Theoretical and Applied Genetics

, Volume 126, Issue 11, pp 2737–2752 | Cite as

An intra-specific linkage map of lettuce (Lactuca sativa) and genetic analysis of postharvest discolouration traits

  • Laura D. Atkinson
  • Leah K. McHale
  • María José Truco
  • Howard W. Hilton
  • James Lynn
  • Johan W. Schut
  • Richard W. Michelmore
  • Paul Hand
  • David A. C. PinkEmail author
Original Paper


Minimally processed salad packs often suffer from discolouration on cut leaf edges within a few days after harvest. This limits shelf life of the product and results in high wastage. Recombinant inbred lines (RILs) derived from a cross between lettuce cvs. Saladin and Iceberg were shown to be suitable for genetic analysis of postharvest discolouration traits in lettuce. An intra-specific linkage map based on this population was generated to enable genetic analysis. A total of 424 markers were assigned to 18 linkage groups covering all nine chromosomes. The linkage map has a total length of 1,040 cM with an average marker distance of 2.4 cM within the linkage groups and was anchored to the ultra-dense, transcript-based consensus map. Significant genetic variation in the postharvest traits ‘pinking’, ‘browning’ and ‘overall discolouration’ was detected among the RILs. Seven significant quantitative trait loci (QTL) were identified for postharvest discolouration traits providing markers linked to the QTL that can be used for marker-assisted selection. Phenotypic stability was confirmed for extreme lines possessing the corresponding QTL parental alleles and which had shown transgressive segregation. This study indicates that a desired phenotype with reduced levels of postharvest discolouration can be achieved by breeding using natural variation.


Quantitative Trait Locus Recombinant Inbred Line Quantitative Trait Locus Analysis Linkage Group Amplify Fragment Length Polymorphism 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The research was primarily conducted at the University of Warwick, Wellesbourne campus, formerly Warwick HRI. We would like to thank a number of laboratory personnel at Warwick HRI, in particular, Sandy McClement and Neale Grant who helped in the planting and maintaining of the field trials in the UK. Rijk Zwaan Ltd. maintained the field site in the Netherlands and we would like to specifically thank Wendy Deijkers for help during harvest and data collection. This work was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) Crop Science Initiative CASE PhD studentship (BBS/S/E/2006/13221) for LDA in collaboration with Rijk Zwaan Ltd, EU GenRes project “Leafy vegetables germplasm, stimulating use” and Department for Environment, Food and Rural Affairs (Defra) project IF0157 “Vegetable Genetic Improvement Network (VeGIN): Pre-breeding research to support sustainable farming of leafy vegetables and salads”. Travel and subsistence for LDA to work at UC Davis was provided by grants from the Vegetable Research Trust, Glasshouse Crop Research Institute Trust, UK Resource Centre for Women in Science, Engineering and Technology, American Study and Student Exchange Committee and a Warwick HRI Student Travel Award. The contributions of LKH, MJT, and RWM were part of the Compositae Genome Project and supported by the National Science Foundation Plant Genome Program Grant # DBI0421630.

Supplementary material

122_2013_2168_MOESM1_ESM.docx (23 kb)
Online Resource 1 Mapped IGG marker name conversions from the Saladin × Iceberg linkage map. Marker information for the Illumina GoldenGate assay available at (DOCX 23 kb)
122_2013_2168_MOESM2_ESM.docx (11 kb)
Online Resource 2 Mapped SPP marker sequences from the Saladin × Iceberg linkage map. Where GeneChip Sequence Assembly ID is the EST/Contig retrieved from and the SPP Position is single positional polymorphism location in that sequence (DOCX 11 kb)


  1. Altunkaya A, Gokmen V (2008) Effect of various inhibitors on enzymatic browning, antioxidant activity and total phenol content of fresh lettuce (Lactuca sativa). Food Chem 107:1173–1179CrossRefGoogle Scholar
  2. Atkinson LD, Hilton HW, Pink DAC (2013) A study of variation in the tendency for postharvest discoloration in a lettuce (Lactuca sativa) diversity set. Int J Food Sci Technol 48(4):801–807CrossRefGoogle Scholar
  3. Barrett D, Garcia E, Wayne J (1998) Textural modification of processing tomatoes. Crit Rev Food Sci Nutr 38:173–258PubMedCrossRefGoogle Scholar
  4. Brecht J, Chau K, Fonseca S, Oliviera F, Silva F, Nunes M, Bender R (2003) Maintaining optimal atmosphere conditions for fruits and vegetables throughout the postharvest handling chain. Postharvest Biol Technol 27:87–111CrossRefGoogle Scholar
  5. Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B Biol Sci 363(1491):557–572CrossRefGoogle Scholar
  6. Cui X, You N, Girke T, Michelmore R, Van Deynze A (2010) Single feature polymorphism detection using recombinant inbred line microarray expression data. Bioinforma 26(16):1983–1989CrossRefGoogle Scholar
  7. Defra (2012) Basic horticultural statistics 2012. Report prepared by Department for Environment and Rural Affairs, UK.
  8. Degl’Innocenti E, Guidi L, Paradossi A, Tognoni F (2005) Biochemical study of leaf browning in minimally processed leaves of lettuce (Lactuca sativa L. var. Acephala). J Agric Food Chem 52:9980–9984CrossRefGoogle Scholar
  9. Fonseca JM (2006) Postharvest quality and microbial population of head lettuce as affected by moisture at harvest. J Food Sci 71(2):M45–M49CrossRefGoogle Scholar
  10. Gurganus M, Nuzhdin S, Leips J, Mackay T (1999) High-resolution mapping of quantitative trait loci for sternopleural bristle number in Drosophila melanogaster. Genetics 152:1585–1604PubMedGoogle Scholar
  11. Hayashi E, Aoyama N, Still DW (2008) Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome 51(11):928–947PubMedCrossRefGoogle Scholar
  12. Hilton HW, Clifford SC, Wurr DCE, Burton KS (2009) The influence of agronomic factors on the visual quality of field-grown, minimally-processed lettuce. J Hortic Sci Biotechnol 84(2):193–198Google Scholar
  13. Hisaminato H, Murata M, Homma S (2001) Relationship between enzymatic browning and phenylalanine ammonia-lyase activity of cut lettuce, and the prevention of browning by inhibitors of polyphenol biosynthesis. Biosci Biotech Biochem 65(5):1016–1021CrossRefGoogle Scholar
  14. Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genet 135(1):205–211Google Scholar
  15. Jansen RC (1994) Controlling the type-I and type-II errors in mapping in quantitative trait loci. Genet 138(3):871–881Google Scholar
  16. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136(4):1447–1455PubMedGoogle Scholar
  17. Jeuken M, van Wijk R, Peleman J, Lindhout P (2001) An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. sativa × L. saligna F-2 populations. Theor Appl Genet 103(4):638–647CrossRefGoogle Scholar
  18. Johnson W, Jackson L, Ochoa O, Peleman J, van Wijk R, St.Clair D, Michelmore R (2000) A shallow-rooted crop and its wild progenitor differ at loci determining root architecture and deep soil water exploitation. Theor Appl Genet 101:1066–1073CrossRefGoogle Scholar
  19. Joslin M, Pointing J (1951) Enzyme-catalyzed oxidative browning of fruit products. Adv Food Res 3:1CrossRefGoogle Scholar
  20. Kesseli R, Paran I, Michelmore R (1994) Analysis of a detailed genetic linkage map of Lactuca sativa (lettuce) constructed from RFLP and RAPD markers. Genetics 136:1435–1446PubMedGoogle Scholar
  21. Kosambi D (1944) The estimation of map distance from recombination values. Ann Eugenet 12(3):172–175Google Scholar
  22. Landry B, Kesseli R, Farrara B, Michelmore R (1987) A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance, and morphological markers. Genetics 116:331–337PubMedGoogle Scholar
  23. Langridge P, Lagudah ES, Holton TA, Appels R, Sharp PJ, Chalmers KJ (2001) Trends in genetic and genome analyses in wheat: a review. Aust J Agric Res 52(11–12):1043–1077CrossRefGoogle Scholar
  24. Lattanzio V, Lattanzio V, Cardinali A (2006) Role of phenolics in the resistance mechanisms of plants against fungal pathogens and insects. In: Imperato F (ed) Phytochemistry: advances in research. Research Signpost Trivandrum, India, pp 23–68Google Scholar
  25. Lopez-Galvez G, Saltveit M, Cantwell M (1996) Wound-induced phenylalanine ammonia lyase activity: factors affecting its induction and correlation with the quality of minimally processed lettuces. Postharvest Biol Technol 9(2):223–233CrossRefGoogle Scholar
  26. Martinez MV, Whitaker JR (1995) The biochemistry and control of enzymatic browning. Trends Food Sci Technol 6(6):195–200CrossRefGoogle Scholar
  27. McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ, Michelmore RW (2009) The genomic architecture of disease resistance in lettuce. Theor Appl Genet 118(3):565–580PubMedCrossRefGoogle Scholar
  28. Mintel International (2009) Salads and Salad Dressings—UK. Independent market analysis report prepared by Mintel Oxygen, Mintel International.
  29. Nicoli MC, Elizalde BE, Pitotti A, Lerici CR (1991) Effect of sugars and maillard reaction products on polyphenol oxidase and peroxidase activity in food. J Food Biochem 15(3):169–184CrossRefGoogle Scholar
  30. Ogundiwin E, Peace C, Nicolet C, Rashbrook V, Gradziel T, Bliss F, Parfitt D, Crisosto C (2008) Leucoanthocyanidin dioxygenase gene (PpLDOX): a potential functional marker for cold storage browning in peach. Tree Genet Genomes 4(3):543–554CrossRefGoogle Scholar
  31. Pavlidis P, Noble WS (2003) Matrix2png: a utility for visualizing matrix data. Bioinforma 19(2):295–296CrossRefGoogle Scholar
  32. Payne R, Murray D, Harding S, Baird D, Soutar D (2009) GenStat for windows (12th Edition) introduction. VSN International, Hemel HempsteadGoogle Scholar
  33. Peiser G, López-Gálvez G, Cantwell M, Saltveit M (1998) Phenylalanine ammonia lyase inhibitors control browning of cut lettuce. Postharvest Biol Technol 14:171–177CrossRefGoogle Scholar
  34. Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7(4):275–291CrossRefGoogle Scholar
  35. Rodenburg CM, Basse H (1960) Varieties of lettuce: an international monograph. Instituut voor de Veredeling van TuinbouwgewassenGoogle Scholar
  36. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, TotowaGoogle Scholar
  37. Ryder EJ (1979) Salinas lettuce. HortScience 14(3):283–284Google Scholar
  38. Sentinelli F, Lovari S, Vitale M, Giorgi G, Di Mario U, Baroni MG (2000) A simple method for non-radioactive PCR-SSCP using MDE™ gel solution and a midi gel format: application for the detection of variants in the GLUT1 and CTLA-4 genes. J Biotechnol 78(2):201–204PubMedCrossRefGoogle Scholar
  39. Solomon E, Sundaram U, Machonkin T (1996) Multicopper oxidases and oxygenases. Chem Rev 96:2563–2605PubMedCrossRefGoogle Scholar
  40. Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S, Truco M-J, Michelmore R, Van Deynze A (2012) Development and application of a 6.5 million feature affymetrix genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.). BMC Genomics 13(1):185PubMedCrossRefGoogle Scholar
  41. Syed NH, Sorensen AP, Antonise R, van de Wiel C, van der Linden CG, van’t Westende W, Hooftman DAP, den Nijs HCM, Flavell AJ (2006) A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theor Appl Genet 112(3):517–527Google Scholar
  42. Toivonen P (2004) Postharvest storage procedures and oxidative stress. HortScience 39:938–942Google Scholar
  43. Toivonen P, Brummell D (2008) Biochemical bases of appearance and texture changes in fresh-cut fruit and vegetables. Postharvest Biol Technol 48(1):1–14CrossRefGoogle Scholar
  44. Tomas-Barberan F, Espin JC (2001) Phenolic compounds and related enzymes as determinants of quality in fruits and vegetables. J Sci Food Agric 81(9):853–876CrossRefGoogle Scholar
  45. Truco MJ, Antonise R, Lavelle D, Ochoa O, Kozik A, Witsenboer H, Fort SB, Jeuken MJW, Kesseli RV, Lindhout P, Michelmore RW, Peleman J (2007) A high-density, integrated genetic linkage map of lettuce (Lactuca spp.). Theor Appl Genet 115(6):735–746PubMedCrossRefGoogle Scholar
  46. Truco MJ, Ashrafi H, Kozik A, van Leeuwen H, Bowers J, Reyes Chin Wo S, Stoffel K, Xu H, Hill T, Van Deynze A, Michelmore RW (2013) An ultra high-density, transcript-based, genetic map of lettuce. Genes Genomes Genet. doi: 10.1534/g3.112.004929
  47. Van Ooijen J (2006) JoinMap® 4, Software for the calculation of genetic maps in experimental populations. Kyazma B.V., WageningenGoogle Scholar
  48. Van Ooijen J, Boer J, Jansen R, Maliepaard C (2002) MapQTL 4.0, Software for the calculation of QTL position on genetic maps. Plant Research International, WageningenGoogle Scholar
  49. Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan G, Caromel B, Ghareeb B, Isidore E, De Jong W, Van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort J, Rousselle-Bourgeois F, Van Vliet J, Waugh R, Visser R, Bakker J, Van Eck H (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087PubMedCrossRefGoogle Scholar
  50. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78PubMedCrossRefGoogle Scholar
  51. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP—a new technique for DNA-fingerprinting. Nucleic Acids Res 23(21):4407–4414PubMedCrossRefGoogle Scholar
  52. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lubberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP (R) linkage maps of Zea mays L.: analysis of distribution of AFLP markers. Theor Appl Genet 99(6):921–935CrossRefGoogle Scholar
  53. Wagstaff C, Clarkson G, Zhang F, Rothwell S, Fry S, Taylor G, Dixon M (2010) Modification of cell wall properties in lettuce improves shelf life. J Exp Bot 61(4):1239–1248PubMedCrossRefGoogle Scholar
  54. Wanner L, Li G, Ware D, Somssich I, Davis K (1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol 27:327–338PubMedCrossRefGoogle Scholar
  55. Watada A, Qi L (1999) Quality of fresh-cut produce. Postharvest Biol Technol 15:201–205CrossRefGoogle Scholar
  56. Waycott W, Fort SB, Ryder EJ, Michelmore RW (1999) Mapping morphological genes relative to molecular markers in lettuce (Lactuca sativa L.). Heredity 82:245–251PubMedCrossRefGoogle Scholar
  57. Werij J, Kloosterman B, Celis-Gamboa C, de Vos C, America T, Visser R, Bachem C (2007) Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis. Theor Appl Genet 115(2):245–252PubMedCrossRefGoogle Scholar
  58. WRAP (2009) Household food and drink waste in the UK. Report prepared by Waste and Resources Action Programme (WRAP). Banbury, UKGoogle Scholar
  59. Yahia EM, Gonzalez-Aguilar G (1998) Use of passive and semi-active atmospheres to prolong the postharvest life of avocado fruit. Food Science and Technology-Lebensmittel-Wissenschaft Technologie 31(7–8):602–606Google Scholar
  60. Zagory D, Kader AA (1988) Modified atmosphere packaging of fresh produce. Food Technol 42(9):70Google Scholar
  61. Zawistowski J, Biliaderis C, Eskin N (1991) Polyphenol oxidase. In: Robinson D, Eskin N (eds) Oxidative enzymes in foods. Elsevier Applied Science Chemistry, London, pp 217–273Google Scholar
  62. Zeng Z (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  63. Zhang F, Wagstaff C, Rae A, Sihota A, Keevil C, Rothwell S, Clarkson G, Michelmore R, Truco M, Dixon M, Taylor G (2007) QTLs for shelf life in lettuce co-locate with those for leaf biophysical properties but not with those for leaf developmental traits. J Exp Bot 58(6):1433–1449PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Laura D. Atkinson
    • 1
  • Leah K. McHale
    • 2
  • María José Truco
    • 3
  • Howard W. Hilton
    • 4
  • James Lynn
    • 5
  • Johan W. Schut
    • 6
  • Richard W. Michelmore
    • 3
  • Paul Hand
    • 7
  • David A. C. Pink
    • 7
    Email author
  1. 1.Monsanto UK LtdCambridgeUK
  2. 2.Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusUSA
  3. 3.Department of Plant Sciences, Genome CenterUniversity of CaliforniaDavisUSA
  4. 4.SGS UK LtdBanburyUK
  5. 5.Applied Statistical SolutionsLeamington SpaUK
  6. 6.Rijk Zwaan Zaadteelt en Zaadhandel B.VDe LierThe Netherlands
  7. 7.Crop and Environment Science DepartmentHarper-Adams UniversityNewportUK

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