Genomic Designing for Climate-Smart Tomato

  • Mathilde CausseEmail author
  • Jiantao Zhao
  • Isidore Diouf
  • Jiaojiao Wang
  • Veronique Lefebvre
  • Bernard Caromel
  • Michel Génard
  • Nadia Bertin


Tomato is the first vegetable consumed in the world. It is grown in very different conditions and areas, mainly in field for processing tomatoes while fresh-market tomatoes are often produced in greenhouses. Tomato faces many environmental stresses, both biotic and abiotic. Today many new genomic resources are available allowing an acceleration of the genetic progress. In this chapter, we will first present the main challenges to breed climate-smart tomatoes. The breeding objectives relative to productivity, fruit quality, and adaptation to environmental stresses will be presented with a special focus on how climate change is impacting these objectives. In the second part, the genetic and genomic resources available will be presented. Then, traditional and molecular breeding techniques will be discussed. A special focus will then be presented on ecophysiological modeling, which could constitute an important strategy to define new ideotypes adapted to breeding objectives. Finally, we will illustrate how new biotechnological tools are implemented and could be used to breed climate-smart tomatoes.


Tomato Breeding Productivity Biotic stress Abiotic stress Ideotypes Modeling 


  1. Aarts J, Hontelez JGJ, Fischer P, Verkerk R, Vankammen A, Zabel P (1991) Acid phosphatase-11, a tightly linked molecular marker for root-knot nematode resistance in tomato—from protein to gene, using pcr and degenerate primers containing deoxyinosine. Plant Mol Biol 16:647–661PubMedCrossRefPubMedCentralGoogle Scholar
  2. Abraitiene A, Girgzdiene R (2013) Impact of the short-term mild and severe ozone treatments on the potato spindle tuber viroid-infected tomato (Lycopersicon esculentum Mill.). Zemdirbyste-Agriculture 100:277–282CrossRefGoogle Scholar
  3. Achuo EA, Prinsen E, Hofte M (2006) Influence of drought, salt stress and abscisic acid on the resistance of tomato to Botrytis cinerea and Oidium neolycopersici. Plant Pathol 55:178–186CrossRefGoogle Scholar
  4. Adams SR, Cockshull KE, Cave CRJ (2001) Effect of temperature on the growth and development of tomato fruits. Ann Bot 88:869–877CrossRefGoogle Scholar
  5. Adams P, Ho LC (1993) Effects of environment on the uptake and distribution of calcium in tomato and on the incidence of blossom-end rot. Plant Soil 154:127–132CrossRefGoogle Scholar
  6. Adato A, Mandel T, Mintz-Oron S, Venger I, Levy D, Yativ M, Domínguez E, Wang Z, De Vos RC, Jetter R, Schreiber L, Heredia A, Rogachev I, Aharoni A (2009) Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genetics. e1000777. Scholar
  7. Adli M (2018) The CRISPR tool kit for genome editing and beyond. Nat Commun 9(1):1911PubMedPubMedCentralCrossRefGoogle Scholar
  8. Agrama HA, Scott JW (2006) Quantitative trait loci for tomato yellow leaf curl virus and tomato mottle virus resistance in tomato. J Am Soc Hort Sci 131:267–272CrossRefGoogle Scholar
  9. Ahmad A, Zhang Y, Cao X-F (2010) Decoding the epigenetic language of plant development. Mol Plant 3:719–728PubMedPubMedCentralCrossRefGoogle Scholar
  10. Al-Abdallat A, Al-Debei H, Ayad J, Hasan S, Al-Abdallat AM, Al-Debei HS et al (2014) Over-expression of SlSHN1 gene improves drought tolerance by increasing cuticular wax accumulation in tomato. Int J Mol Sci 15:19499–19515PubMedPubMedCentralCrossRefGoogle Scholar
  11. Albacete A, Cantero-Navarro E, Großkinsky DK, Arias CL, Balibrea ME, Bru R, Fragner L, Ghanem ME, González MDLC, Hernández JA et al (2015) Ectopic overexpression of the cell wall invertase gene CIN1 leads to dehydration avoidance in tomato. J Exp Bot 66:863–878PubMedCrossRefPubMedCentralGoogle Scholar
  12. Albacete A, Martínez-Andújar C, Ghanem ME, Acosta M, Sánchez-Bravo J, Asins MJ, et al (2009) Rootstock-mediated changes in xylem ionic and hormonal status are correlated with delayed leaf senescence, and increased leaf area and crop productivity in salinized tomato. Plant Cell Environ 32:928–938CrossRefGoogle Scholar
  13. Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V et al (2018) Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J 96(3):635–650PubMedCrossRefGoogle Scholar
  14. Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby J-P, Bitton F, Causse M (2016a) Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. Theor Appl Genet 129:395–418PubMedCrossRefGoogle Scholar
  15. Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M (2016b) Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. J Exp Bot 67:6413–6430PubMedPubMedCentralCrossRefGoogle Scholar
  16. Albrecht E, Escobar M, Chetelat RT (2010) Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens. Ann Bot 105:535–554PubMedPubMedCentralCrossRefGoogle Scholar
  17. Alian A, Altman A, Heuer B (2000) Genotypic difference in salinity and water stress tolerance of fresh market tomato cultivars. Plant Sci 152:59–65CrossRefGoogle Scholar
  18. Allwood JW, De Vos RCH, Moing A, Deborde C, Erban A, Kopka J, Goodacre R, Hall RD (2011) Plant metabolomics and its potential for systems biology research: background concepts, technology, and methodology. In: Methods Enzymol, 1st edn. Scholar
  19. Almeida J, Quadrana L, Asís R et al (2011) Genetic dissection of vitamin E biosynthesis in tomato. J Exp Bot 62(11):3781–3798PubMedPubMedCentralCrossRefGoogle Scholar
  20. Alpert KB, Tanksley SD (1996) High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato. Proc Natl Acad Sci USA 93:15503–15507PubMedCrossRefGoogle Scholar
  21. Alseekh S, Fernie AR (2018) Metabolomics 20 years on: what have we learned and what hurdles remain? Plant J 94:933–942PubMedCrossRefGoogle Scholar
  22. Alseekh S, Ofner I, Pleban T, Tripodi P, Di Dato F, Cammareri M, Mohammad A, Grandillo S, Fernie AR, Zamir D (2013) Resolution by recombination: breaking up Solanum pennellii introgressions. Trends Plant Sci 18:536–538PubMedCrossRefGoogle Scholar
  23. Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T et al (2017) Canalization of tomato fruit metabolism. Plant Cell 29(11):2753–2765PubMedPubMedCentralCrossRefGoogle Scholar
  24. Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T et al (2017) Canalization of tomato fruit metabolism. Plant Cell 29(11):2753–2765PubMedPubMedCentralCrossRefGoogle Scholar
  25. Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355CrossRefGoogle Scholar
  26. Andolfo G, Jupe F, Witek K, Etherington GJ, Ercolano MR, Jones JDG (2014) Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biol 14Google Scholar
  27. Anfoka G, Moshe A, Fridman L, Amrani L, Rotem O, Kolot M, Zeidan M, Czosnek H, Gorovits R (2016) Tomato yellow leaf curl virus infection mitigates the heat stress response of plants grown at high temperatures. Sci Rep 6:19715PubMedCrossRefGoogle Scholar
  28. Apse MP, Aharon GS, Snedden WA, Blumwald E (1999) Salt tolerance conferred by overexpression of a vacuolar Na+/H+ antiport in Arabidopsis. Science 285:1256–1258PubMedCrossRefGoogle Scholar
  29. Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K (2017) Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLoS ONE 12:e0189951PubMedPubMedCentralCrossRefGoogle Scholar
  30. Archak S, Karihaloo JL, Jain A (2002) RAPD markers reveal narrowing genetic base of Indian tomato cultivars. Curr Sci 82:1139–1143Google Scholar
  31. Arms EM, Lounsbery JK, Bloom AJ, St. Clair DA (2016) Complex relationships among water use efficiency-related traits, yield, and maturity in tomato lines subjected to deficit irrigation in the field. Crop Sci 56:1698CrossRefGoogle Scholar
  32. Ashrafi H, Kinkade MP, Merk HL, Foolad MR (2012) Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population. Mol Breed 30:549–567CrossRefGoogle Scholar
  33. Ashrafi-Dehkordi E, Alemzadeh A, Tanaka N, Razi H (2018) Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato. PeerJ 6:e4631PubMedPubMedCentralCrossRefGoogle Scholar
  34. Asins MJ, Albacete A, Martinez-Andujar C, Pérez-Alfocea F, Dodd IC, Carbonell EA, Dieleman JA (2017) Genetic analysis of rootstock-mediated nitrogen (N) uptake and root-to-shoot signalling at contrasting N availabilities in tomato. Plant Sci 263:94–106PubMedCrossRefGoogle Scholar
  35. Asins MJ, Bolarín MC, Pérez-Alfocea F, Estañ MT, Martínez-Andújar C, Albacete A et al (2010) Genetic analysis of physiological components of salt tolerance conferred by Solanum rootstocks. What is the rootstock doing for the scion? Theor Appl Genet 121:105–115PubMedCrossRefGoogle Scholar
  36. Asins MJ, Raga V, Roca D, Belver A, Carbonell EA (2015) Genetic dissection of tomato rootstock effects on scion traits under moderate salinity. Theor Appl Genet 128:667–679PubMedCrossRefGoogle Scholar
  37. Asins MJ, Villalta I, Aly MM, Olías R, Álvarez De Morales P, Huertas R et al (2013) Two closely linked tomato HKT coding genes are positional candidates for the major tomato QTL involved in Na+/K+ homeostasis. Plant Cell Environ 36:1171–1191CrossRefGoogle Scholar
  38. Atanassova B (1999) Functional male sterility (ps2) in tomato (Lycopersicon esculentum Mill.) and its application in breeding and seed production. Euphytica 107: 1, 13–21Google Scholar
  39. Auerswald H, Schwarz D, Kornelson C, Krumbein A, Brückner B (1999) Sensory analysis, sugar and acid content of tomato at different EC values of the nutrient solution. Sci Hort (Amsterdam) 82:227–242CrossRefGoogle Scholar
  40. Bai Y, Lindhout P (2007) Domestication and breeding of tomatoes: what have we gained and what can we gain in the future? Ann Bot 100(5):1085–1094PubMedPubMedCentralCrossRefGoogle Scholar
  41. Bai YL, Huang CC, van der Hulst R, Meijer-Dekens F, Bonnema G, Lindhout P (2003) QTLs for tomato powdery mildew resistance (Oidium lycopersici) in Lycopersicon parviflorum G1.1601 co-localize with two qualitative powdery mildew resistance genes. Mol Plant-Microbe Interact 16:169–176PubMedCrossRefGoogle Scholar
  42. Bai YL, Kissoudis C, Yan Z, Visser RGF, van der Linden G (2018) Plant behaviour under combined stress: tomato responses to combined salinity and pathogen stress. Plant J 93:781–793PubMedCrossRefGoogle Scholar
  43. Bai YL, Pavan S, Zheng Z, Zappel NF, Reinstadler A, Lotti C, De Giovanni C, Ricciardi L, Lindhout P, Visser R, Theres K, Panstruga R (2008) Naturally occurring broad-spectrum powdery mildew resistance in a central American tomato accession is caused by loss of Mlo function. Mol Plant-Microbe Interact 21:30–39PubMedCrossRefGoogle Scholar
  44. Baldazzi V, Bertin N, Jong H, Genard M (2012) Towards multiscale plant models: integrating cellular networks. Trends Plant Sci 17:728–736PubMedCrossRefGoogle Scholar
  45. Baldazzi V, Génard M, Bertin N (2017) Cell division, endoreduplication and expansion processes: setting the cell and organ control into an integrated model of tomato fruit development. Acta Hort 1182Google Scholar
  46. Baldazzi V, Pinet A, Vercambre G, Benard C, Biais B, Génard M (2013) In-silico analysis of water and carbon relations under stress conditions. A multi-scale perspective centered on fruit. Front Plant Sci 4.
  47. Baldazzi V, Valsesia P, Génard M, Bertin N (2019) Organ-wide and ploidy-dependent regulations both contribute to cell size determination: evidence from a computational model of tomato fruit. J Exp Bot. Scholar
  48. Baldet P, Stevens R, Causse M, Duffe P, Buret M, Rothan C, Garchery C, Duffé P, Carchery C, Baldet P et al (2007) Candidate genes and quantitative trait loci affecting fruit ascorbicacid content in three tomato populations. Plant Physiol 143:1943–1953PubMedPubMedCentralCrossRefGoogle Scholar
  49. Baldwin E, Scott J, Shewmaker C, Schuch W (2000) Flavor trivia and tomato aroma: biochemistry and possible mechanisms for control of important aroma components. HortScience 35:1013–1022CrossRefGoogle Scholar
  50. Baldwin EA, Nisperos-Carriedo MO, Baker R, Scott JW (1991) Quantitative analysis of flavor parameters in six Florida tomato cultivars (Lycopersicon esculentum Mill). J Agri Food Chem 39:1135–1140CrossRefGoogle Scholar
  51. Baldwin EA, Scott JW, Einstein MA, Malundo TMM, Carr BT, Shewfelt RL, Tandon KS (1998) Relationship between sensory and instrumental analysis for tomato flavor. J Am Soc Hort Sci 123:906–915CrossRefGoogle Scholar
  52. Ballester A-R, Bovy AG, Viquez-Zamora M, Tikunov Y, Grandillo S, de Vos R, de Maagd RA, van Heusden S, Molthoff J (2016) Identification of loci affecting accumulation of secondary metabolites in tomato fruit of a Solanum lycopersicum × Solanum chmielewskii introgression line population. Front Plant Sci 7:1428PubMedPubMedCentralCrossRefGoogle Scholar
  53. Bandillo N, Raghavan C, Muyco P, Sevilla MAL, Lobina IT, Dilla-Ermita C, Tung C-W, McCouch S, Thomson M, Mauleon R et al (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6:11PubMedPubMedCentralCrossRefGoogle Scholar
  54. Bastet A, Zafirov D, Giovinazzo N, Guyon-Debast A, Nogué F, Robaglia C, Gallois J-L (2019) Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses. Plant Biotechnol J. Scholar
  55. Bauchet G, Causse M (2012) Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Caliskan M (ed) Genetic Divers Plants. ISBN: 978-953-51-0185-7, InTech, Scholar
  56. Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M (2017a) Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor Appl Genet 130:875–889PubMedCrossRefGoogle Scholar
  57. Bauchet G, Grenier S, Samson N, Segura V, Kende A, Beekwilder J, Cankar K, Gallois J-L, Gricourt J, Bonnet J et al (2017b) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytol 215:624–641PubMedCrossRefGoogle Scholar
  58. Baxter CJ, Liu JL, Fernie AR, Sweetlove LJ (2007) Determination of metabolic fluxes in a non-steady-state system. Phytochemistry 68:2313–2319PubMedCrossRefGoogle Scholar
  59. Beauvoit B, Belouah I, Bertin N, Belmys Cakpo C, Colombié S, Dai Z, Gautier H, Génard M, Moing A, Roch L, Vercambre G, Gibon Y (2018) Putting primary metabolism into perspective to obtain better fruits. Ann Bot 122(1):1–21PubMedPubMedCentralCrossRefGoogle Scholar
  60. Beauvoit BP, Colombié S, Monier A, Andrieu MH, Biais B, Bérnard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat JP et al (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant cell 26(8):3224–3242PubMedPubMedCentralCrossRefGoogle Scholar
  61. Belfanti E, Malatrasi M, Orsi I, Boni AG (2015) Isolated nucleotide sequence from solanum lycopersicum for improved resistance to tomato spotted wilt virus, TSWV. Patent WO/2015/090468; International Application No: PCT/EP2013/077799Google Scholar
  62. Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D, Tanksley S (1998) Advanced backcross QTL analysis in tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97(1/2): 170–180; erratum 97(7): 1191–1196CrossRefGoogle Scholar
  63. Bernacchi D, Beck-Bunn T, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley S (1998b) Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet 97:381–397CrossRefGoogle Scholar
  64. Berr A, Shafiq S, Shen WH (2011) Histone modifications in transcriptional activation during plant development. Biochim Biophys Acta Gene Regul Mech 1809:567–576CrossRefGoogle Scholar
  65. Bertin N, Borel C, Brunel B, Cheniclet C, Causse M (2003) Do genetic make-up and growth manipulation affect tomato fruit size by cell number, or cell size and DNA endoreduplication? Ann Bot 92(3):415–424PubMedPubMedCentralCrossRefGoogle Scholar
  66. Bertin N, Guichard S, Leonardi C, Longuenesse JJ, Langlois D, Navez B (2000) Seasonal evolution of the quality of fresh glasshouse tomatoes under mediterranean conditions, as affected by air vapour pressure deficit and plant fruit load. Ann Bot 85:741–750CrossRefGoogle Scholar
  67. Bertin N, Gautier H, Roche C (2002) Number of cells in tomato fruit depending on fruit position and source-sink balance during plant development. Plant Growth Regul 36(2):105–112CrossRefGoogle Scholar
  68. Bertin N, Martre P, Génard M, Quilot B, Salon C (2010) Why and how can process-based simulation models link genotype to phenotype for complex traits? Case-study of fruit and grain quality traits. J Exp Bot 61:955–967PubMedCrossRefGoogle Scholar
  69. Bhatia P, Ashwath N, Senaratna T, Midmore D (2004) Tissue culture studies of tomato (Lycopersicon esculentum). Plant Cell Tiss Org Cult 78(1):1–21CrossRefGoogle Scholar
  70. Bhatt RM, Srinivasa Rao NK (1987) Seed germination and seedling growth responses of tomato cultivars to imposed water stress. J Hort Sci 62:221–225CrossRefGoogle Scholar
  71. Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA (2010) Heterosis. Plant Cell 22:2105–2112PubMedPubMedCentralCrossRefGoogle Scholar
  72. Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F (2012) Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7:e48198PubMedPubMedCentralCrossRefGoogle Scholar
  73. Blanca J, Montero-Pau J, Sauvage C, Bauchet G, Illa E, Díez MJ, Francis D, Causse M, van der Knaap E, Cañizares J (2015) Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genom 16:257CrossRefGoogle Scholar
  74. Bloom AJ, Zwieniecki MA, Passioura JB, Randall LB, Holbrook NM, St. Clair DA (2004) Water relations under root chilling in a sensitive and tolerant tomato species. Plant, Cell Environ 27:971–979CrossRefGoogle Scholar
  75. Boison SA, Utsunomiya ATH, Santos DJA, Neves HHR, Carvalheiro R, Mészáros G, Utsunomiya YT, do Carmo AS, MA RS, Machado SA et al (2017) Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle. J Dairy Sci 100:5479–5490PubMedCrossRefGoogle Scholar
  76. Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G et al (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46:1034–1038PubMedCrossRefGoogle Scholar
  77. Boote K (2016) Modelling crop growth and yield in tomato cultivation. ID: 9781786760401-010Google Scholar
  78. Boureau L, How-Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J, Stammitti L, Pribat A, Bowler C, Hong Y et al (2016) A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. Plant Mol Biol 90:485–501PubMedCrossRefGoogle Scholar
  79. Bovy A, de Vos R, Kemper M, Schijlen E, Pertejo MA, Muir S, Collins G, Robinson S, Verhoeyen M, Hughes S, Santos-Buelga C (2002) High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1. Plant Cell 14:2509–2526PubMedPubMedCentralCrossRefGoogle Scholar
  80. Bovy A, Schijlen E, Hall RD (2007) Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics. Metabolomics 3:399–412PubMedPubMedCentralCrossRefGoogle Scholar
  81. Boote KJ, Rybak MR, Scholberg JM, Jones JW (2012) Improving the CROPGRO-Tomato model for predicting growth and yield response to temperature. HortScience 47:1038–1049CrossRefGoogle Scholar
  82. Brachi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232PubMedPubMedCentralCrossRefGoogle Scholar
  83. Bramley PM (2000) Is lycopene beneficial to human health? Phytochemistry 54:233–236PubMedCrossRefGoogle Scholar
  84. Brandwagt BF, Mesbah LA, Takken FLW, Laurent PL, Kneppers TJA, Hille J, Nijkamp HJJ (2000) A longevity assurance gene homolog of tomato mediates resistance to Alternaria alternata f. sp lycopersici toxins and fumonisin B(1). In: Proceedings of the national academy of sciences of the United States of America 97:4961-4966CrossRefGoogle Scholar
  85. Breiman L (2001) Random forests. Mach Learn 45:5–32CrossRefGoogle Scholar
  86. Brommonschenkel SH, Frary A, Tanksley SD (2000) The broad-spectrum tospovirus resistance gene Sw-5 of tomato is a homolog of the root-knot nematode resistance gene Mi. Mol Plant-Microbe Interact 13:1130-1138PubMedCrossRefPubMedCentralGoogle Scholar
  87. Brooks C, Nekrasov V, Lippman ZB, Van Eck J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol 166(3):1292–1297PubMedPubMedCentralCrossRefGoogle Scholar
  88. Brouwer DJ, Jones ES, St Clair DA (2004) QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato. Genome 47:475–492PubMedCrossRefGoogle Scholar
  89. Brouwer DJ, St Clair DA (2004) Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs. Theor Appl Genet 108:628–638PubMedCrossRefGoogle Scholar
  90. Browning BL, Browning SR (2016) Genotype imputation with millions of reference samples. Amer J Hum Genet 98:116–126PubMedCrossRefGoogle Scholar
  91. Bruhn CM, Feldman N, Garlitz C, Harwood J, Ivans E, Marshall M, Riley A, Thurber D, Williamson E (1991) Consumer perceptions of quality: apricots, cantaloupes, peaches, pears, strawberries, and tomatoes. J Food Qual 14:187–195CrossRefGoogle Scholar
  92. Brummell DA, Harpster MH, Civello PM, Palys JM, Bennett AB, Dunsmuir P (1999) Modification of expansin protein abundance in tomato fruit alters softening and cell wall polymer metabolism during ripening. Plant Cell 11(11):2203–2216PubMedPubMedCentralCrossRefGoogle Scholar
  93. Bucheli P, Voirol E, De La Torre R, López J, Rytz A, Tanksley SD, Pétiard V (1999) Definition of nonvolatile markers for flavor of tomato (Lycopersicon esculentum Mill.) as tools in selection and breeding. J Agri Food Chem 47:659–664CrossRefGoogle Scholar
  94. Budiman MA, Chang S-B, Lee S, Yang TJ, Zhang H-B, de Jong H, Wing RA (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108:190–196PubMedCrossRefGoogle Scholar
  95. Bush DS (1995) Calcium regulation in plant cells and its role in signaling. Annu Rev Plant Physiol 46:95–122CrossRefGoogle Scholar
  96. Bussières P (1994) Water import rate in tomato fruit: a resistance model. Ann Bot 73:75–82CrossRefGoogle Scholar
  97. Butler L (1952) The linkage map of the tomato. J Hered 43:25–36CrossRefGoogle Scholar
  98. Cagas CC, Lee ON, Nemoto K, Sugiyama N (2008) Quantitative trait loci controlling flowering time and related traits in a Solanum lycopersicum × S. pimpinellifolium cross. Sci Hort (Amsterdam) 116:144–151CrossRefGoogle Scholar
  99. Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866PubMedCrossRefGoogle Scholar
  100. Callaway E (2018) CRISPR plants now subject to t ough GM l aws in European Union. Nature 560:16. Scholar
  101. Calus MPL, Meuwissen THE, de Roos APW, Veerkamp RF (2008) Accuracy of genomic selection using different methods to define haplotypes. Genetics 178:553–561PubMedPubMedCentralCrossRefGoogle Scholar
  102. Canady MA, Meglic V, Chetelat RT (2005) A library of Solanum lycopersicoides introgression lines in cultivated tomato. Genome 48:685–697PubMedCrossRefGoogle Scholar
  103. Cantero-Navarro E, Romero-Aranda R, Fernández-Muñoz R, Martínez-Andújar C, Pérez-Alfocea F, Albacete A (2016) Improving agronomic water use efficiency in tomato by rootstock-mediated hormonal regulation of leaf biomass. Plant Sci 251:90–100PubMedCrossRefPubMedCentralGoogle Scholar
  104. Cao K, Xu H, Zhang R, Xu D, Yan L, Sun Y, Xia L, Zhao J, Zou Z, Bao E (2019) Renewable and sustainable strategies for improving the thermal environment of Chinese solar greenhouses. Energy Build. In PressGoogle Scholar
  105. Cárdenas PD, Sonawane PD, Pollier J, Vanden Bossche R, Dewangan V, Weithorn E, Tal L, Meir S, Rogachev I, Malitsky S, Giri AP, Goossens A, Burdman S, Aharoni A (2016) GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway. Nat Commun 7:10654Google Scholar
  106. Carelli BP, Gerald LTS, Grazziotin FG, Echeverrigaray S (2006) Genetic diversity among Brazilian cultivars and landraces of tomato Lycopersicon esculentum Mill. revealed by RAPD markers. Genet Resour Crop Evol 53:395–400CrossRefGoogle Scholar
  107. Carmeille A, Caranta C, Dintinger J, Prior P, Luisetti J, Besse P (2006) Identification of QTLs for Ralstonia solanacearum race 3-phylotype II resistance in tomato. Theor Appl Genet 113:110–121PubMedCrossRefPubMedCentralGoogle Scholar
  108. Carmel-Goren L, Liu YS, Lifschitz E, Zamir D (2003) The SELF-PRUNING gene family in tomato. Plant Mol Biol 52:1215–1222PubMedCrossRefPubMedCentralGoogle Scholar
  109. Caro M, Cruz V, Cuartero J, Estañ MT, Bolarin MC (1991) Salinity tolerance of normal-fruited and cherry tomato cultivars. Plant Soil 136:249–255CrossRefGoogle Scholar
  110. Caromel B, Hamers C, Touhami N, Renaudineau A, Bachellez A, Massire A, Damidaux R, Lefebvre V (2015) Screening tomato germplasm for resistance to late blight. In: INNOHORT, innovation in integrated & organic horticulture. ISHS International Symposium, Avignon, France, 8–12 June 2015, pp 15–16Google Scholar
  111. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor M-I, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M et al (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142:1380–1396PubMedPubMedCentralCrossRefGoogle Scholar
  112. Casteel CL, Walling LL, Paine TD (2007) Effect of Mi-1.2 gene in natal host plants on behavior and biology of the tomato psyllid Bactericerca cockerelli (Sulc) (Hemiptera: Psyllidae). J Entomol Sci 42:155–162CrossRefGoogle Scholar
  113. Catanzariti AM, Do HTT, Bru P, de Sain M, Thatcher LF, Rep M, Jones DA (2017) The tomato I gene for Fusarium wilt resistance encodes an atypical leucine-rich repeat receptor-like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1. Plant J 89:1195–1209PubMedCrossRefPubMedCentralGoogle Scholar
  114. Catanzariti AM, Lim GTT, Jones DA (2015) The tomato I-3 gene: a novel gene for resistance to Fusarium wilt disease. New Phytol 207:106–118PubMedCrossRefPubMedCentralGoogle Scholar
  115. Catchen JM, Boone JQ, Davey JW, Hohenlohe PA, Etter PD, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510PubMedCrossRefPubMedCentralGoogle Scholar
  116. Causse M, Buret M, Robini K, Verschave P (2003) Inheritance of nutritional and sensory quality traits in fresh market tomato and relation to consumer preferences. J Food Sci 68:2342–2350CrossRefGoogle Scholar
  117. Causse M, Friguet C, Coiret C, Lépicier M, Navez B, Lee M, Holthuysen N, Sinesio F, Moneta E, Grandillo S (2010) Consumer preferences for fresh tomato at the European scale: a common segmentation on taste and firmness. J Food Sci 75(9):531–541CrossRefGoogle Scholar
  118. Causse M, Chaïb J, Lecomte L, Buret M, Hospital F (2007a) Both additivity and epistasis control the genetic variation for fruit quality traits in tomato. Theor Appl Genet 115:429–442PubMedCrossRefPubMedCentralGoogle Scholar
  119. Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685PubMedCrossRefPubMedCentralGoogle Scholar
  120. Causse M, Damidaux R, Rousselle P (2007) Traditional and enhanced breeding for fruit quality traits in tomato. In: Razdan MK, Mattoo AK (eds) Genetic improvement of solanaceous crops, Vol. 2: Tomato. Science Publishers, Enfield, USA, pp 153–192Google Scholar
  121. Causse M, Saliba-Colombani V, Lesschaeve I, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato. 2. Mapping QTLs for sensory attributes. Theor Appl Genet 102:273–283CrossRefGoogle Scholar
  122. Causse M, Saliba-Colombani V, Lecomte L, Duffé P, Rousselle P, Buret M (2002) QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits. J Exp Bot 53:2089–2098PubMedCrossRefPubMedCentralGoogle Scholar
  123. Causse M, Desplat N, Pascual L et al (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14, 791PubMedPubMedCentralCrossRefGoogle Scholar
  124. Chakrabarti M, Zhang N, Sauvage C, Muños S, Blanca J, Cañizares J, Diez MJ, Schneider R, Mazourek M, McClead J et al (2013) A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci USA 110:17125–17130PubMedCrossRefPubMedCentralGoogle Scholar
  125. Chen FQ, Foolad MR, Hyman J, St. Clair DA, Beelaman RB (1999) Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species. Mol Breed 5:283–299CrossRefGoogle Scholar
  126. Chen J, Kang S, Du T, Qiu R, Guo P, Chen R (2013) Quantitative response of greenhouse tomato yield and quality to water deficit at different growth stages. Agri Water Manag 129:152–162CrossRefGoogle Scholar
  127. Chen X (2005) microRNA biogenesis and function in plants. FEBS Lett 579:5923PubMedPubMedCentralCrossRefGoogle Scholar
  128. Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44PubMedPubMedCentralCrossRefGoogle Scholar
  129. Chetelat RT, DeVerna JW, Bennett AB (1995) Introgression into tomato (Lycopersicon esculentum) of the L. chmielewskii sucrose accumulator gene (sucr) controlling fruit sugar composition. Theor Appl Genet 91:327–333PubMedCrossRefPubMedCentralGoogle Scholar
  130. Cho SK, Ben Chaabane S, Shah P, Poulsen CP, Yang SW (2014) COP1 E3 ligase protects HYL1 to retain microRNA biogenesis. Nat Commun 5:5867PubMedCrossRefPubMedCentralGoogle Scholar
  131. Chunwongse J, Chunwongse C, Black L, Hanson P (2002) Molecular mapping of the Ph-3 gene for late blight resistance in tomato. J Hort Sci Biotechnol 77:281–286CrossRefGoogle Scholar
  132. Clark AG (2004) The role of haplotypes in candidate gene studies. Genet Epidemiol 27:321–333PubMedCrossRefPubMedCentralGoogle Scholar
  133. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J16(6):735–743Google Scholar
  134. Coaker GL, Francis DM (2004) Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum. Theor Appl Genet 108:1047–1055PubMedCrossRefPubMedCentralGoogle Scholar
  135. Colliver S, Bovy A, Collins G, Muir S, Robinson S, de Vos CHR, Verhoeyen ME (2002) Improving the nutritional content of tomatoes through reprogramming their flavonoid biosynthetic pathway. Phytochem Rev 1:113–123CrossRefGoogle Scholar
  136. Colombié S, Beauvoit B, Nazaret C, Bénard C, Vercambre G, Le Gall S, Biais B, Cabasson C, Maucourt M, Bernillon S, Moing A, Dieuaide-Noubhani M, Mazat J-P, Gibon Y (2017) Respiration climacteric in tomato fruits elucidated by constraint-based modelling. New Phytol 213:1726–1739PubMedCrossRefPubMedCentralGoogle Scholar
  137. Colombié S, Nazaret C, Bénard C, Biais B, Mengin V, Solé M, Fouillen L, Dieuaide-Noubhani M, Mazat J-P, Beauvoit B, Gibon Y (2015) Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit. Plant J 81:24–39PubMedCrossRefPubMedCentralGoogle Scholar
  138. Comai L, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45:684–694PubMedCrossRefPubMedCentralGoogle Scholar
  139. Coneva V, Frank MH, Balaguer MAL, Li M, Sozzani R, Chitwood DH (2017) Genetic architecture and molecular networks underlying leaf thickness in desert-adapted Tomato Solanum pennellii. Plant Physiol 175(1):376–391PubMedPubMedCentralCrossRefGoogle Scholar
  140. Constantinescu D, Memmah M-M, Vercambre G, Génard M, Baldazzi V, Causse M et al (2016) Model-assisted estimation of the genetic variability in physiological parameters related to tomato fruit growth under contrasted water conditions. Front Plant Sci 7:1841. Scholar
  141. Costa JM, Ortuño MF, Chaves MM (2007) Deficit irrigation as a strategy to save water: physiology and potential application to horticulture. J Integr Plant Biol 49:1421–1434CrossRefGoogle Scholar
  142. Cournède P-H et al (2013) Development and evaluation of plant growth models: methodology and implementation in the pygmalion platform. Math Mod Nat Phen 8(4):112–130CrossRefGoogle Scholar
  143. Cowger C, Brown JKM (2019) Durability of quantitative resistance in crops: greater than we know? Annu Rev Phytopathol 57:253–277PubMedCrossRefGoogle Scholar
  144. Crain J, Mondal S, Rutkoski J, Singh RP, Poland J (2018) Combining high-Throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding. Plant Genome 11: 0CrossRefGoogle Scholar
  145. Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de los Campos G, Burgueño J, Camacho-González JM, Pérez-Elizalde S, Beyene Y, et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci. Scholar
  146. Cui J, Jiang N, Zhou X, Hou X, Yang G, Meng J, Luan Y (2018) Tomato MYB49 enhances resistance to Phytophthora infestans and tolerance to water deficit and salt stress. Planta 248:1487–1503PubMedCrossRefGoogle Scholar
  147. Cui J, You C, Chen X (2017a) The evolution of microRNAs in plants. Curr Opin Plant Biol 35:61–67PubMedCrossRefGoogle Scholar
  148. Cui J, Zhou B, Ross SA, Zempleni J (2017b) Nutrition, microRNAs, and human health. Adv Nutr 8:105–112PubMedPubMedCentralCrossRefGoogle Scholar
  149. Cuyabano BC, Su G, Lund MS (2014) Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population. BMC Genom. Scholar
  150. Cuyabano BCD, Su G, Lund MS (2015a) Selection of haplotype variables from a high-density marker map for genomic prediction. Genet Sel Evol 47:61PubMedPubMedCentralCrossRefGoogle Scholar
  151. Cuyabano BCD, Su G, Rosa GJM, Lund MS, Gianola D (2015b) Bootstrap study of genome-enabled prediction reliabilities using haplotype blocks across Nordic Red cattle breeds. J Dairy Sci 98:7351–7363PubMedCrossRefGoogle Scholar
  152. Dal Cin V, Kevany B, Fei Z, Klee HJ (2009) Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. Theor Appl Genet 119:1183–1192CrossRefGoogle Scholar
  153. Danecek P, Huang J, Min JL, Timpson NJ, Trabetti E, Richards JB, Durbin R, Howie B, Gambaro G, Zheng H-F et al (2015) Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nat Commun 6:8111PubMedPubMedCentralCrossRefGoogle Scholar
  154. Danilo B, Perrot L, Botton E, Nogué F, Mazier M (2018) The DFR locus: a smart landing pad for targeted transgene insertion in tomato. PLoS ONE 13(12):e0208395PubMedPubMedCentralCrossRefGoogle Scholar
  155. Danilo B, Perrot L, Mara K, Botton E, Nogué F, Mazier M (2019) Efficient and transgene-free gene targeting using Agrobacterium-mediated delivery of the CRISPR/Cas9 system in tomato. Plant Cell Rep 38(4):459–462PubMedCrossRefGoogle Scholar
  156. Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M et al (2016) Next-generation genotype imputation service and methods. Nat Genet 48:1284–1287PubMedPubMedCentralCrossRefGoogle Scholar
  157. Davies JN, Hobson GE (1981) The constituents of tomato fruit—the influence of environment, nutrition, and genotype. Crit Rev Food Sci Nutr 15:205–280PubMedCrossRefGoogle Scholar
  158. Davila Olivas NH, Kruijer W, Gort G, Wijnen CL, van Loon JJA, Dicke M (2017) Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana. New Phytol 213:838–851PubMedCrossRefGoogle Scholar
  159. Davis J, Yu DZ, Evans W, Gokirmak T, Chetelat RT, Stotz HU (2009) Mapping of loci from Solanum lycopersicoides conferring resistance or susceptibility to Botrytis cinerea in tomato. Theor Appl Genet 119:305–314PubMedPubMedCentralCrossRefGoogle Scholar
  160. de Freitas ST, Martinelli F, Feng B, Reitz NF, Mitcham EJ (2018) Transcriptome approach to understand the potential mechanisms inhibiting or triggering blossom-end rot development in tomato fruit in response to plant growth regulators. J Plant Growth Regul 37:183–198Google Scholar
  161. de Groot CC, Marcelis LFM, van den Boogaard R, Lambers H (2004) Response of growth of tomato to phosphorus and nitrogen nutrition. Acta Hort 357–364Google Scholar
  162. de Jong CF, Takken FLW, Cai XH, de Wit P, Joosten M (2002) Attenuation of Cf-mediated defense responses at elevated temperatures correlates with a decrease in elicitor-binding sites. Mol Plant-Microbe Interact 15:1040–1049PubMedCrossRefGoogle Scholar
  163. de Los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MPL, Kirst M, Huber D, Peter GF (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193:327–345CrossRefGoogle Scholar
  164. De Swaef T, Mellisho CD, Baert A, De Schepper V, Torrecillas A, Conejero W, Steppe K (2014) Model-assisted evaluation of crop load effects on stem diameter variations and fruit growth in peach. Trees 28:1607–1622CrossRefGoogle Scholar
  165. Delhaize E, Gruber BD, Ryan PR (2007) The roles of organic anion permeases in aluminium resistance and mineral nutrition. FEBS Lett 581:2255–2262PubMedCrossRefGoogle Scholar
  166. DeVicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596PubMedPubMedCentralGoogle Scholar
  167. Dileo MV, Pye MF, Roubtsova TV, Duniway JM, MacDonald JD, Rizzo DM, Bostock RM (2010) Abscisic acid in salt stress predisposition to Phytophthora root and crown rot in tomato and chrysanthemum. Phytopathology 100:871–879PubMedCrossRefGoogle Scholar
  168. Diouf IA, Derivot L, Bitton F, Pascual L, Causse M (2018) Water deficit and salinity stress reveal many specific QTL for plant growth and fruit quality traits in tomato. Front Plant Sci 9:279PubMedPubMedCentralCrossRefGoogle Scholar
  169. Dixon MS, Hatzixanthis K, Jones DA, Harrison K, Jones JDG (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell 10:1915–1925PubMedPubMedCentralCrossRefGoogle Scholar
  170. Dixon MS, Jones DA, Keddie JS, Thomas CM, Harrison K, Jones JD (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell 84:451–459PubMedCrossRefGoogle Scholar
  171. Do PT, Prudent M, Sulpice R, Causse M, Fernie AR (2010) The influence of fruit load on the tomato pericarp metabolome in a Solanum chmielewskii introgression line population. Plant Physiol 154:1128–1142PubMedPubMedCentralCrossRefGoogle Scholar
  172. Doganlar S, Dodson J, Gabor B, Beck-Bunn T, Crossman C, Tanksley SD (1998) Molecular mapping of the py-1 gene for resistance to corky root rot (Pyrenochaeta lycopersici) in tomato. Theor Appl Genet 97:784–788CrossRefGoogle Scholar
  173. Doganlar S, Frary A, Ku H-M, Tanksley SD (2003) Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). Genome 45:1189–1202CrossRefGoogle Scholar
  174. Domínguez T, Hernández ML, Pennycooke JC, Jiménez P, Martínez-Rivas JM, Sanz C, Stockinger EJ, Sánchez-Serrano JJ, Sanmartín M (2010) Increasing ω-3 desaturase expression in tomato results in altered aroma profile and enhanced resistance to cold stress. Plant Physiol 153(2):655–665PubMedPubMedCentralCrossRefGoogle Scholar
  175. Donald 1968 C.M. The breeding of crop idéotypes. Euphytica, 17 (1968), pp. 385–403Google Scholar
  176. Dong QL, Liu DD, An XH, Hu DG, Yao YX, Hao YJ (2011) MdVHP1 encodes an apple vacuolar H+-PPase and enhances stress tolerance in transgenic apple callus and tomato. JPlant Physiol 168(17):2124–2133CrossRefGoogle Scholar
  177. Dong Z, Men Y, Li Z, Zou Q, Ji J (2019) Chlorophyll fluorescence imaging as a tool for analyzing the effects of chilling injury on tomato seedlings. Sci Hort (Amsterdam) 246:490–497CrossRefGoogle Scholar
  178. Dorais M, Papadopoulos AP, Gosselin A (2001) Greenhouse tomato fruit quality. Hortic Rev 26:239–319Google Scholar
  179. Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A (2017) Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J 91(4):565–573PubMedPubMedCentralCrossRefGoogle Scholar
  180. Driedonks N, Wolters-Arts M, Huber H, de Boer G-J, Vriezen W, Mariani C, Rieu I (2018) Exploring the natural variation for reproductive thermotolerance in wild tomato species. Euphytica 214:67CrossRefGoogle Scholar
  181. Du Y-D, Niu W-Q, Gu X-B, Zhang Q, Cui B-J (2018) Water- and nitrogen-saving potentials in tomato production: a meta-analysis. Agri Water Manag 210:296–303CrossRefGoogle Scholar
  182. Duangjit J, Causse M, Sauvage C (2016) Efficiency of genomic selection for tomato fruit quality. Mol Breed 36(36):29CrossRefGoogle Scholar
  183. Edwards SM, Buntjer JB, Jackson R, Bentley AR, Lage J, Byrne E, Burt C, Jack P, Berry S, Flatman E et al (2019) The effects of training population design on genomic prediction accuracy in wheat. Theor Appl Genet 443267Google Scholar
  184. El-hady E, Haiba A, El-hamid NRA, Rizkalla A, Phylogenetic AR (2010) Phylogenetic diversity and relationships of some tomato varieties by electrophoretic protein and RAPD analysis. J Amer Sci 6:434–441Google Scholar
  185. Elvanidi A, Katsoulas N, Augoustaki D, Loulou I, Kittas C (2018) Crop reflectance measurements for nitrogen deficiency detection in a soilless tomato crop. Biosyst Eng 176:1–11CrossRefGoogle Scholar
  186. Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome J 4:250CrossRefGoogle Scholar
  187. Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L (2012) Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. Plant Cell Rep 31:973–985PubMedPubMedCentralCrossRefGoogle Scholar
  188. Eriksson EM, Bovy A, Manning K, Harrison L, Andrews J, De Silva J, Tucker GA, Seymour GB, Thompson J, Tor M et al (2004) Effect of the colorless non-ripening mutation on cell wall biochemistry and gene expression during tomato fruit development and ripening 1[w]. Plant Physiol 136:4184–4197PubMedPubMedCentralCrossRefGoogle Scholar
  189. Ernst K, Kumar A, Kriseleit D, Kloos DU, Phillips MS, Ganal MW (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31:127–136PubMedCrossRefPubMedCentralGoogle Scholar
  190. Eshed Y, Gera G, Zamir D (1996) A genome-wide search for wild-species alleles that increase horticultural yield of processing tomato. Theor Appl Genet 93:877–886PubMedPubMedCentralCrossRefGoogle Scholar
  191. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivatedtomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162PubMedPubMedCentralGoogle Scholar
  192. Estañ MT, Villalta I, Bolarín MC, Carbonell EA, Asins MJ (2009) Identification of fruit yield loci controlling the salt tolerance conferred by solanum rootstocks. Theor Appl Genet 118:305–312PubMedCrossRefPubMedCentralGoogle Scholar
  193. Evangelou E, Ioannidis JPA (2013) Meta-analysis methods for genome-wide association studies and beyond. Nat Rev Genet 14:379–389PubMedCrossRefGoogle Scholar
  194. Fan ZQ, Ba LJ, Shan W, Xiao YY, Lu WJ, Kuang JF, Chen JY (2018) A banana R2R3-MYB transcription factor MaMYB3 is involved in fruit ripening through modulation of starch degradation by repressing starch degradation-related genes and MabHLH6. Plant J 96(6):1191–1205PubMedCrossRefGoogle Scholar
  195. Fang X, Cui Y, Li Y, Qi Y (2015) Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis. Nat Plants 1:15075PubMedCrossRefGoogle Scholar
  196. Fanwoua J, de Visser PHB, Heuvelink E, Yin X, Struik PC, Marcelis LFM (2013) A dynamic model of tomato fruit growth integrating cell division, cell growth and endoreduplication. Funct Plant Biol 40(11):1098–1114CrossRefGoogle Scholar
  197. FAO (2015) Coping with climate change—the roles of genetic resources for food and agricultureGoogle Scholar
  198. Farashi S, Kryza T, Clements J, Batra J (2019) Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 19:46–59PubMedCrossRefGoogle Scholar
  199. Fereres E, Soriano MA (2006) Deficit irrigation for reducing agricultural water use. J Exp Bot 58:147–159PubMedCrossRefGoogle Scholar
  200. Fernandes SB, Dias KOG, Ferreira DF, Brown PJ (2018) Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum. Theor Appl Genet 131:747–755PubMedCrossRefGoogle Scholar
  201. Fernandez AI, Viron N, Alhagdow M, Karimi M, Jones M, Amsellem Z, Sicard A, Czerednik A, Angenent G, Grierson D, May S (2009) Flexible tools for gene expression and silencing in tomato. Plant Physiol 151(4):1729–1740PubMedPubMedCentralCrossRefGoogle Scholar
  202. Fernie AR, Aharoni A, Willmitzer L, Stitt M, Tohge T, Kopka J, Carroll AJ, Saito K, Fraser PD, DeLuca V (2011) Recommendations for reporting metabolite data. Plant Cell 23:2477–2482PubMedPubMedCentralCrossRefGoogle Scholar
  203. Fernie AR, Schauer N (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends Genet 25:39–48PubMedCrossRefGoogle Scholar
  204. Finkers R, Bai YL, van den Berg P, van Berloo R, Meijer-Dekens F, ten Have A, van Kan J, Lindhout P, van Heusden AW (2008) Quantitative resistance to Botrytis cinerea from Solanum neorickii. Euphytica 159:83–92CrossRefGoogle Scholar
  205. Finkers R, van den Berg P, van Berloo R, ten Have A, van Heusden AW, van Kan JAL, Lindhout P (2007a) Three QTLs for Botrytis cinerea resistance in tomato. Theor Appl Genet 114:585–593PubMedCrossRefGoogle Scholar
  206. Finkers R, Van Heusden AW, Meijer-Dekens F, Van Kan JAL, Maris P, Lindhout P (2007b) The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea. Theor Appl Genet 114:1071–1080PubMedPubMedCentralCrossRefGoogle Scholar
  207. Fishman S, Génard M (1998) A biophysical model of fruit growth: simulation of seasonal and diurnal dynamics of mass. Plant Cell Environ 21:739–752CrossRefGoogle Scholar
  208. Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358PubMedPubMedCentralGoogle Scholar
  209. Foolad MR, Merk HL, Ashrafi H (2008) Genetics, genomics and breeding of late blight and early blight resistance in tomato. Crit Rev Plant Sci 27:75–107CrossRefGoogle Scholar
  210. Foolad MR, Panthee DR (2012) Marker-assisted selection in tomato breeding. Crit Rev Plant Sci 31:93–123CrossRefGoogle Scholar
  211. Foolad MR, Sullenberger MT, Ohlson EW, Gugino BK (2014) Response of accessions within tomato wild species, Solanum pimpinellifolium to late blight. Plant Breed 133:401–411CrossRefGoogle Scholar
  212. Foolad MR, Zhang LP, Khan AA, Nino-Liu D, Lin GY (2002) Identification of QTLs for early blight (Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross. Theor Appl Genet 104:945–958PubMedCrossRefPubMedCentralGoogle Scholar
  213. Fragkostefanakis S, Mesihovic A, Simm S, Paupière MJ, Hu Y, Paul P, Mishra SK, Tschiersch B, Theres K, Bovy A et al (2016) HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues. Plant Physiol 170:2461–2477PubMedPubMedCentralCrossRefGoogle Scholar
  214. Fragkostefanakis S, Röth S, Schleiff E, Scharf KD (2015) Prospects of engineering thermotolerance in crops through modulation of heat stress transcription factor and heat shock protein networks. Plant, Cell Environ 38:1881–1895CrossRefGoogle Scholar
  215. Frary A, Doganlar S, Daunay MC, Tanksley SD (2003) QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species. Theor Appl Genet 107:359–370PubMedCrossRefPubMedCentralGoogle Scholar
  216. Frary A, Fulton TM, Zamir D, Tanksley SD (2004) Advanced backcross QTL analysis of a Lycopersicon esculentum × L. pennellii cross and identification of possible orthologs in the Solanaceae. Theor Appl Genet 108:485–496PubMedCrossRefPubMedCentralGoogle Scholar
  217. Frary A, Keleş D, Pinar H, Göl D, Doğanlar S (2011) NaCl tolerance in Lycopersicon pennellii introgression lines: QTL related to physiological responses. Biol Plant 55:461–468CrossRefGoogle Scholar
  218. Frary A, Nesbitt TC, Frary A, Grandillo S, Van Der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB et al (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science (80-) 289: 85–88PubMedCrossRefPubMedCentralGoogle Scholar
  219. Frary A, Göl D, Keleş D, Ökmen B, Pınar H, Şığva HÖ et al (2010) Salt tolerance in Solanum pennellii: antioxidant response and related QTL. BMC Plant Biol 10:58PubMedPubMedCentralCrossRefGoogle Scholar
  220. Fridman E, Carrari F, Liu YS, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science (80-) 305: 1786–1789PubMedCrossRefPubMedCentralGoogle Scholar
  221. Fridman E, Liu YS, Carmel-Goren L, Gur A, Shoresh M, Pleban T, Eshed Y, Zamir D (2002) Two tightly linked QTLs modify tomato sugar content via different physiological pathways. Mol Genet Genom 266: 821–826PubMedCrossRefPubMedCentralGoogle Scholar
  222. Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723PubMedPubMedCentralCrossRefGoogle Scholar
  223. Fridman E, Zamir D (2003) Functional divergence of a syntenic invertase gene family in tomato, potato, and Arabidopsis. Plant Physiol 131:603–609PubMedPubMedCentralCrossRefGoogle Scholar
  224. Fry WE, Goodwin SB (1997) Re-emergence of potato and tomato late blight in the United States. Plant Dis 81:1349–1357PubMedCrossRefPubMedCentralGoogle Scholar
  225. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol 9:436–442PubMedPubMedCentralCrossRefGoogle Scholar
  226. Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, et al. (2016) A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification. G3: GenesGenomesGenet 6:3169–3184PubMedPubMedCentralCrossRefGoogle Scholar
  227. Fulton TM (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467PubMedPubMedCentralCrossRefGoogle Scholar
  228. Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894CrossRefGoogle Scholar
  229. Fulton TM, Grandillo S, Beck-Bunn T, Fridman E, Frampton A, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (2000) Advanced backcross QTL analysis of a Lycopersicon esculentum × Lycopersicon parviflorum cross. Theor Appl Genet 100:1025–1042CrossRefGoogle Scholar
  230. Gaion LA, Muniz JC, Barreto RF, D’Amico-Damião V, de Mello Prado R, Carvalho RF (2019) Amplification of gibberellins response in tomato modulates calcium metabolism and blossom end rot occurrence. Sci Hortic (Amsterdam) 246:498–505CrossRefGoogle Scholar
  231. Gaj T, Gersbach CA, Barbas CF (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405PubMedPubMedCentralCrossRefGoogle Scholar
  232. Gallusci P, Hodgman C, Teyssier E, Seymour GB (2016) DNA methylation and chromatin regulation during fleshy fruit development and ripening. Front Plant Sci 7:807PubMedPubMedCentralCrossRefGoogle Scholar
  233. Gao C, Ju Z, Cao D, Zhai B, Qin G, Zhu H, Fu D, Luo Y, Zhu B (2015) MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation. Plant Biotechnol J 13:370–382PubMedCrossRefPubMedCentralGoogle Scholar
  234. Gao L, Gonda I, Sun H et al (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51:1044–1051PubMedCrossRefGoogle Scholar
  235. Garcia V, Bres C, Just D, Fernandez L, Tai FWJ, Mauxion JP, Le Paslier MC, Bérard A, Brunel D, Aoki K et al (2016) Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing. Nat Protoc 11:2401–2418PubMedCrossRefPubMedCentralGoogle Scholar
  236. Gauffier C, Lebaron C, Moretti A, Constant C, Moquet F, Bonnet G, Caranta C, Gallois J-L (2016) A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy. Plant J 85:717–729PubMedCrossRefPubMedCentralGoogle Scholar
  237. Gautier H, Diakou-Verdin V, Bénard C, Reich M, Buret M, Bourgaud F, Poëssel JL, Caris-Veyrat C, Génard M (2008) How does tomato quality (sugar, acid, and nutritional quality) vary with ripening stage, temperature, and irradiance? J Agri Food Chem 56:1241–1250CrossRefGoogle Scholar
  238. Génard M, Bertin N, Gautier H, Lescourret F, Quilot B (2010) Virtual profiling: a new way to analyse phenotypes. Plant J 62:344–355PubMedCrossRefPubMedCentralGoogle Scholar
  239. Génard M, Lescourret F (2004) Modelling fruit quality: ecophysiological, agronomical and ecological perspectives. In: Dris R, Jain SM (eds) Production practices and quality assessment of food crops, vol 1. Preharvest practice. Kluwer Academic Publisher, Netherlands, pp 47–82CrossRefGoogle Scholar
  240. Génard M, Memmah M-M, Quilot-Turion B, Vercambre G, Baldazzi V, Le Bot J, Bertin N, Gautier H, Lescourret F, Pagès L (2016) Process-based simulation models are essential tools for virtual profiling and design of ideotypes: example of fruit and root. In: Yin X, Struik PC (eds) Crop systems biology: narrowing the gaps between crop modelling and genetics, pp 83–104CrossRefGoogle Scholar
  241. Gerszberg A, Hnatuszko-Konka K, Kowalczyk T, Kononowicz AK (2015) Tomato (Solanum lycopersicum L.) in the service of biotechnology. Plant Cell Tiss Org Cult 120(3):881–902CrossRefGoogle Scholar
  242. Geshnizjani N, Ghaderi-Far F, Willems LAJ, Hilhorst HWM, Ligterink W (2018) Characterization of and genetic variation for tomato seed thermo-inhibition and thermo-dormancy. BMC Plant Biol 18:229PubMedPubMedCentralCrossRefGoogle Scholar
  243. Gest N, Gautier H, Stevens R (2013) Ascorbate as seen through plant evolution: the rise of a successful molecule? J Exp Bot 64:33–53PubMedCrossRefPubMedCentralGoogle Scholar
  244. Gianola D, van Kaam JBCHM (2008) Reproducing Kernel Hilbert spaces regression methods for genomic assisted prediction of quantitative traits. Genetics 178:2289PubMedPubMedCentralCrossRefGoogle Scholar
  245. Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol 68:61–84PubMedCrossRefPubMedCentralGoogle Scholar
  246. Giovannucci E (1999) Tomatoes, tomato-based products, lycopene, and cancer: review of the epidemiologic literature. J Natl Cancer Inst 91:317–331PubMedCrossRefPubMedCentralGoogle Scholar
  247. Giroux RW, Filion WG (1992) A comparison of the chilling-stress response in two differentially tolerant cultivars of tomato (Lycopersicon esculentum). Biochem Cell Biol 70:191–198PubMedCrossRefPubMedCentralGoogle Scholar
  248. Goff SA, Klee HJ (2006) Plant volatile compounds: sensory cues for health and nutritional value? Science 311:815–819PubMedCrossRefPubMedCentralGoogle Scholar
  249. Gonatopoulos-Pournatzis T, Cowling VH (2015) Cap-binding complex (CBC). Biochem J 458:185CrossRefGoogle Scholar
  250. Gonzalez-Cendales Y, Catanzariti AM, Baker B, McGrath DJ, Jones DA (2016) Identification of I-7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes. Mol Plant Pathol 17:448–463PubMedPubMedCentralCrossRefGoogle Scholar
  251. Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351PubMedCrossRefPubMedCentralGoogle Scholar
  252. Grandillo S, Cammareri M (2016) Molecular mapping of quantitative trait loci in tomato. In: Causse M, Giovannoni J, Bouzayen M, Zouine M (eds) The tomato genome. Springer, Berlin, pp 39–73CrossRefGoogle Scholar
  253. Grandillo S, Chetelat R, Knapp S, Spooner D, Peralta I, Cammareri M, Perez O, Termolino P, Tripodi P, Chiusano ML et al (2011) Solanum sect. Lycopersicon. In: Kole C (ed) Wild crop relatives: genomic and breeding resources. Springer, Berlin, pp 129–215CrossRefGoogle Scholar
  254. Grandillo S, Ku HM, Tanksley SD (1996) Characterization of fs8.1, a major QTL influencing fruit shape in tomato. Mol Breed 2:251–260CrossRefGoogle Scholar
  255. Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99:978–987CrossRefGoogle Scholar
  256. Grandillo S, Tanksley SD (1996a) Genetic analysis of RFLPs, GATA microsatellites and RAPDs in a cross between L. esculentum and L. pimpinellifolium. Theor Appl Genet 92:957–965PubMedCrossRefPubMedCentralGoogle Scholar
  257. Grandillo S, Tanksley SD (1996b) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951PubMedCrossRefPubMedCentralGoogle Scholar
  258. Grandillo S, Termolino P, van der Knaap E (2013) Molecular mapping of complex traits in tomato. In: Liedl BE, Labate JA, Stommel JR, Slade A, Kole C (eds) Genetics, genomics and breeding of tomato. CRC Press, Boca Raton, FL, pp 150–227CrossRefGoogle Scholar
  259. Grierson D (2016) Identifying and silencing tomato ripening genes with antisense genes. Plant Biotechnol J14(3):835–838CrossRefGoogle Scholar
  260. Grilli G, Trevizan Braz L, Gertrudes E, Lemos M (2007) QTL identification for tolerance to fruit set in tomatoby fAFLP markers. Crop Breed Appl Biotechnol 7:234–241CrossRefGoogle Scholar
  261. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193–1197PubMedCrossRefPubMedCentralGoogle Scholar
  262. Guan Y, Stephens M (2008) Practical issues in imputation-based association mapping. PLoS Genet. Scholar
  263. Guichard S, Bertin N, Leonardi C, Gary C (2001) Tomato fruit quality in relation to water and carbon fluxes. Agronomie 21:385–392CrossRefGoogle Scholar
  264. Guichard S, Gary C, Leonardi C, Bertin N (2005) Analysis of growth and water relations of tomato fruits in relation to air vapor pressure deficit and plant fruit load. J Plant Growth Regul 24:201–213CrossRefGoogle Scholar
  265. Gupta A, Pal RK, Rajam MV (2013) Delayed ripening and improved fruit processing quality in tomato by RNAi-mediated silencing of three homologs of 1-aminopropane-1-carboxylate synthase gene. JPlant Physiol 170(11):987–995CrossRefGoogle Scholar
  266. Gur A, Osorio S, Fridman E, Fernie AR, Zamir D (2010) hi2-1, A QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes. Theor Appl Genet 121:1587–1599PubMedPubMedCentralCrossRefGoogle Scholar
  267. Gur A, Semel Y, Osorio S, Friedmann M, Seekh S, Ghareeb B et al (2011) Yield quantitative trait loci from wild tomato are predominately expressed by the shoot. Theor Appl Genet 122:405–420PubMedCrossRefGoogle Scholar
  268. Gur A, Zamir D (2015) Mendelizing all components of a pyramid of three yield QTL in tomato. Front Plant Sci 6:1096. Scholar
  269. Haanstra JPW, Wye C, Verbakel H, Meijer-Dekens F, Van Den Berg P, Odinot P, Van Heusden AW, Tanksley S, Lindhout P, Peleman J (1999) An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum x L. pennellii F2 populations. Theor Appl Genet 99:254–271CrossRefGoogle Scholar
  270. Habier D, Fernando RL, Kizilkaya K, Garrick DJ (2011) Extension of the bayesian alphabet for genomic selection. BMC Bioinformatics 12:186PubMedPubMedCentralCrossRefGoogle Scholar
  271. Hagassou D, Francia E, Ronga D, Buti M (2019) Blossom end-rot in tomato (Solanum lycopersicum L.): A multi-disciplinary overview of inducing factors and control strategies. Sci Hortic (Amsterdam) 249:49–58CrossRefGoogle Scholar
  272. Haggard JE, Johnson EB, St. Clair DA (2013) Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato solanum habrochaites. G3: GenesGenomes|Genet 3: 2131–2146Google Scholar
  273. Halperin E, Stephan DA (2009) SNP imputation in association studies. Nat Biotechnol 27:349–351PubMedCrossRefGoogle Scholar
  274. Hamilton JP, Sim S-C, Stoffel K, Van Deynze A, Buell CR, Francis DM (2012) Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome J 5:17CrossRefGoogle Scholar
  275. Han P, Lavoir A-V, Le Bot J, Amiens-Desneux E, Desneux N (2015) Nitrogen and water availability to tomato plants triggers bottom-up effects on the leafminer Tuta absoluta. Sci Rep 4:4455CrossRefGoogle Scholar
  276. Hanson PM, Yang R, Wu J, Chen J, Ledesma D, Tsou SCS, Lee T-C (2004) Variation for antioxidant activity and antioxidants in tomato. J Amer Soc Hort Sci 129:704–711CrossRefGoogle Scholar
  277. Hanssen IM, Thomma B (2010) Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops. Mol Plant Pathol 11:179–189PubMedCrossRefGoogle Scholar
  278. Hanssens J, De Swaef T, Steppe K (2015) High light decreases xylem contribution to fruit growth in tomato. Plant Cell Environ 38:487–498PubMedCrossRefGoogle Scholar
  279. Harborne JB (1994) The flavonoids. Advances in research since 1986, 1st edn. Chapman Hall, LondonGoogle Scholar
  280. Harvell CD, Mitchell CE, Ward JR, Altizer S, Dobson AP, Ostfeld RS, Samuel MD (2002) Climate warming and disease risks for terrestrial and marine biota. Science 296:2158–2162PubMedCrossRefGoogle Scholar
  281. Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KFX, et al. (2011) From RNA-seq to large-scale genotyping—genomics resources for rye (Secale cereale L.). BMC Plant Biol 11: 131PubMedPubMedCentralCrossRefGoogle Scholar
  282. Hayashi T, Iwata H (2010) EM algorithm for Bayesian estimation of genomic breeding values. BMC Genet 11:3PubMedPubMedCentralCrossRefGoogle Scholar
  283. He S, Schulthess AW, Mirdita V, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y (2016) Genomic selection in a commercial winter wheat population. Theor Appl Genet 129:641–651PubMedCrossRefGoogle Scholar
  284. He Y (2012) Chromatin regulation of flowering. Trends Plant Sci 17:556–562PubMedCrossRefGoogle Scholar
  285. Hepler PK (2005) Calcium: a central regulator of plant growth and development. Plant Cell 17:2142–2155PubMedPubMedCentralCrossRefGoogle Scholar
  286. Heslot N, Yang HP, Sorrells ME, Jannink JL (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146–160CrossRefGoogle Scholar
  287. Hess M, Druet T, Hess A, Garrick D (2017) Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population. Genet Sel Evol 49:54PubMedPubMedCentralCrossRefGoogle Scholar
  288. Heuvelink E (2005) Tomatoes. CABI Publishers, Wallingford, UKCrossRefGoogle Scholar
  289. Heuvelink E, Bertin N (1994) Dry matter partitioning in a tomato crop: comparison of two simulation models. J Hort Sci 69:885–903CrossRefGoogle Scholar
  290. Hill M, Tran N (2018) MicroRNAs regulating MicroRNAs in cancer. Trends Cancer 4:465–468PubMedCrossRefGoogle Scholar
  291. Hirschi KD (2004) The calcium conundrum. Both versatile nutrient and specific signal. Plant Physiol 136:2438–2442PubMedPubMedCentralCrossRefGoogle Scholar
  292. Ho LC (1996) The mechanism of assimilate partitioning and carbohydrate compartmentation in fruit in relation to the quality and yield of tomato. J Exp Bot 47:1239–1243PubMedCrossRefGoogle Scholar
  293. Hobson G, Grierson D (1993) Tomato. In: Biochemistry of fruit ripening. Springer, Dordrecht, pp 405–442CrossRefGoogle Scholar
  294. Hobson GE, Bedford L (1989) The composition of cherry tomatoes and its relation to consumer acceptability. J Hort Sci 64:321–329CrossRefGoogle Scholar
  295. Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147:1469–1485PubMedPubMedCentralGoogle Scholar
  296. Hospital F, Chevalet C, Mulsant P (1992) Using markers in gene introgression breeding programs. Genetics 132:1199–1210PubMedPubMedCentralGoogle Scholar
  297. How Kit A, Boureau L, Stammitti-Bert L, Rolin D, Teyssier E, Gallusci P (2010) Functional analysis of SlEZ1 a tomato Enhancer of zeste (E(z)) gene demonstrates a role in flower development. Plant Mol Biol 74:201–213PubMedCrossRefGoogle Scholar
  298. Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10:826–839PubMedCrossRefGoogle Scholar
  299. Huang WJ, Liu HK, McCormick S, Tang WH (2014) Tomato pistil factor STIG1 promotes in vivo pollen tube growth by binding to phosphatidylinositol 3-phosphate and the extracellular domain of the pollen receptor kinase LePRK2. Plant Cell 26(6):2505–2523PubMedPubMedCentralCrossRefGoogle Scholar
  300. Huang Z, van der Knaap E (2011) Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor Appl Genet 123:465–474PubMedCrossRefGoogle Scholar
  301. Hutton SF, Scott JW, Yang WC, Sim SC, Francis DM, Jones JB (2010) Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet 121:1275–1287PubMedCrossRefGoogle Scholar
  302. Ishibashi K, Masuda K, Naito S, Meshi T, Ishikawa M (2007) An inhibitor of viral RNA replication is encoded by a plant resistance gene. In: Proceedings of the national academy of sciences of the United States of America 104:13833–13838CrossRefGoogle Scholar
  303. Isidro J, Jannink J-L, Akdemir D, Poland J, Heslot N, Sorrells ME (2015) Training set optimization under population structure in genomic selection. Theor Appl Genet 128:145–158PubMedCrossRefGoogle Scholar
  304. Islam MN, Hasanuzzaman ATM, Zhang Z-F, Zhang Y, Liu T-X (2017) High level of nitrogen makes tomato plants releasing less volatiles and attracting more Bemisia tabaci (Hemiptera: Aleyrodidae). Front Plant Sci 8:466PubMedPubMedCentralGoogle Scholar
  305. Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Shima Y, Nakamura N, Kotake-Nara E, Kawasaki S, Toki S (2017) Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. Nat Plants 3(11):866–874PubMedCrossRefGoogle Scholar
  306. Iwata H, Jannink JL (2010) Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines. Crop Sci 50:1269–1278CrossRefGoogle Scholar
  307. Janse J, Schols M (1995) Une préférence pour un goût sucré et non farineux. Groenten Fruit 26:16–17Google Scholar
  308. Jatoi SA, Fujimura T, Yamanaka S, Watanabe J, Watanabe KN, Watanabe KN (2008) Potential loss of unique genetic diversity in tomato landraces by genetic colonization of modern cultivars at a non-center of origin. Plant Breed 127:189–196CrossRefGoogle Scholar
  309. Jha UC, Bohra A, Jha R (2017) Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. Plant Cell Rep 36:1–35PubMedCrossRefGoogle Scholar
  310. Jiang Y, Schmidt RH, Reif JC (2018) Haplotype-based genome-wide prediction models exploit local epistatic interactions among markers. G3: GenesGenomesGenet 8: g3.300548.2017Google Scholar
  311. Jiménez-Gómez JM, Alonso-Blanco C, Borja A, Anastasio G, Angosto T, Lozano R, Martínez-Zapater JM (2007) Quantitative genetic analysis of flowering time in tomato. Genome 50:303–315PubMedCrossRefGoogle Scholar
  312. Johansson L, Haglund Å, Berglund L, Lea P, Risvik E (1999) Preference for tomatoes, affected by sensory attributes and information about growth conditions. Food Qual Prefer 10:289–298CrossRefGoogle Scholar
  313. Johnstone PR, Hartz TK, LeStrange M, Nunez JJ, Miyao EM (2005) Managing fruit soluble solids with late-season deficit irrigation in drip-irrigated processing tomato production. HortScience 40:1857–1861CrossRefGoogle Scholar
  314. Jonas E, de Koning D-J (2013) Does genomic selection have a future in plant breeding? Trends Biotechnol 31:497–504PubMedCrossRefPubMedCentralGoogle Scholar
  315. Jones JB (1986) Survival of Xanthomonas campestris pv. vesicatoria in Florida on tomato crop residue, weeds, seeds, and volunteer tomato plants. Phytopathology 76: 430CrossRefGoogle Scholar
  316. Jones JW, Dayan E, Allen LH, Van Keulen H, Challa H (1991) A dynamic tomato growth and yield model (Tomgro). Am Soc Agri Eng 34: 663–672Google Scholar
  317. Jones DA, Thomas CM, Hammondkosack KE, Balintkurti PJ, Jones JDG (1994) Isolation of the tomato cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266:789–793PubMedCrossRefGoogle Scholar
  318. Kabelka E, Franchino B, Francis DM (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp michiganensis. Phytopathology 92:504–510PubMedCrossRefPubMedCentralGoogle Scholar
  319. Kamal HM, Takashina T, Egashira H, Satoh H, Imanishi S (2001) Introduction of aromatic fragrance into cultivated tomato from the “peruvianum complex”. Plant Breed 120:179–181CrossRefGoogle Scholar
  320. Kang BC, Yeam I, Li HX, Perez KW, Jahn MM (2007) Ectopic expression of a recessive resistance gene generates dominant potyvirus resistance in plants. Plant Biotechnol J 5:526–536PubMedCrossRefPubMedCentralGoogle Scholar
  321. Karimi Z, Sargolzaei M, Robinson JAB, Schenkel FS (2018) Assessing haplotype-based models for genomic evaluation in Holstein cattle. Can J Sci 1–10Google Scholar
  322. Karlova R, Van Haarst JC, Maliepaard C, Van De Geest H, Bovy AG, Lammers M, Angenent GC, De Maagd RA (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 64:1863–1878PubMedPubMedCentralCrossRefGoogle Scholar
  323. Kawchuk LM, Hachey J, Lynch DR, Kulcsar F, Van Rooijen G, Waterer DR, Robertson A, Kokko E, Byers R, Howard RJ et al (2001) Tomato Ve disease resistance genes encode cell surface-like receptors. Proc Natl Acad Sci USA 98:6511–6515PubMedCrossRefPubMedCentralGoogle Scholar
  324. Kazmi RH, Khan N, Willems LAJ, Van Heusden AW, Ligterink W, Hilhorst HWM (2012) Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium. Plant Cell Environ 35:929–951PubMedCrossRefPubMedCentralGoogle Scholar
  325. Keller M, Simm S (2018) The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen. BMC Genom 19:447CrossRefGoogle Scholar
  326. Kenchanmane Raju SK, Barnes AC, Schnable JC, Roston RL (2018) Low-temperature tolerance in land plants: are transcript and membrane responses conserved? Plant Sci 276:73–86PubMedCrossRefPubMedCentralGoogle Scholar
  327. Kimbara J, Ohyama A, Chikano H, Ito H, Hosoi K, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Fukuoka H et al (2018) QTL mapping of fruit nutritional and flavor components in tomato (Solanum lycopersicum) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross. Euphytica 214:210CrossRefGoogle Scholar
  328. King SR, Davis AR, Zhang X, Crosby K (2010) Genetics, breeding and selection of rootstocks for Solanaceae and Cucurbitaceae. Sci Hortic (Amsterdam) 127:106–111CrossRefGoogle Scholar
  329. Kinkade MP, Foolad MR (2013) Validation and fine mapping of lyc12.1, a QTL for increased tomato fruit lycopene content. Theor Appl Genet 126:2163–2175PubMedCrossRefPubMedCentralGoogle Scholar
  330. Kissoudis C, Chowdhury R, van Heusden S, van de Wiel C, Finkers R, Visser RGF, Bai Y, van der Linden G (2015) Combined biotic and abiotic stress resistance in tomato. Euphytica 202:317–332CrossRefGoogle Scholar
  331. Klay I, Gouia S, Liu M, Mila I, Khoudi H, Bernadac A et al (2018) Ethylene Response Factors (ERF) are differentially regulated by different abiotic stress types in tomato plants. Plant Sci 274:137–145PubMedCrossRefGoogle Scholar
  332. Klee HJ (2010) Improving the flavor of fresh fruits: genomics, biochemistry, and biotechnology. New Phytol 187:44–56PubMedCrossRefPubMedCentralGoogle Scholar
  333. Klee HJ (2013) Purple tomatoes: Longer lasting, less disease, and better for you. Curr Biol 23:R520–R521PubMedCrossRefPubMedCentralGoogle Scholar
  334. Klee HJ, Tieman DM (2013) Genetic challenges of flavor improvement in tomato. Trends Genet 29:257–262PubMedCrossRefPubMedCentralGoogle Scholar
  335. Klee HJ, Tieman DM (2018) The genetics of fruit flavour preferences. Nat Rev Genet 19:347–356PubMedCrossRefPubMedCentralGoogle Scholar
  336. Klein RJ, Zeiss C, Chew EY, Tsai J-Y, Sackler RS, Haynes C, Henning AK, Paul SanGiovanni J, Mane SM, Mayne ST et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308:385–389PubMedPubMedCentralCrossRefGoogle Scholar
  337. Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H et al (2016) Genome-wide association mapping and genomic prediction elucidate the genetic architecture of morphological traits in arabidopsis. Plant Physiol 170:2187–2203PubMedPubMedCentralCrossRefGoogle Scholar
  338. Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M (2012) A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 44:1066–1071PubMedPubMedCentralCrossRefGoogle Scholar
  339. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551PubMedPubMedCentralCrossRefGoogle Scholar
  340. Kramer M, Sanders R, Bolkan H, Waters C, Sheeny RE, Hiatt WR (1992) Postharvest evaluation of transgenic tomatoes with reduced levels of polygalacturonase: processing, firmness and disease resistance. Postharv Biol Technol 1(3):241–255CrossRefGoogle Scholar
  341. Kramer MG, Redenbaugh K (1994) Commercialization of a tomato with an antisense polygalacturonase gene: the FLAVR SAVR? tomato story. Euphytica 79:293–297CrossRefGoogle Scholar
  342. Krieger U, Lippman ZB, Zamir D (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42:459–463PubMedCrossRefPubMedCentralGoogle Scholar
  343. Kromdijk J, Bertin N, Heuvelink E, Molenaar J, de Visser PHB, Marcelis LFM, Struik PC (2013) Crop management impacts the efficiency of QTL detection and use—case study of fruit load x QTL interactions. J Exp Bot. Scholar
  344. Kropff MJ, Haverkort AJ, Aggarwal PK, Kooman PL (1995) Using systems approaches to design and evaluate ideotypes for specific environments. In: Bouma J, Bouman BAM, Luyten JC, Zandstra HG (eds) Eco-regional approaches for sustainable land use and food production. Kluwer Academic Publ, Dordrecht, Netherlands, pp 417–435CrossRefGoogle Scholar
  345. Kumar M, Ashok I, Chandrawat S (2016) Gene pyramiding: an overview. Intl J Curr Res Biosci Plant Biol. Scholar
  346. Kusmec A, Srinivasan S, Nettleton D, Schnable PS (2017) Distinct genetic architectures for phenotype means and plasticities in Zea mays. Nat Plants 3:715–723PubMedPubMedCentralCrossRefGoogle Scholar
  347. Kyriacou MC, Rouphael Y, Colla G, Zrenner R, Schwarz D (2017) Vegetable grafting: the implications of a growing agronomic imperative for vegetable fruit quality and nutritive value. Front Plant Sci 8:741Google Scholar
  348. Labate JA, Grandillo S, Fulton T, Muños S, Caicedo AL, Peralta I, Ji Y, Chetelat RT, Scott JW, Gonzalo MJ et al (2007) Tomato. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 5. Vegetables. Springer, Berlin, pp 1–125Google Scholar
  349. Lanfermeijer FC, Warmink J, Hille J (2005) The products of the broken Tm-2 and the durable Tm-2(2) resistance genes from tomato differ in four amino acids. J Exp Bot 56:2925–2933PubMedCrossRefPubMedCentralGoogle Scholar
  350. Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J, Zhang Y, Handa AK, Zhu JK (2017) Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci USA 114(22):E4511–E4519PubMedCrossRefPubMedCentralGoogle Scholar
  351. Lapidot M, Karniel U, Gelbart D, Fogel D, Evenor D, Kutsher Y, Makhbash Z, Nahon S, Shlomo H, Chen L, Reuveni M, Levin I (2015) A novel route controlling begomovirus resistance by the messenger RNA surveillance factor Pelota. PLoS Genetics 11PubMedPubMedCentralCrossRefGoogle Scholar
  352. Larbat R, Olsen KM, Slimestad R, Løvdal T, Bénard C, Verheul M, Bourgaud F, Robin C, Lillo C (2012) Influence of repeated short-term nitrogen limitations on leaf phenolics metabolism in tomato. Phytochemistry 77:119–128PubMedCrossRefPubMedCentralGoogle Scholar
  353. Laterrot H (1996) Twenty-one near isogenic lines in Moneymaker type with different genes for disease resistances. Rep Tomato Genet Coop 46:34Google Scholar
  354. Laterrot H (2000) Disease resistance in tomato: practical situation. Acta Physiol Plant 22:328–331CrossRefGoogle Scholar
  355. Laterrot H, Moretti A (1989) Linkage between Pto and susceptibility to fenthion. Tomato Genet Coop Rep 39:21–22Google Scholar
  356. Le Nguyen K, Grondin A, Courtois B, Gantet P (2018) Next-generation sequencing accelerates crop gene discovery. Trends Plant Sci 24:263–274Google Scholar
  357. Le LQ, Lorenz Y, Scheurer S, Fötisch K, Enrique E, Bartra J, Biemelt S, Vieths S, Sonnewald U (2006) Design of tomato fruits with reduced allergenicity by dsRNAi-mediated inhibition of ns-LTP (Lyc e 3) expression. Plant Biotechnol J 4(2):231–242PubMedCrossRefPubMedCentralGoogle Scholar
  358. Lecompte F, Abro MA, Nicot PC (2010) Contrasted responses of Botrytis cinerea isolates developing on tomato plants grown under different nitrogen nutrition regimes. Plant Pathol 59:891–899CrossRefGoogle Scholar
  359. Lecompte F, Nicot PC, Ripoll J, Abro MA, Raimbault AK, Lopez-Lauri F, Bertin N (2017) Reduced susceptibility of tomato stem to the necrotrophic fungus Botrytis cinerea is associated with a specific adjustment of fructose content in the host sugar pool. Ann Bot 119:931–943PubMedPubMedCentralGoogle Scholar
  360. Lecomte L, Saliba-Colombani V, Gautier A, Gomez-Jimenez MC, Duffé P, Buret M, Causse M (2004a) Fine mapping of QTLs for the fruit architecture and composition in fresh market tomato, on the distal region of the long arm of chromosome 2. Mol Breed 13:1–14CrossRefGoogle Scholar
  361. Lecomte L, Duffé P, Buret M, Servin B, Hospital F, Causse M (2004b) Marker-assisted introgression of 5 QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds. Theor Appl Genet 109:658–668PubMedCrossRefPubMedCentralGoogle Scholar
  362. Lee DR (1990) A unidirectional water flux model of fruit growth. Can J Bot 68:1286–1290CrossRefGoogle Scholar
  363. Lee JM, Oh CS, Yeam I (2015) Molecular markers for selecting diverse disease resistances in tomato breeding programs. Plant Breed Biotechnol 3:308–322CrossRefGoogle Scholar
  364. Lee JT, Prasad V, Yang PT, Wu JF, David Ho TH, Charng YY, Chan MT (2003) Expression of Arabidopsis CBF1 regulated by an ABA/stress inducible promoter in transgenic tomato confers stress tolerance without affecting yield. Plant Cell Environ 26(7):1181–1190CrossRefGoogle Scholar
  365. Lee SY, Luna-Guzman I, Chang S, Barrett DM, Guinard JX (1999) Relating descriptive analysis and instrumental texture data of processed diced tomatoes. Food Qual Pref 10:447–455CrossRefGoogle Scholar
  366. Lefebvre V, Boissot N, Gallois J-L (2018) Host plant resistance to pests and pathogens, the genetic leverage in integrated pest and disease management. In: Gullino ML, Albajes R, Nicot P, van Lenteren JC (eds) Pest and disease management in greenhouse crops. Developments in Plant Pathology. Springer International Publishing, ChamGoogle Scholar
  367. Length F (2011) Genetic diversity in 14 tomato (Lycopersicon esculentum Mill.) varieties in Nigerian markets by RAPD-PCR technique. Afr J Biotechnol 10(11):4961–4967Google Scholar
  368. Letort V, Mahe P, Cournede PH, De Reffye P, Courtois B (2008) Quantitative genetics and functional-structural plant growth models: Simulation of quantitative trait loci detection for model parameters and application to potential yield optimization. Ann Bot-London 101:1243–1254CrossRefGoogle Scholar
  369. Levin I, Gilboa N, Yeselson E, Shen S, Schaffer AA (2000) Fgr, a major locus that modulates the fructose to glucose ratio in mature tomato fruits. Theor Appl Genet 100:256–262CrossRefGoogle Scholar
  370. Li YM, Gabelman WH (1990) Inheritance of calcium use efficiency in tomatoes grown under low-calcium stress. J Am Soc Hortic Sci 115:835–838CrossRefGoogle Scholar
  371. Li J, Liu L, Bai Y, Zhang P, Finkers R, Du Y et al (2011) Seedling salt tolerance in tomato. Euphytica 178:403–414CrossRefGoogle Scholar
  372. Li T, Yang X, Yu Y, Si X, Zhai X, Zhang H, Dong W, Gao C, Xu C (2018) Domestication of wild tomato is accelerated by genome editing. Nat Biotechnol 36:1160–1163CrossRefGoogle Scholar
  373. Lin KH, Yeh WL, Chen HM, Lo HF (2010) Quantitative trait loci influencing fruit-related characteristics of tomato grown in high-temperature conditions. Euphytica 174:119–135CrossRefGoogle Scholar
  374. Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226PubMedCrossRefPubMedCentralGoogle Scholar
  375. Lindemose S, O’Shea C, Jensen M, Skriver K, Lindemose S, O’Shea C et al (2013) Structure, function and networks of transcription factors involved in abiotic stress responses. Int J Mol Sci 14:5842–5878PubMedPubMedCentralCrossRefGoogle Scholar
  376. Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23:60–66PubMedPubMedCentralCrossRefGoogle Scholar
  377. Liu Z, Alseekh S, Brotman Y, Zheng Y, Fei Z, Tieman DM, Giovannoni JJ, Fernie AR, Klee HJ (2016b) Identification of a Solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL. Front Plant Sci 7:1–15Google Scholar
  378. Liu H, Genard M, Guichard S, Bertin N (2007) Model-assisted analysis of tomato fruit growth in relation to carbon and water fluxes. J Exp Bot 58:3567–3580PubMedCrossRefPubMedCentralGoogle Scholar
  379. Liu J, Van Eck J, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306PubMedCrossRefPubMedCentralGoogle Scholar
  380. Liu HJ, Yan J (2019) Crop genome-wide association study: a harvest of biological relevance. Plant J 97:8–18PubMedCrossRefPubMedCentralGoogle Scholar
  381. Liu H, Yu C, Li H, Ouyang B, Wang T, Zhang J et al (2015) Overexpression of SHDHN, a dehydrin gene from Solanum habrochaites enhances tolerance to multiple abiotic stresses in tomato. Plant Sci 231:198–211PubMedCrossRefGoogle Scholar
  382. Liu M, Yu H, Zhao G et al (2017) Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 18:481Google Scholar
  383. Liu Y, Zhou T, Ge H, Pang W, Gao L, Ren L et al (2016a) SSR mapping of QTLs conferring cold tolerance in an interspecific cross of tomato. Intl J Genom 2016:1–6CrossRefGoogle Scholar
  384. Lobit P, Génard M, Soing P, Habib R (2006) Modelling malic acid accumulation in fruits: relationships with organic acids, potassium, and temperature. J Exp Bot 57:1471–1483PubMedCrossRefPubMedCentralGoogle Scholar
  385. Lobit P, Génard M, Wu BH, Soing P, Habib R (2003) Modelling citrate metabolism in fruits: responses to growth and temperature. J Exp Bot 54:2489–2501PubMedCrossRefPubMedCentralGoogle Scholar
  386. Lü P, Yu S, Zhu N, Chen Y-R, Zhou B, Pan Y, Tzeng D, Fabi JP, Argyris J, Garcia-Mas J et al. (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nat Plants 1Google Scholar
  387. Luo J (2015) Metabolite-based genome-wide association studies in plants. Curr Opin Plant Biol 24:31–38PubMedCrossRefGoogle Scholar
  388. Maayan Y, Pandaranayaka EPJ, Srivastava DA, Lapidot M, Levin I, Dombrovsky A, Harel A (2018) Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus. Arch Virol 163:1863–1875PubMedCrossRefGoogle Scholar
  389. Mackay IJ, Bansept-Basler P, Barber T, Bentley AR, Cockram J, Gosman N, Greenland AJ, Horsnell R, Howells R, O’Sullivan DM et al (2014) An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation. G3: GenesGenomGenet 4: 1603–1610PubMedPubMedCentralCrossRefGoogle Scholar
  390. Madhavi DL, Salunkhe DK (1998) Handbook of vegetable science and technology. In: Salunkhe DK, Kadam SS (eds) Production, composition, storage, and processing, New York, USA. Scholar
  391. Malundo TMM, Shewfelt RL, Scott JW (1995) Flavor quality of fresh tomato (Lycopersicon esculentum Mill.) as affected by sugar and acid levels. Postharv BiolTechnol 6:103–110CrossRefGoogle Scholar
  392. Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151:859–870PubMedCrossRefGoogle Scholar
  393. Mangin B, Rincent R, Rabier CE, Moreau L, Goudemand-Dugue E (2019) Training set optimization of genomic prediction by means of EthAcc. PLoS ONE 14:e0205629PubMedPubMedCentralCrossRefGoogle Scholar
  394. Mangin B, Thoquet P, Olivier J, Grimsley NH (1999) Temporal and multiple quantitative trait loci analyses of resistance to bacterial wilt in tomato permit the resolution of linked loci. Genetics 151:1165–1172PubMedPubMedCentralGoogle Scholar
  395. Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952PubMedCrossRefGoogle Scholar
  396. Mao L, Begum D, Chuang H, Budiman MA, Szymkowiak EJ, Irish EE, Wing RA (2000) JOINTLESS is a MADS-box gene controlling tomato flower abscissionzone development. Nature 406:910–913PubMedCrossRefGoogle Scholar
  397. Marchini J, Howie B (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499–511PubMedCrossRefGoogle Scholar
  398. Marques de Carvalho L, Benda ND, Vaughan MM, Cabrera AR, Hung K, Cox T, Abdo Z, Allen LH, Teal PE (2015) Mi-1-mediated nematode resistance in tomatoes is broken by short-term heat stress but recovers over time. J Nematol 47:133–140PubMedPubMedCentralGoogle Scholar
  399. Marschner H (1983) General introduction to the mineral nutrition of plants. In: Lauchli A, Bieleski R (eds) Inorganic plant nutrition. Springer, Berlin, pp 5–60CrossRefGoogle Scholar
  400. Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD, Sipvey R et al (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science (80-) 262:1432–1436PubMedCrossRefGoogle Scholar
  401. Martin GB, Frary A, Wu T, Brommonschenkel S, Chunwongse J, Earle ED, Tanksley SD (1994) A member of the tomato Pto gene family confers sensitivity to fenthion resulting in rapid cell death. Plant Cell 6:1543–1552PubMedPubMedCentralGoogle Scholar
  402. Martre P, Bertin N, Salon C, Génard M (2011) Modelling the size and composition of fruit, grain and seed by process-based simulation models. New Phytolt Tansley Review 191:601–618CrossRefGoogle Scholar
  403. Martre P, Quilot-Turion B, Luquet D, Ould-Sidi M-M, Chenu K, Debaeke P (2015) Model-assisted phenotyping and ideotype design. In: Sadras V, Calderini D (eds) Crop physiology: applications for genetic improvement and agronomy. Academic Press, London, pp 349–373CrossRefGoogle Scholar
  404. Mazzucato A, Cellini F, Bouzayen M, Zouine M, Mila I, Minoia S, Petrozza A, Picarella ME, Ruiu F, Carriero F (2015) A TILLING allele of the tomato Aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. Mol Breed 35:22CrossRefGoogle Scholar
  405. Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B et al (2008) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 116:657–669PubMedCrossRefGoogle Scholar
  406. Mboup M, Fischer I, Lainer H, Stephan W (2012) Trans-species polymorphism and Allele-Specific expression in the CBF gene family of wild tomatoes. Mol Biol Evol 29:3641–3652PubMedCrossRefGoogle Scholar
  407. McCormick S, Niedermeyer J, Fry J, Barnason A, Horsch R, Fraley R (1986) Leaf disc transformation of cultivated tomato (L. esculentum) using Agrobacterium tumefaciens. Plant Cell Rep 5(2):81–84PubMedCrossRefGoogle Scholar
  408. McCouch SR, Wright MH, Tung C-W, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P et al (2016) Open access resources for genome-wide association mapping in rice. Nat Commun 7:10532PubMedPubMedCentralCrossRefGoogle Scholar
  409. McGlasson WB, Last JH, Shaw KJ, Meldrum SK (1987) Influence of the non-ripening mutant rin and nor on the aroma of tomato fruits. HortScience 22:632–634Google Scholar
  410. Meena YK, Khurana DS, Singh K (2018) Towards enhanced low temperature stress tolerance in tomato : an approach. J Environ Biol. Scholar
  411. Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12:1612–1619PubMedPubMedCentralCrossRefGoogle Scholar
  412. Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) Insilico screening of a saturated mutation library of tomato. Plant J 38:861–872PubMedCrossRefGoogle Scholar
  413. Menda N, Strickler SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP et al (2014) Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biol 14:287PubMedPubMedCentralCrossRefGoogle Scholar
  414. Mendell JT, Olson EN (2012) MicroRNAs in stress signaling and human disease. Cell 148:1172–1187PubMedPubMedCentralCrossRefGoogle Scholar
  415. Meng C, Yang D, Ma X, Zhao W, Liang X, Ma N, Meng Q (2016) Suppression of tomato SlNAC1 transcription factor delays fruit ripening. J Plant Physiol 193:88–96PubMedCrossRefPubMedCentralGoogle Scholar
  416. Meng FJ, Xu XY, Huang FL, Li JF (2010) Analysis of genetic diversity in cultivated and wild tomato varieties in Chinese market by RAPD and SSR. Agri Sci China 9:1430–1437CrossRefGoogle Scholar
  417. Messeguer R, Ganal M, de Vicente MC, Young ND, Bolkan H, Tanksley SD (1991) High resolution RFLP map around the root knot nematode resistance gene (Mi) in tomato. Theor Appl Genet 82:529–536PubMedCrossRefPubMedCentralGoogle Scholar
  418. Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedPubMedCentralGoogle Scholar
  419. Migault V, Pallas B, Costes E (2017) Combining genome-wide information with a functional structural plant model to simulate 1-year-old apple tree architecture. Front Plant Sci. Scholar
  420. Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448PubMedCrossRefPubMedCentralGoogle Scholar
  421. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10:1307–1319PubMedPubMedCentralCrossRefGoogle Scholar
  422. Milner S et al (2011) Bioactivities of glycoalkaloids and their aglycones from Solanum species. J Agri Food Chem 59:3454–3484CrossRefGoogle Scholar
  423. Minamikawa MF, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S, Yoshioka T, Imai A, Hamada H, Hayashi T et al (2017) Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Sci Rep 7:4721PubMedPubMedCentralCrossRefGoogle Scholar
  424. Minoïa S, Bendahmane A, Piron F, Salgues A, Moretti A, Caranta C, Piednoir E, Nicolaï M, Zamir D (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS ONE 5:e11313PubMedPubMedCentralCrossRefGoogle Scholar
  425. Minoia S, Cellini F, Bendahmane A, D’Onofrio O, Petrozza A, Carriero F, Piron F, Mosca G, Sozio G (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes. Scholar
  426. Mirnezhad M, Romero-Gonzalez RR, Leiss KA, Choi YH, Verpoorte R, Klinkhamer PG (2010) Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes. Phytochem Analys 21(1):110–117CrossRefGoogle Scholar
  427. Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14:267–274PubMedCrossRefPubMedCentralGoogle Scholar
  428. Mitchell J, Shennan C, Grattan S (1991) Developmental-changes in tomato fruit composition in response to water deficit and salinity. Physiol Plant 83:177–185CrossRefGoogle Scholar
  429. Mohorianu I, Schwach F, Jing R, Lopez-Gomollon S, Moxon S, Szittya G, Sorefan K, Moulton V, Dalmay T (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J 67:232–246PubMedCrossRefPubMedCentralGoogle Scholar
  430. Molgaard P, Ravn H (1988) Evolutionary aspects of caffeoyl ester distribution in dicotyledons. Phytochemistry 27:2411–2421CrossRefGoogle Scholar
  431. Monforte AJ, Asíns MJ, Carbonell EA (1996) Salt tolerance in Lycopersicon species. IV. Efficiency of marker-assisted selection for salt tolerance improvement. Theor Appl Genet 93–93:765–772CrossRefGoogle Scholar
  432. Monforte AJ, Asíns MJ, Carbonell EA (1997a) Salt tolerance in Lycopersicon species VI. Genotype-by-salinity interaction in quantitative trait loci detection: constitutive and response QTLs. Theor Appl Genet 95:706–713CrossRefGoogle Scholar
  433. Monforte AJ, Asíns MJ, Carbonell EA (1997b) Salt tolerance in Lycopersicon species. V. Does genetic variability at quantitative trait loci affect their analysis? Theor Appl Genet 95:284–293CrossRefGoogle Scholar
  434. Monforte AJ, Tanksley SD (2000) Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield. Theor Appl Genet 100:471–479CrossRefGoogle Scholar
  435. Montesinos-López OA, Montesinos-López A, Crossa J, Toledo FH, Pérez-Hernández O, Eskridge KM, Rutkoski J (2016) A genomic Bayesian MULTI-TRAIT AND MULTI-ENVIRONMENT MODEL. G3: GenesGenomGenet 6: 2725–2744PubMedPubMedCentralCrossRefGoogle Scholar
  436. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18:1602–1609PubMedPubMedCentralCrossRefGoogle Scholar
  437. Mu Q, Huang Z, Chakrabarti M, Illa-Berenguer E, Liu X, Wang Y, Ramos A, van der Knaap E (2017) Fruit weight is controlled by cell size regulator encoding a novel protein that is expressed in maturing tomato fruits. PLoS Genet 13:e1006930PubMedPubMedCentralCrossRefGoogle Scholar
  438. Muir SR, Collins GJ, Robinson S, Hughes S, Bovy A, Ric De Vos CH, van Tunen AJ, Verhoeyen ME (2001) Overexpression of petunia chalcone isomerase in tomato results in fruit containing increased levels of flavonols. Nat Biotechnol 19:470–474PubMedCrossRefPubMedCentralGoogle Scholar
  439. Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen M, Cheng Z, Li C, Ling H, Xue Y, Seymour G, Bishop G, Bryan G, Sharma R, Khurana J, Tyagi A, Chattopadhyay D, Singh NK, Stiekema W, Lindhout P, Jesse T, Lankhorst RK, Bouzayen M, Shibata D, Tabata S, Granell A, Botella MA, Giuliano G, Frusciante L, Causse M, Zamir D (2005) The tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics 6(3):153–158PubMedPubMedCentralCrossRefGoogle Scholar
  440. Müller BSF, Neves LG, de Almeida Filho JE, Resende MFR, Muñoz PR, dos Santos PET, Filho EP, Kirst M, Grattapaglia D (2017) Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genom 18:524CrossRefGoogle Scholar
  441. Munns R, Gilliham M (2015) Salinity tolerance of crops - what is the cost? New Phytol 208:668–673PubMedCrossRefPubMedCentralGoogle Scholar
  442. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681CrossRefGoogle Scholar
  443. Muños S, Ranc N, Botton E, Bérard A, Rolland S, Duffé P, Carretero Y, Le Paslier MC, Delalande C, Bouzayen M, Brunel D, Causse M (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156(4):2244–2254PubMedPubMedCentralCrossRefGoogle Scholar
  444. Mutshinda CM, Sillanpää MJ (2010) Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction. Genetics 186:1067–1075PubMedPubMedCentralCrossRefGoogle Scholar
  445. Nadeem M, Li J, Wang M, Shah L, Lu S, Wang X, Ma C, Nadeem M, Li J, Wang M et al (2018) Unraveling field crops sensitivity to heat stress: mechanisms, approaches, and future prospects. Agronomy 8:128CrossRefGoogle Scholar
  446. Nakazato T, Warren DL, Moyle LC (2010) Ecological and geographic modes of species divergence in wild tomatoes. Amer J Bot 97:680–693CrossRefGoogle Scholar
  447. Navarro JM, Flores P, Carvajal M, Martinez V (2005) Changes in quality and yield of tomato fruit with ammonium, bicarbonate and calcium fertilisation under saline conditions. J Hort Sci Biotechnol 80:351–357CrossRefGoogle Scholar
  448. Naves ER, de Ávila Silva L, Sulpice R, Araújo WL, Nunes-Nesi A, Peres LE, Zsögön A (2019) Capsaicinoids: pungency beyond capsicum. Trends Plant Sci 24:109–120PubMedCrossRefPubMedCentralGoogle Scholar
  449. Nawaz MA, Imtiaz M, Kong Q, Cheng F, Ahmed W, Huang Y et al (2016) Grafting: a technique to modify ion accumulation in horticultural crops. Front Plant Sci 7:1457Google Scholar
  450. Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S (2017) Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 7:482PubMedPubMedCentralCrossRefGoogle Scholar
  451. Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162:365–379PubMedPubMedCentralGoogle Scholar
  452. Nombela G, Williamson VM, Muniz M (2003) The root-knot nematode resistance gene Mi-1.2 of tomato is responsible for resistance against the whitefly Bemisia tabaci. Mol Plant-Microbe Interact 16:645–649PubMedCrossRefPubMedCentralGoogle Scholar
  453. Nuruddin MM, Madramootoo CA, Dodds GT (2003) Effects of water stress at different growth stages on greenhouse tomato yield and quality. HortScience 38:1389–1393CrossRefGoogle Scholar
  454. Ofner I, Lashbrooke J, Pleban T, Aharoni A, Zamir D (2016) Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits. Plant J 87:151–160PubMedCrossRefPubMedCentralGoogle Scholar
  455. Ohlson EW, Ashrafi H, Foolad MR (2018) Identification and mapping of late blight resistance quantitative trait loci in tomato accession PI 163245. Plant Genome 11Google Scholar
  456. Ohlson EW, Foolad MR (2016) Genetic analysis of resistance to tomato late blight in Solanum pimpinellifolium accession PI 163245. Plant Breed 135:391–398CrossRefGoogle Scholar
  457. Okabe Y, Asamizu E, Saito T, Matsukura C, Ariizumi T, Brès C, Rothan C, Mizoguchi T, Ezura H (2011) Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Physiol 52:1994–2005PubMedPubMedCentralCrossRefGoogle Scholar
  458. Okello RCO, Heuvelink E, de Visser PHB, Struik PC, Marcelis LFM (2015) What drives fruit growth? Funct Plant Biol 42:817–827CrossRefGoogle Scholar
  459. Oliver JE, Whitfield AE (2016) The genus tospovirus: emerging bunyaviruses that threaten food security. In: Enquist LW (ed) Annu Rev Virol 3:101–124Google Scholar
  460. Ongom PO, Ejeta G (2017) Mating design and genetic structure of a multi-parent advanced generation intercross (MAGIC) population of Sorghum (Sorghum bicolor (L.) Moench). G3 Genes|Genomes|Genetics 8:331–341PubMedCentralCrossRefGoogle Scholar
  461. Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley S, Zamir D, Fluhr R (1997) The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes. Plant Cell (The) 9:521–532PubMedPubMedCentralGoogle Scholar
  462. Osorio S, Ruan Y-L, Fernie AR (2014) An update on source-to-sink carbon partitioning in tomato. Front Plant Sci 5:516PubMedPubMedCentralCrossRefGoogle Scholar
  463. Ould-Sidi M-M, Lescourret F (2011) Model-based design of innovative cropping systems: state of the art and new prospects. AgronSustain Dev 31(3):571–588Google Scholar
  464. Overy SA, Walker HJ, Malone S, Howard TP, Baxter CJ, Sweetlove LJ, Hill SA, Quick WP (2004) Application of metabolite profiling to the identification of traits in a population of tomato introgression lines. J Exp Bot 56:287–296PubMedCrossRefPubMedCentralGoogle Scholar
  465. Pailles Y, Ho S, Pires IS, Tester M, Negrão S, Schmöckel SM (2017) Genetic diversity and population structure of two tomato species from the Galapagos Islands. Front Plant Sci 8:138PubMedPubMedCentralCrossRefGoogle Scholar
  466. Panthee DR, Piotrowski A, Ibrahem R (2017) Mapping Quantitative Trait Loci (QTL) for resistance to late blight in tomato. Int J Mol Sci 18 (7). pii: E1589.
  467. Papadopoulos I, Rendig VV (1983) Interactive effects of salinity and nitrogen on growth and yield of tomato plants. Plant Soil 73:47–57CrossRefGoogle Scholar
  468. Paran I, Goldman I, Tanksley SD, Zamir D (1995) Recombinant inbred lines for genetic mapping in tomato. Theor Appl Genet 90:542–548PubMedCrossRefPubMedCentralGoogle Scholar
  469. Park T, Casella G (2008) The Bayesian lasso. J Amer Stat Assoc 103:681–686CrossRefGoogle Scholar
  470. Park YH, West MA, St. Clair DA (2004) Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.). Genome 47:510–518PubMedCrossRefPubMedCentralGoogle Scholar
  471. Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P et al (2012) Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet 44:631–635PubMedPubMedCentralCrossRefGoogle Scholar
  472. De Pascale S, Maggio A, Fogliano V, Ambrosino P, Ritieni A (2001) Irrigation with saline water improves carotenoids content and antioxidant activity of tomato. J Hort Sci Biotechnol 76:447–453CrossRefGoogle Scholar
  473. Pascual L, Desplat N, Huang BE, Desgroux A, Bruguier L, Bouchet JP, Le QH, Chauchard B, Verschave P, Causse M (2015) Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol J 13:565–577PubMedCrossRefPubMedCentralGoogle Scholar
  474. Patanè C, Cosentino SL (2010) Effects of soil water deficit on yield and quality of processing tomato under a mediterranean climate. Agri Water Manag 97:131–138CrossRefGoogle Scholar
  475. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Loncoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197PubMedPubMedCentralGoogle Scholar
  476. Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742PubMedPubMedCentralGoogle Scholar
  477. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726PubMedCrossRefPubMedCentralGoogle Scholar
  478. Pattison RJ, Csukasi F, Zheng Y, Fei Z, van der Knaap E, Catalá C (2015) Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiol 168(4):1684–1701PubMedPubMedCentralCrossRefGoogle Scholar
  479. Peralta IE, Knapp S, Spooner DM (2005) New species of wild tomatoes (Solanum Section Lycopersicon: Solanaceae) from Northern Peru. Syst Bot 30:424–434CrossRefGoogle Scholar
  480. Pertuzé RA, Ji Y, Chetelat RT (2003) Comparative linkage map of the Solanum lycopersicoides and S. sitiens genomes and their differentiation from tomato. Genome 45:1003–1012CrossRefGoogle Scholar
  481. Petró-Turza M (1986) Flavor of tomato and tomato products. Food Rev Intl 2:309–351CrossRefGoogle Scholar
  482. Pettigrew WT (2008) Potassium influences on yield and quality production for maize, wheat, soybean and cotton. Physiol Plant 133:670–681PubMedCrossRefPubMedCentralGoogle Scholar
  483. Philouze J (1991) Description of isogenic lines, except for one, or two, monogenically controlled morphological traits in tomato, Lycopersicon esculentum Mill. Euphytica 56:121–131CrossRefGoogle Scholar
  484. Pillen K, Ganal MW, Tanksley SD (1996) Construction of a high-resolution genetic map and YAC-contigs in the tomato Tm-2a region. Theor Appl Genet 93:228–233PubMedCrossRefPubMedCentralGoogle Scholar
  485. Piron F, Nicolai M, Minoia S, Piednoir E, Moretti A, Salgues A, Zamir D, Caranta C, Bendahmane A (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PloS One 5PubMedPubMedCentralCrossRefGoogle Scholar
  486. Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Zamir D, Lifschitz E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125(11):1979–1989PubMedPubMedCentralGoogle Scholar
  487. Poiroux-Gonord F, Bidel LPR, Fanciullino A-L, Gautier H, Lauri-Lopez F, Urban L (2010) Health benefits of vitamins and secondary metabolites of fruits and vegetables and prospects to increase their concentrations by agronomic approaches. J Agri Food Chem 58:12065–12082CrossRefGoogle Scholar
  488. Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14:21–29PubMedCrossRefGoogle Scholar
  489. Prudent M, Lecomte A, Bouchet JP, Bertin N, Causse M, Génard M (2011) Combining ecophysiological modelling and quantitative trait loci analysis to identify key elementary processes underlying tomato fruit sugar concentration. J Exp Bot 62:907–919PubMedCrossRefPubMedCentralGoogle Scholar
  490. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183PubMedPubMedCentralCrossRefGoogle Scholar
  491. Quadrana L, Almeida J, Asís R, Duffy T, Dominguez PG, Bermúdez L, Conti G, Corrêa da Silva JV, Peralta IE, Colot V et al (2014) Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun 5:4027CrossRefGoogle Scholar
  492. Quilot B, Kervella J, Genard M, Lescourret F (2005) Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach. J Exp Bot 56:3083–3092PubMedCrossRefPubMedCentralGoogle Scholar
  493. Quilot-Turion B, Génard M, Valsesia P, Memmah M-M (2016) Optimization of allelic combinations controlling parameters of a Peach quality model. Front Plant Sci 7:1873PubMedPubMedCentralCrossRefGoogle Scholar
  494. Quilot-Turion B, Ould-Sidi M-M, Kadrani A, Hilgert N, Génard M, Lescourret F (2012) Optimization of parameters of the ‘Virtual Fruit’ model to design peach genotype for sustainable production systems. Eur J Agron 42:34–48CrossRefGoogle Scholar
  495. Quinet M, Kinet J-M, Lutts S (2011) Flowering response of the uniflora: blind: self-pruning and jointless: uniflora: self-pruning tomato (Solanum lycopersicum) triple mutants. Physiol Plant 141:166–176PubMedCrossRefPubMedCentralGoogle Scholar
  496. Rached M, Pierre B, Yves G, Matsukura C, Ariizumi T, Ezura H et al (2018) Differences in blossom-end rot resistance in tomato cultivars is associated with total ascorbate rather than calcium concentration in the distal end part of fruits per se Hortic J 87:372–381Google Scholar
  497. Rajasekaran LR, Aspinall D, Paleg LG (2000) Physiological mechanism of tolerance of Lycopersicon spp. exposed to salt stress. Can J Plant Sci 80:151–159CrossRefGoogle Scholar
  498. Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38:S8–S13PubMedCrossRefPubMedCentralGoogle Scholar
  499. Rambla JL, Tikunov YM, Monforte AJ, Bovy AG, Granell A (2014) The expanded tomato fruit volatile landscape. J Exp Bot 65:4613–4623PubMedCrossRefPubMedCentralGoogle Scholar
  500. Ramstein GP, Jensen SE, Buckler ES (2018) Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theor Appl Genet 132:559–567PubMedPubMedCentralCrossRefGoogle Scholar
  501. Ranc N, Muños S, Xu J, Le Paslier M-C, Chauveau A, Bounon R, Rolland S, Bouchet J-P, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3: GenesGenomesGenet 2: 853–864Google Scholar
  502. Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L et al (2016) eQTL regulating transcript levels associated with diverse biological processes in tomato. Plant Physiol 172(1):328–340PubMedPubMedCentralCrossRefGoogle Scholar
  503. Rao ES, Kadirvel P, Symonds RC, Ebert AW (2013) Relationship between survival and yield related traits in Solanum pimpinellifolium under salt stress. Euphytica 190:215–228CrossRefGoogle Scholar
  504. Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J (2013) Transcriptome responses to combinations of stresses in arabidopsis. Plant Physiol 161:1783–1794PubMedPubMedCentralCrossRefGoogle Scholar
  505. Rengel Z (1992) The role of calcium in salt toxicity. Plant Cell Environ 15:625–663CrossRefGoogle Scholar
  506. Reymond M, Muller B, Leonardi A, Charcosset A, Tardieu F (2003) Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit. Plant Physiol 131:664–675PubMedPubMedCentralCrossRefGoogle Scholar
  507. Rick CM, Chetelat RT (1995) Utilization of related wild species for tomato improvement. In: FernandezMunoz R, Cuartero J, GomezGuillamon ML (eds) First international symposium on solanaceae for fresh market. Acta Hort 412:21–38Google Scholar
  508. Ripoll J, Urban L, Brunel B, Bertin N (2016) Water deficit effects on tomato quality depend on fruit developmental stage and genotype. J Plant Physiol 190:26–35PubMedCrossRefGoogle Scholar
  509. Ripoll J, Urban L, Staudt M, Lopez-Lauri F, Bidel LPR, Bertin N (2014) Water shortage and quality of fleshy fruits—making the most of the unavoidable. J Exp Bot 65:4097–4117PubMedCrossRefGoogle Scholar
  510. Rivero RM, Mestre TC, Mittler R, Rubio F, Garcia-Sanchez F, Martinez V (2014) The combined effect of salinity and heat reveals a specific physiological, biochemical and molecular response in tomato plants. Plant Cell Environ 37:1059–1073PubMedCrossRefGoogle Scholar
  511. Robbins MD, Masud MAT, Panthee DR, Gardner RG, Francis DM, Stevens MR (2010) Marker-assisted selection for coupling phase resistance to Tomato spotted wilt virus and Phytophthora infestans (Late Blight) in tomato. HortScience 45:1424–1428CrossRefGoogle Scholar
  512. Robert VJM, West MAL, Inai S, Caines A, Arntzen L, Smith JK, St Clair DA (2001) Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Mol Breed 8:217–233CrossRefGoogle Scholar
  513. Rodríguez GR, Muños S, Anderson C, Sim S-C, Michel A, Causse M, Gardener BBM, Francis D, van der Knaap E (2011) Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity. Plant Physiol 156:275–285PubMedPubMedCentralCrossRefGoogle Scholar
  514. Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB (2017) Engineering quantitative trait variation for crop improvement by genome editing. Cell 171:470–480PubMedCrossRefGoogle Scholar
  515. Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant MicroRNAs. Plant Cell 25:2383–2399PubMedPubMedCentralCrossRefGoogle Scholar
  516. Ronen G, Cohen M, Zamir D, Hirschberg J (1999) Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta. Plant J17:341–351Google Scholar
  517. Rosales MA, Rubio-Wilhelmi MM, Castellano R, Castilla N, Ruiz JM, Romero L (2007) Sucrolytic activities in cherry tomato fruits in relation to temperature and solar radiation. Sci Hort (Amsterdam) 113:244–249CrossRefGoogle Scholar
  518. Rosental L, Perelman A, Nevo N, Toubiana D, Samani T, Batushansky A, Sikron N, Saranga Y, Fait A (2016) Environmental and genetic effects on tomato seed metabolic balance and its association with germination vigor. BMC Genom 17:1047CrossRefGoogle Scholar
  519. Rossi M, Goggin FL, Milligan SB, Kaloshian I, Ullman DE, Williamson VM (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. Proc Natl Acad Sci USA 95:9750–9754PubMedCrossRefGoogle Scholar
  520. Rothan C, Diouf I, Causse M (2019) Trait discovery and editing in tomato. Plant J 97:73–90PubMedCrossRefGoogle Scholar
  521. Rousseaux MC, Jones CM, Adams D, Chetelat R, Bennett A, Powell A (2005) QTL analysis of fruit antioxidants in tomato using Lycopersicon pennellii introgression lines. Theor Appl Genet 111:1396–1408PubMedCrossRefGoogle Scholar
  522. Ruan Y-L, Patrick JW, Bouzayen M, Osorio S, Fernie AR (2012) Molecular regulation of seed and fruit set. Trends Plant Sci 17:656–665PubMedCrossRefGoogle Scholar
  523. Ruffel S, Gallois JL, Lesage ML, Caranta C (2005) The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Genet Genom 274:346–353CrossRefGoogle Scholar
  524. Ruggieri V, Francese G, Sacco A, Alessandro AD, Rigano MM, Parisi M, Milone M, Cardi T, Mennella G, Barone A (2014) An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC Plant Biol 14:1–15CrossRefGoogle Scholar
  525. Sacco A, Di Matteo A, Lombardi N, Trotta N, Punzo B, Mari A, Barone A (2013) Quantitative trait loci pyramiding for fruit quality traits in tomato. Mol Breed 31(1):217–222PubMedCrossRefPubMedCentralGoogle Scholar
  526. Sahu KK, Chattopadhyay D (2017) Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping. BMC Genom 18:430CrossRefGoogle Scholar
  527. Sainju UM, Dris R, Singh B (2003) Mineral nutrition of tomato. Food Agri Environ 1:176–183Google Scholar
  528. Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato: 1. Mapping QTLs for physical and chemical traits. Theor Appl Genet 102:259–272CrossRefGoogle Scholar
  529. Sallam A, Martsch R (2015) Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.). Genetica 143:501–514PubMedCrossRefPubMedCentralGoogle Scholar
  530. Salmeron JM, Oldroyd GE, Rommens CM, Scofield SR, Kim H-S, Lavelle DT, Dahlbeck D, Staskawicz BJ (1996) Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto Kinase gene cluster. Cell 86:123–133PubMedCrossRefPubMedCentralGoogle Scholar
  531. Sanei M, Chen X (2015) Mechanisms of microRNA turnover. Curr Opin Plant Biol 27:199–206PubMedPubMedCentralCrossRefGoogle Scholar
  532. Sarlikioti V, de Visser PHB, Buck-Sorlin GH, Marcelis LFM (2011) How plant architecture affects light absorption and photosynthesis in tomato: towards an ideotype for plant architecture using a functional–structural plant model. Ann Bot 108(6):1065–1073PubMedPubMedCentralCrossRefGoogle Scholar
  533. Sato S, Tabata S, Hirakawa H et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  534. Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant J 91:631–645PubMedCrossRefPubMedCentralGoogle Scholar
  535. Sauvage C, Segura V, Bauchet G, Stevens R, Do PT, Nikoloski Z, Fernie AR, Causse M (2014) Genome-wide association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiol 165:1120–1132PubMedPubMedCentralCrossRefGoogle Scholar
  536. Schachtman DP, Shin R (2007) Nutrient sensing and signaling: NPKS. Annu Rev Plant Biol 58:47–69PubMedCrossRefPubMedCentralGoogle Scholar
  537. Schaffer AA, Levin I, Oguz I, Petreikov M, Cincarevsky F, Yeselson Y, Shen S, Gilboa N, Bar M (2000) ADPglucose pyrophosphorylase activity and starch accumulation in immature tomato fruit: the effect of a Lycopersicon hirsutum-derived introgression encoding for the large subunit. Plant Sci 152:135–144CrossRefGoogle Scholar
  538. Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454PubMedCrossRefPubMedCentralGoogle Scholar
  539. Schauer N, Zamir D, Fernie AR (2005) Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J Exp Bot 56:297–307PubMedCrossRefPubMedCentralGoogle Scholar
  540. Scheben A, Batley J, Edwards D (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149–161PubMedPubMedCentralCrossRefGoogle Scholar
  541. Schijlen EG, de Vos CR, Martens S, Jonker HH, Rosin FM, Molthoff JW, Tikunov YM, Angenent GC, van Tunen AJ, Bovy AG (2007) RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits. Plant Physiol 144(3):1520–1530PubMedPubMedCentralCrossRefGoogle Scholar
  542. Scholberg JMS, Locascio SJ (1999) Growth response of snap bean and tomato as affected by salinity and irrigation method. HortScience 34:259–264CrossRefGoogle Scholar
  543. Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M (2012) An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet 44:825–830PubMedPubMedCentralCrossRefGoogle Scholar
  544. Semel Y, Nissenbaum J, Menda N, Zinder M, Krieger U, Issman N, Pleban T, Lippman Z, Gur A, Zamir D (2006) Overdominant quantitative trait loci for yield and fitness in tomato. Proc Natl Acad Sci USA 103:12981–12986PubMedCrossRefPubMedCentralGoogle Scholar
  545. Semel Y, Schauer N, Roessner U, Zamir D, Fernie AR (2007) Metabolite analysis for the comparison of irrigated and non-irrigated field grown tomato of varying genotype. Metabolomics 3:289–295CrossRefGoogle Scholar
  546. Shahlaei A, Torabi S, Khosroshahli M (2014) Efficiacy of SCoT and ISSR marekers in assesment of tomato (Lycopersicum esculentum Mill.) genetic diversity. Intl J Biosci 5:14–22Google Scholar
  547. Shalit A, Rozman A, Goldshmidt A, Alvarez JP, Bowman JL, Eshed Y, Lifschitz E (2009) The flowering hormone florigen functions as a general systemic regulator of growth and termination. Proc Natl Acad Sci USA 106:8392–8397PubMedCrossRefPubMedCentralGoogle Scholar
  548. Shammai A, Petreikov M, Yeselson Y, Faigenboim A, Moy-Komemi M, Cohen S, Cohen D, Besaulov E, Efrati A, Houminer N et al (2018) Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit. Plant J 96:343–357PubMedCrossRefPubMedCentralGoogle Scholar
  549. Sharada MS, Kumari A, Pandey AK, Sharma S, Sharma P, Sreelakshmi Y, Sharma R (2017) Generation of genetically stable transformants by Agrobacterium using tomato floral buds. Plant Cell Tiss Org Cult 129(2):299–312CrossRefGoogle Scholar
  550. Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature Biotechnol 35(5):441–443CrossRefGoogle Scholar
  551. Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich DJ, Shi Y, Xu Y, Zheng Y, Snyder SI, Martin LBB et al (2018) High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nat Commun 9:364PubMedPubMedCentralCrossRefGoogle Scholar
  552. Sim S-C, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, et al. (2012a) High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS One 7:e45520PubMedPubMedCentralCrossRefGoogle Scholar
  553. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S et al (2012b) Development of a large snp genotyping array and generation of high-density genetic maps in tomato. PLoS One. Scholar
  554. Sim S-C, Robbins MD, Van Deynze A, Agee M, Francis DM (2010) Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity (Edinb) 106:927–935CrossRefGoogle Scholar
  555. Sim SC, Robbins MD, Wijeratne S, Wang H, Yang WC, Francis DM (2015) Association analysis for bacterial spot resistance in a directionally selected complex breeding population of tomato. Phytopathology 105:1437–1445PubMedCrossRefPubMedCentralGoogle Scholar
  556. Simons G, Groenendijk J, Wijbrandi J, Reijans M, Groenen J, Diergaarde P, Van der Lee T, Bleeker M, Onstenk J, de Both M, Haring M, Mes J, Cornelissen B, Zabeau M, Vos P (1998) Dissection of the Fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. Plant Cell (The) 10:1055–1068PubMedPubMedCentralCrossRefGoogle Scholar
  557. Smart CD, Tanksley SD, Mayton H, Fry WE (2007) Resistance to Phytophthora infestans in Lycopersicon pennellii. Plant Dis 91:1045–1049PubMedCrossRefPubMedCentralGoogle Scholar
  558. Smirnoff N, Wheeler GL (2000) Ascorbic acid in plants: biosynthesis and function. Crit Rev Biochem Mol Biol 35:291–314PubMedCrossRefPubMedCentralGoogle Scholar
  559. Smith DL, Abbott JA, Gross KC (2002) Down-regulation of tomato β-galactosidase 4 results in decreased fruit softening. Plant Physiol 129(4):1755–1762PubMedPubMedCentralCrossRefGoogle Scholar
  560. Soyk S, Lemmon ZH, Oved M et al (2017a) Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169:1142–1155PubMedCrossRefPubMedCentralGoogle Scholar
  561. Soyk S, Müller NA, Park SJ, Schmalenbach I, Jiang K, Hayama R, Zhang L, Van Eck J, Jiménez-Gómez JM, Lippman ZB (2017b) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet 49:162–168PubMedCrossRefPubMedCentralGoogle Scholar
  562. Spano R, Mascia T, Kormelink R, Gallitelli D (2015) Grafting on a non-transgenic tolerant tomato variety confers resistance to the infection of a Sw5-breaking strain of tomato spotted wilt virus via RNA silencing. PloS One 10PubMedPubMedCentralCrossRefGoogle Scholar
  563. Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 11:1–25Google Scholar
  564. Stamova BS, Chetelat RT (2000) Inheritance and genetic mapping of cucumber mosaic virus resistance introgressed from Lycopersicon chilense into tomato. TheorAppl Genet 101:527–537CrossRefGoogle Scholar
  565. Stevens MA (1986) Inheritance of tomato fruit quality components. Plant Breed Rev 4:273–311Google Scholar
  566. Stevens MA, Kader AA, Albright M (1979) Potential for increasing tomato flavor via increased sugar and acid content. J Amer Soc Hort Sci 104:40–42Google Scholar
  567. Stevens MA, Kader AA, Albright-Holton M (1977) Intercultivar variation in composition of locular and pericarp portions of fresh market tomatoes. J Amer Soc Hort Sci 102:689–692Google Scholar
  568. Stevens MR, Lamb EM, Rhoads DD (1995) Mapping the Sw-5 locus for tomato spotted wilt virus-resistance in tomatoes using RAPD and RFLP analyses. Theor Appl Genet 90:451–456PubMedCrossRefPubMedCentralGoogle Scholar
  569. Stikic R, Popovic S, Srdic M, Savic D, Jovanovic Z, Zdravkovic J (2003) Partial root drying (PRD): a new technique for growing plants that saves water and improves the quality of fruit. Bulg J Plant Physiol 164–171Google Scholar
  570. Stricker SH, Köferle A, Beck S (2017) From profiles to function in epigenomics. Nat Rev Genet 18:51–66PubMedCrossRefPubMedCentralGoogle Scholar
  571. Struik PC, Yin XY, de Visser P (2005) Complex quality traits: now time to model. Trends Plant Sci 10:513–516PubMedCrossRefPubMedCentralGoogle Scholar
  572. Suliman-Pollatschek S, Kashkush K, Shats H, Hillel J, Lavi U (2002) Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum. Cell Mol Biol Lett 7:583–597PubMedPubMedCentralGoogle Scholar
  573. Sun J, Poland JA, Mondal S, Crossa J, Juliana P, Singh RP, Rutkoski JE, Jannink J-L, Crespo-Herrera L, Velu G et al (2019) High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage. Theor Appl Genet 1–16Google Scholar
  574. Sun X, Gao Y, Li H, Yang S, Liu Y (2015) Over-expression of SlWRKY39 leads to enhanced resistance to multiple stress factors in tomato. J Plant Biol 58:52–60CrossRefGoogle Scholar
  575. Suzuki N, Rivero RM, Shulaev V, Blumwald E, Mittler R (2014) Abiotic and biotic stress combinations. New Phytol 203:32–43PubMedCrossRefPubMedCentralGoogle Scholar
  576. Tadmor Y, Fridman E, Gur A, Larkov O, Lastochkin E, Ravid U, Zamir D, Lewinsohn E (2002) Identification of malodorous, a wild species allele affecting tomato aroma that was selected against during domestication. J Agri Food Chem 50:2005–2009CrossRefGoogle Scholar
  577. Takken FLW, Thomas CM, Joosten M, Golstein C, Westerink N, Hille J, Nijkamp HJJ, De Wit P, Jones JDG (1999) A second gene at the tomato Cf-4 locus confers resistance to Cladosporium fulvum through recognition of a novel avirulence determinant. Plant J 20:279–288PubMedCrossRefPubMedCentralGoogle Scholar
  578. Takken FLW, Schipper D, Nijkamp HJJ, Hille J (1998) Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. Plant J 14:401–411PubMedCrossRefGoogle Scholar
  579. Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831PubMedCrossRefPubMedCentralGoogle Scholar
  580. Tanksley SD (2004) The genetic, developmental, and molecular bases of fruit size in tomato and shape variation. Plant Cell 16:181–190CrossRefGoogle Scholar
  581. Tanksley SD, Ganal MW, Prince JP, De Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedPubMedCentralGoogle Scholar
  582. Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224PubMedCrossRefPubMedCentralGoogle Scholar
  583. Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203PubMedCrossRefPubMedCentralGoogle Scholar
  584. Tardieu F (2003) Virtual plants: modelling as a tool for the genomics of tolerance to water deficit. Trends Plant Sci 8:9–14PubMedCrossRefPubMedCentralGoogle Scholar
  585. Tashkandi M, Ali Z, Aljedaani F, Shami A, Mahfouz MM (2018) Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. Plant Signal Behav 13Google Scholar
  586. Taudt A, Colomé-Tatché M, Johannes F (2016) Genetic sources of population epigenomic variation. Nat Rev Genet 17:319–332PubMedCrossRefPubMedCentralGoogle Scholar
  587. The 100 Tomato Genome Sequencing Consortium (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148Google Scholar
  588. The 100 Tomato Genome Sequencing Consortium (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148Google Scholar
  589. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073Google Scholar
  590. The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491Google Scholar
  591. The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491Google Scholar
  592. The 3000 rice genomes project (2014) The 3,000 rice genomes project. Gigascience 3: 7Google Scholar
  593. The UK10K Consortium (2015) The UK10K project identifies rare variants in health and disease. Nature 526:82–89Google Scholar
  594. Thoen MPM, Davila Olivas NH, Kloth KJ, Coolen S, Huang PP, Aarts MGM, Bac-Molenaar JA, Bakker J, Bouwmeester HJ, Broekgaarden C et al (2017) Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping. New Phytol 213:1346–1362PubMedPubMedCentralCrossRefGoogle Scholar
  595. Tieman D, Bliss P, McIntyre LMM, Blandon-Ubeda A, Bies D, Odabasi AZZ, Rodríguez GRR, Van Der Knaap E, Taylor MGG, Goulet C et al (2012) The chemical interactions underlying tomato flavor preferences. Curr Biol 22:1035–1039PubMedCrossRefPubMedCentralGoogle Scholar
  596. Tieman D, Taylor M, Schauer N, Fernie AR, Hanson AD, Klee HJ (2006) Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc Natl Acad Sci USA 103:8287–8292PubMedCrossRefPubMedCentralGoogle Scholar
  597. Tieman D, Zhu G, Resende MFR, Lin T, Nguyen C, Bies D, Rambla JL, Beltran KSO, Taylor M, Zhang B et al (2017) A chemical genetic roadmap to improved tomato flavor. Science (80-) 355:391–394PubMedCrossRefPubMedCentralGoogle Scholar
  598. Tieman DM, Handa AK (1994) Reduction in pectin methylesterase activity modifies tissue integrity and cation levels in ripening tomato (Lycopersicon esculentum Mill.) fruits. Plant Physiol 106(2):429–36PubMedPubMedCentralCrossRefGoogle Scholar
  599. Tikunov Y, Lommen A, Vos CHR, de Verhoeven HA, Bino RJ, Hall RD, Bovy AG (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol 139:1125–1137PubMedPubMedCentralCrossRefGoogle Scholar
  600. Tikunov YM, Molthoff J, de Vos RCH, Beekwilder J, van Houwelingen A et al (2013) Non-smoky glycosyltransferase1 prevents the release of smoky aroma from tomato fruit. Plant Cell 25(8):3067–3078PubMedPubMedCentralCrossRefGoogle Scholar
  601. Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuono C, Bostan H, Termolino P, Aversano R, Batelli G et al (2018) Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. DNA Res 25:149–160PubMedCrossRefPubMedCentralGoogle Scholar
  602. Tuna AL, Kaya C, Ashraf M, Altunlu H, Yokas I, Yagmur B (2007) The effects of calcium sulphate on growth, membrane stability and nutrient uptake of tomato plants grown under salt stress. Environ Exp Bot 59:173–178CrossRefGoogle Scholar
  603. Turina M, Kormelink R, Resende RO (2016) Resistance to tospoviruses in vegetable crops: epidemiological and molecular aspects. In: Leach JE, Lindow S (eds) Annu Rev Phytopathol 54:347–371Google Scholar
  604. Uluisik S, Chapman NH, Smith R, Poole M, Adams G, Gillis RB, Besong TM, Sheldon J, Stiegelmeyer S, Perez L, Samsulrizal N (2016) Genetic improvement of tomato by targeted control of fruit softening. Nature Biotechnol 34(9):950CrossRefGoogle Scholar
  605. Usadel B, Chetelat R, Koren S, Maumus F, Fernie AR, Aury J-M, Maß J, Schmidt MH-W, Denton AK, Wormit A et al (2017) De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell 29:2336–2348PubMedPubMedCentralCrossRefGoogle Scholar
  606. Vakalounakis DJ, Laterrot H, Moretti A, Ligoxigakis EK, Smardas K (1997) Linkage between Frl (Fusarium oxysporum f sp radicis-lycopersici resistance) and Tm-2 (tobacco mosaic virus resistance-2) loci in tomato (Lycopersicon esculentum). Ann Appl Biol 130:319–323CrossRefGoogle Scholar
  607. van Berloo R, Stam P (1998) Marker-assisted selection in autogamous RIL populations: a simulation study. Theor Appl Genet 96:147–154CrossRefGoogle Scholar
  608. van Berloo R, Stam P (1999) Comparison between marker-assisted selection and phenotypical selection in a set of Arabidopsis thaliana recombinant inbred lines. Theor Appl Genet 98:113–118CrossRefGoogle Scholar
  609. Van Berloo R, Zhu A, Ursem R, Verbakel H, Gort G, van Eeuwijk FA (2008) Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. Theor Appl Genet 117:89–101PubMedPubMedCentralCrossRefGoogle Scholar
  610. van der Knaap E, Tanksley SD (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato. Theor Appl Genet 107:139–147PubMedCrossRefPubMedCentralGoogle Scholar
  611. van Eeuwijk Fred A, Bustos-Korts D, Millet EJ, Boer MP, Kruijer W, Thompson A et al (2019) Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding. Plant Sci 282:23–39PubMedCrossRefGoogle Scholar
  612. Vargas-Ponce O, Pérez-Álvarez LF, Zamora-Tavares P, Rodríguez A (2011) Assessing genetic diversity in mexican husk tomato species. Plant Mol Biol Rep 29:733–738CrossRefGoogle Scholar
  613. Veillet F, Perrot L, Chauvin L, Kermarrec M-P, Guyon-Debast A, Chauvin J-E, Nogué F, Mazier M (2019) Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Intl J Mol Sci 20(2):402CrossRefGoogle Scholar
  614. Venter F (1977) Solar radiation and vitamin C content of tomato fruits. Acta Hortic 58:121–127Google Scholar
  615. Verkerke W, Janse J, Kersten M (1998) Instrumental measurement and modelling of tomato fruit taste. Acta Hort 199–206Google Scholar
  616. Verlaan MG, Hutton SF, Ibrahem RM, Kormelink R, Visser RGF, Scott JW, Edwards JD, Bai YL (2013) The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA-Dependent RNA Polymerases. PLoS Genetics 9PubMedPubMedCentralCrossRefGoogle Scholar
  617. Villalta I, Bernet GP, Carbonell EA, Asins MJ (2007) Comparative QTL analysis of salinity tolerance in terms of fruit yield using two solanum populations of F7 lines. Theor Appl Genet 114:1001–1017PubMedCrossRefGoogle Scholar
  618. Víquez-Zamora M, Vosman B, van de Geest H, Bovy A, Visser RGF, Finkers R, van Heusden AW (2013) Tomato breeding in the genomics era: insights from a SNP array. BMC Genom 14:354CrossRefGoogle Scholar
  619. Vos P, Simons G, Jesse T, Wijbrandi J, Heinen L, Hogers R, Frijters A, Groenendijk J, Diergaarde P, Reijans M, Fierens-Onstenk J, de Both M, Peleman J, Liharska T, Hontelez J, Zabeau M (1998) The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids. Nat Biotechnol 16:1365–1369PubMedCrossRefGoogle Scholar
  620. Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science (80-) 296:343–346PubMedCrossRefGoogle Scholar
  621. Wahid A, Gelani S, Ashraf M, Foolad MR (2007) Heat tolerance in plants: an overview. Environ Exp Bot 61:199–223CrossRefGoogle Scholar
  622. Wang D, Salah El-Basyoni I, Stephen Baenziger P, Crossa J, Eskridge KM, Dweikat I (2012) Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations. Heredity (Edinb) 109:313–319CrossRefGoogle Scholar
  623. Wang DR, Agosto-Pérez FJ, Chebotarov D, Shi Y, Marchini J, Fitzgerald M, McNally KL, Alexandrov N, McCouch SR (2018) An imputation platform to enhance integration of rice genetic resources. Nat Commun 9:3519PubMedPubMedCentralCrossRefGoogle Scholar
  624. Wang JF, Ho FI, Truong HTH, Huang SM, Balatero CH, Dittapongpitch V, Hidayati N (2013a) Identification of major QTLs associated with stable resistance of tomato cultivar ‘Hawaii 7996’ to Ralstonia solanacearum. Euphytica 190:241–252CrossRefGoogle Scholar
  625. Wang K, Li M, Hakonarson H (2010) ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164PubMedPubMedCentralCrossRefGoogle Scholar
  626. Wang L, Song X, Gu L, Li X, Cao S, Chu C, Cui X, Chen X, Cao X (2013b) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis. Plant Cell 25:715–727PubMedPubMedCentralCrossRefGoogle Scholar
  627. Wang R, Tavano ECDR, Lammers M, Martinelli AP, Angenent GC, de Maagd RA (2019) Re-evaluation of transcription factor function in tomato fruit development and ripening with CRISPR/Cas9-mutagenesis. Sci Rep 8:1696CrossRefGoogle Scholar
  628. Wang Y, Wu W-H (2015) Genetic approaches for improvement of the crop potassium acquisition and utilization efficiency. Curr Opin Plant Biol 25:46–52PubMedCrossRefPubMedCentralGoogle Scholar
  629. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedPubMedCentralCrossRefGoogle Scholar
  630. Waters AJ, Makarevitch I, Noshay J, Burghardt LT, Hirsch CN, Hirsch CD, Springer NM (2017) Natural variation for gene expression responses to abiotic stress in maize. Plant J 89:706–717PubMedCrossRefPubMedCentralGoogle Scholar
  631. Wells T, Ward JL, Corol DI, Baker JM, Gerrish C, Michael H, Seymour GB, Fraser PD and Bramley PM (2013) Metabolite profiling of introgression lines of Solanum habrochaites using targeted and non-targeted approaches reveals novel quantitative trait loci. PhD Max Planck Institute Postdam, Germany, 149 pGoogle Scholar
  632. Wilkins KA, Matthus E, Swarbreck SM, Davies JM (2016) Calcium-mediated abiotic stress signaling in roots. Front Plant Sci 7:1296Google Scholar
  633. Willits MG, Kramer CM, Prata RT, De Luca V, Potter BG, Steffens JC, Graser G (2005) Utilization of the genetic resources of wild species to create a nontransgenic high flavonoid tomato. J Agri Food Chem 53:1231–1236CrossRefGoogle Scholar
  634. Won SY, Yumul RE, Chen X (2014) Small RNAs in plants. Molecular biology. Springer, New York, pp 95–127Google Scholar
  635. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–1530PubMedCrossRefGoogle Scholar
  636. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138:2145–2154PubMedPubMedCentralCrossRefGoogle Scholar
  637. Xu J, Driedonks N, Rutten MJM, Vriezen WH, de Boer GJ, Rieu I (2017a) Mapping quantitative trait loci for heat tolerance of reproductive traits in tomato (Solanum lycopersicum). Mol Breed 37:58PubMedPubMedCentralCrossRefGoogle Scholar
  638. Xu J, Ranc N, Muños S, Rolland S, Bouchet J-PP, Desplat N, Le Paslier M-CC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126:567–581PubMedCrossRefGoogle Scholar
  639. Xu J, Wolters-Arts M, Mariani C, Huber H, Rieu I (2017b) Heat stress affects vegetative and reproductive performance and trait correlations in tomato (Solanum lycopersicum). Euphytica 213:156CrossRefGoogle Scholar
  640. Xu WF, Shi WM, Yan F (2012) Temporal and tissue-specific expression of tomato 14-3-3 gene family in response to phosphorus deficiency. Pedosphere 22:735–745CrossRefGoogle Scholar
  641. Yamaguchi H, Ohnishi J, Saito A, Ohyama A, Nunome T, Miyatake K, Fukuoka H (2018) An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. Theoret Appl Genet 131:1345–1362PubMedCrossRefPubMedCentralGoogle Scholar
  642. Yamamoto E, Matsunaga H, Onogi A, Kajiya-Kanegae H, Minamikawa M, Suzuki A, Shirasawa K, Hirakawa H, Nunome T, Yamaguchi H et al (2016) A simulation-based breeding design that uses whole-genome prediction in tomato. Sci Rep 6:19454PubMedPubMedCentralCrossRefGoogle Scholar
  643. Yamamoto E, Matsunaga H, Onogi A, Ohyama A, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H (2017) Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity (Edinb) 118:202–209CrossRefGoogle Scholar
  644. Yang D-Y, Li M, Ma N-N, Yang X-H, Meng Q-W (2017) Tomato SlGGP-LIKE gene participates in plant responses to chilling stress and pathogenic infection. Plant Physiol Biochem 112:218–226PubMedCrossRefPubMedCentralGoogle Scholar
  645. Yang X, Caro M, Hutton SF, Scott JW, Guo Y, Wang X, Rashid MH, Szinay D, de Jong H, Visser RGF et al (2014) Fine mapping of the tomato yellow leaf curl virus resistance gene Ty-2 on chromosome 11 of tomato. Mol Breed 34:749–760PubMedPubMedCentralGoogle Scholar
  646. Yasmeen A, Mirza B, Inayatullah S, Safdar N, Jamil M, Ali S, Choudhry MF (2009) In planta transformation of tomato. Plant Mol Biol Rep 27(1):20–28CrossRefGoogle Scholar
  647. Ye J, Wang X, Hu T, Zhang F, Wang B, Li C, Yang T, Li H, Lu Y, Giovannoni JJ et al (2017) An InDel in the promoter of Al-ACTIVATED MALATE TRANSPORTER9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. Plant Cell 29:2249–2268PubMedPubMedCentralCrossRefGoogle Scholar
  648. Yin X, Kropff MJ, Stam P (1999) The role of ecophysiological models in QTL analysis: the example of specific leaf area in barley. Heredity 82:415–421PubMedCrossRefPubMedCentralGoogle Scholar
  649. You C, Cui J, Wang H, Qi X, Kuo L-Y, Ma H, Gao L, Mo B, Chen X (2017) Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biol 18:158PubMedPubMedCentralCrossRefGoogle Scholar
  650. Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around the Tm-2 locus of tomato during backcross breeding. Theor Appl Genet 77:353–359PubMedCrossRefPubMedCentralGoogle Scholar
  651. Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC et al (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA105: 10073–10078CrossRefGoogle Scholar
  652. Yu Y, Jia T, Chen X (2017) The ‘how’ and ‘where’ of plant microRNAs. New Phytol 216:1002–1017PubMedPubMedCentralCrossRefGoogle Scholar
  653. Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:3–9CrossRefGoogle Scholar
  654. Zanor MI, Rambla JL, Chaïb J, Steppa A, Medina A, Granell A, Fernie AR, Causse M (2009) Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. J Exp Bot 60:2139–2154PubMedPubMedCentralCrossRefGoogle Scholar
  655. Zegbe-Domı́nguez J, Behboudian M, Lang A, Clothier B (2003) Deficit irrigation and partial rootzone drying maintain fruit dry mass and enhance fruit quality in ‘Petopride’ processing tomato (Lycopersicon esculentum, Mill.). Sci Hort (Amsterdam) 98:505–510CrossRefGoogle Scholar
  656. Zhang B, Tieman DM, Chen J, Xu Y, Chen K, Fei Z, Giovannoni J, Klee HJ (2016) Loss of tomato flavor quality during chilling is associated with reduced expression of volatile biosynthetic genes and a transient alteration in DNA methylation. Proc Natl Acad Sci USA113:12580–12584Google Scholar
  657. Zhang C, Liu L, Wang X, Vossen J, Li G, Li T, Zheng Z, Gao J, Guo Y, Visser RGF et al (2014) The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor Appl Genet 127:1353–1364PubMedPubMedCentralCrossRefGoogle Scholar
  658. Zhang J, Zhao J, Liang Y, Zou Z (2016b) Genome-wide association-mapping for fruit quality traits in tomato. Euphytica 207:439–451CrossRefGoogle Scholar
  659. Zhang J, Zhao J, Xu Y, Liang J, Chang P, Yan F, Li M, Liang Y, Zou Z (2015a) Genome-wide association mapping for tomato volatiles positively contributing to tomato flavor. Front Plant Sci 6:1042PubMedPubMedCentralGoogle Scholar
  660. Zhang S, Xie M, Ren G, Yu B (2013) CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts. Proc Natl Acad Sci USA 110:17588–17593PubMedCrossRefPubMedCentralGoogle Scholar
  661. Zhang Y, Butelli E, Alseekh S, Tohge T, Rallapalli G, Luo J, Kawar PG, Hill L, Santino A, Fernie AR, Martin C (2015b) Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nat Commun 6:8635PubMedPubMedCentralCrossRefGoogle Scholar
  662. Zhang Z, Guo X, Ge C, Ma Z, Jiang M, Li T, Koiwa H, Yang SW, Zhang X (2017) KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci USA 114:4011–4016PubMedCrossRefPubMedCentralGoogle Scholar
  663. Zhao C, Liu B, Piao S, Wang X, Lobell DB, Huang Y, Huang M, Yao Y, Bassu S, Ciais P et al (2017) Temperature increase reduces global yields of major crops in four independent estimates. Proc Natl Acad Sci USA114: 9326–9331CrossRefGoogle Scholar
  664. Zhao J, Sauvage C, Zhao J, Bitton F, Bauchet G, Liu D, Huang S, Tieman DM, Klee HJ, Causse M (2019) Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Nat Commun 10:1534PubMedPubMedCentralCrossRefGoogle Scholar
  665. Zhao X, Liu Y, Liu X, Jiang J (2018) Comparative transcriptome profiling of two tomato genotypes in response to potassium-deficiency stress. Int J Mol Sci 19:2402PubMedCentralCrossRefGoogle Scholar
  666. Zhong S, Fei Z, Chen Y, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J et al (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31:154–159PubMedCrossRefPubMedCentralGoogle Scholar
  667. Zhou R, Wu Z, Cao X, Jiang F (2015) Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers. Genet Mol Res 14:13868–13879PubMedCrossRefPubMedCentralGoogle Scholar
  668. Zhou R, Yu X, Ottosen C-O, Rosenqvist E, Zhao L, Wang Y, Yu W, Zhao T, Wu Z (2017) Drought stress had a predominant effect over heat stress on three tomato cultivars subjected to combined stress. BMC Plant Biol 17:24PubMedPubMedCentralCrossRefGoogle Scholar
  669. Zhu G, Gou J, Klee H, Huang S (2019) Next-gen approaches to flavor-related metabolism. Ann Rev Plant Biol 70:187–212CrossRefGoogle Scholar
  670. Zhu G, Wang S, Huang Z, Zhang S, Liao Q et al (2018) Rewiring of the fruit metabolome in tomato breeding. Cell 172:249–261PubMedCrossRefPubMedCentralGoogle Scholar
  671. Zhuang K, Kong F, Zhang S, Meng C, Yang M, Liu Z, Wang Y, Ma N, Meng Q (2019) Whirly1 enhances tolerance to chilling stress in tomato via protection of photosystem II and regulation of starch degradation. New Phytol 221:1998–2012PubMedCrossRefPubMedCentralGoogle Scholar
  672. Zsögön A, Čermák T, Naves ER, Notini MM, Edel KH, Weinl S, Freschi L, Voytas DF, Kudla J, Peres LE (2018) De novo domestication of wild tomato using genome editing. Nat Biotechnol 36:1211–1216CrossRefGoogle Scholar
  673. Zsögön A, Cermak T, Voytas D, Pereira Peres LE (2017) Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: case study in tomato. Plant Sci 256:120–130PubMedCrossRefPubMedCentralGoogle Scholar
  674. Zuo J, Fu D, Zhu Y, Qu G, Tian H, Zhai B, Ju Z, Gao C, Wang Y, Luo Y et al (2013) SRNAome parsing yields insights into tomato fruit ripening control. Physiol Plant 149:540–553PubMedCrossRefPubMedCentralGoogle Scholar
  675. Zuo J, Zhu B, Fu D, Zhu Y, Ma Y, Chi L, Ju Z, Wang Y, Zhai B, Luo Y (2012) Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. BMC Genom 13:7CrossRefGoogle Scholar
  676. Zuriaga E, Blanca J, Nuez F (2009) Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences. Genet Resour Crop Evol 56:663–678CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Mathilde Causse
    • 1
    Email author
  • Jiantao Zhao
    • 1
  • Isidore Diouf
    • 1
  • Jiaojiao Wang
    • 2
  • Veronique Lefebvre
    • 1
  • Bernard Caromel
    • 1
  • Michel Génard
    • 3
  • Nadia Bertin
    • 3
  1. 1.INRA, Centre de Recherche PACA, Génétique et Amélioration Des Fruits et Légumes, Domaine Saint MauriceMontfavetFrance
  2. 2.INRA and University of Bordeaux, UMR 1332 Biologie Du Fruit et PathologieVillenave D’Ornon CedexFrance
  3. 3.INRA, Plantes et Systèmes de Culture Horticoles, Institut National de La Recherche Agronomique - Centre de Recherche PACAAvignonFrance

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