, Volume 197, Issue 2, pp 211–228 | Cite as

QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis

  • Amy Frary
  • Anne Frary
  • Marie-Christine Daunay
  • Koen Huvenaars
  • Rolf Mank
  • Sami Doğanlar


Fifty-eight F2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P ≤ 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies.


Solanum melongena Quantitative trait loci Gene conservation Solanaceae 



This work was supported by a Career Project (TUBITAK 104T224) from the Scientific and Technical Research Council of Turkey to Sami Doğanlar. This execution of the AFLP marker work was financially supported by DeRuiterZonen C.V., Rijk Zwaan Zaadteelt and Zaadhandel B.V., and Vilmorin Clause & Cie S.A. The AFLP® technology is covered by patents and/or patent applications of Keygene N.V. AFLP and KeyGene are registered trademarks of Keygene N.V. Other trademarks are the property of their respective owners.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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  1. Alpert K, Grandillo S, Tanksley SD (1995) fw2.2: a major QTL controlling fruit weight is common to both red- and green-fruited tomato species. Theor Appl Genet 91:994–1000PubMedGoogle Scholar
  2. Barchi L, Lefebvre V, Sage-Palloix A-M, Lanteri S, Palloix A (2009) QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping. Theor Appl Genet 118:1157–1171PubMedCrossRefGoogle Scholar
  3. Barchi L, Lanteri S, Portis E, Vale G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L, Rotino GL (2012) A RAD tag derived marker based eggplant linkage map and location of QTLs determining anthocyanin pigmentation. PLoS ONE 7:e43740PubMedCentralPubMedCrossRefGoogle Scholar
  4. Ben Chaim A, Paran I, Grube RC, Jahn M, van Wijk R, Peleman J (2001) QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor Appl Genet 102:1016–1028CrossRefGoogle Scholar
  5. Bonierbale MW, Plaisted RL, Pineda O, Tanksley SD (1994) QTL analysis of trichome-mediated insect resistance in potato. Theor Appl Genet 87:973–987PubMedCrossRefGoogle Scholar
  6. Busch BL, Schmitz G, Rossmann S, Piron F, Ding J, Bendahmane A, Theres K (2011) Shoot branching and leaf dissection in tomato are regulated by homologous gene modules. Plant Cell 23:3595–3609PubMedCentralPubMedCrossRefGoogle Scholar
  7. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedCentralPubMedGoogle Scholar
  8. Clayberg CD (1962) Inheritance and linkage of fruit stripe Fs. Rep Tomato Genet Coop 12:22–23Google Scholar
  9. Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196CrossRefGoogle Scholar
  10. Daunay MC, Aubert S, Frary A, Doganlar S, Lester RN, Barendse G, van der Weerden G, Hennart JW, Haanstra J, Dauphin F, Jullian E (2004) Eggplant (Solanum melongena) fruit colour: pigments measurements and genetics. In: Proceedings of the XIIth EUCARPIA meeting on genetics and breeding of Capsicum and eggplant, 17–19 May 2004, Noordwijkerhout, The Netherlands, pp 108–116Google Scholar
  11. De Jong WS, Eannetta NT, De Jong DM, Bodis M (2004) Candidate gene analysis of anthocyanin pigmentation loci in the Solanaceae. Theor Appl Genet 108:423–432PubMedCrossRefGoogle Scholar
  12. deVicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596PubMedCentralPubMedGoogle Scholar
  13. Doganlar S, Frary A, Daunay M, Lester R, Tanksley S (2002a) A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae. Genetics 161:1697–1711PubMedCentralPubMedGoogle Scholar
  14. Doganlar S, Frary A, Daunay MC, Lester RN, Tanksley SD (2002b) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161:1713–1726PubMedCentralPubMedGoogle Scholar
  15. Doganlar S, Frary A, Daunay MC, Huvenaars K, Mank R, Frary A (in press) High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae. Euphytica Google Scholar
  16. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine-mapping of yield-associated QTL. Genetics 141:1147–1162PubMedCentralPubMedGoogle Scholar
  17. FAO Statistics (2013) Accessed 15 Jan 2013
  18. Frary A, Nesbitt TC, Frary A, Grandillo S, van der Knapp E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanskley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88PubMedCrossRefGoogle Scholar
  19. Frary A, Doganlar S, Daunay MC, Tanksley SD (2003a) QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of Solanaceous species. Theor Appl Genet 107:359–370PubMedCrossRefGoogle Scholar
  20. Frary A, Doganlar S, Frampton A, Fulton T, Uhlig J, Yates H, Tanksley S (2003b) Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1. Genome 46:235–243PubMedCrossRefGoogle Scholar
  21. Frary A, Fritz LA, Tanksley SD (2004) A comparative study of the genetic bases of natural variation in tomato leaf sepal and petal morphology. Theor Appl Genet 109:523–533PubMedCrossRefGoogle Scholar
  22. 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. Mon Genet Genomics 266:821–826CrossRefGoogle Scholar
  23. Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A (2012) Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. Theor Appl Genet 125:47–56PubMedCrossRefGoogle Scholar
  24. Grandillo S, Tanksley SD (1996) Analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951PubMedCrossRefGoogle Scholar
  25. 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
  26. Hareven D, Gutfinger T, Parnis A, Eshed Y, Lifschitz E (1996) The making of a compound tomato leaf: genetic manipulation of leaf architecture in tomato. Cell 84:735–744PubMedCrossRefGoogle Scholar
  27. Joehanes R, Nelson JC (2008) QGene 4.0 an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789PubMedCrossRefGoogle Scholar
  28. Kimura S, Koenig D, Kang J, Yoong FY, Sinha N (2008) Natural variation in leaf morphology results from mutation of a novel KNOX gene. Curr Biol 18:672–677PubMedCrossRefGoogle Scholar
  29. Ku H-M, Doganlar S, Chen K-Y, Tanksley SD (1999) The genetic basis of pear-shaped tomato fruit. Theor Appl Genet 9:844–850CrossRefGoogle Scholar
  30. Liharska TB, Hontelez J, van Kammen A, Zabel P, Koornneef M (1997) Molecular mapping around the centromere of tomato chromosome 6 using irradiation-induced deletions. Theor Appl Genet 95:969–974CrossRefGoogle Scholar
  31. Lippman Z, Tanksley SD (2001) Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 158:413–422PubMedCentralPubMedGoogle Scholar
  32. 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 99:13302–13306PubMedCentralPubMedCrossRefGoogle Scholar
  33. Livingstone KD, Lackney VK, Blauth JR, van Wijk R, Jahn MK (1999) Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152:1183–1202PubMedCentralPubMedGoogle Scholar
  34. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459–473PubMedCentralPubMedGoogle Scholar
  35. MacArthur JW (1934) Linkage groups in the tomato. J Genet 29:123–133CrossRefGoogle Scholar
  36. Maliepaard C, Bas N, van Heusden S, Kos J, Pet G, Verkerk R, Vrielink R, Zabel P, Lindhout P (1995) Mapping of QTLs for glandular trichome densities and Trialeurodes vaporariorum (greenhouse whitefly) resistance in an F2 from Lycopersicon esculentum × Lycopersicon hirsutum f. glabratum. Heredity 75:425–433CrossRefGoogle Scholar
  37. Mathews H, Clendennen SK, Caldwell CG, Liu XL, Connors K, Matheis N, Schuster DK, Menasco DJ, Wagoner W, Lightnew J, Wagner DR (2003) Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis modification and transport. Plant Cell 15:1689–1703PubMedCentralPubMedCrossRefGoogle Scholar
  38. Monforte A, Friedman E, Zamir D, Tanksley SD (2001) Comparison of a set of allelic QTL-NILs for chromosome 4 of tomato: deductions about natural variation and implications for germplasm collection. Theor Appl Genet 102:572–590CrossRefGoogle Scholar
  39. Nagelkerke NJD (1991) A note on a general definition of the coefficient of determination. Biometrika 78:691–692CrossRefGoogle Scholar
  40. Nelson JC (1997) QGene: software for marker-based genomic analysis and breeding. Mol Breed 3:229–235CrossRefGoogle Scholar
  41. Nunome T, Yoshida T, Hirai M (1998) Genetic linkage map of eggplant. In: Proceedings of the 10th Eucarpia meeting on genetics and breeding of Capsicum and eggplant, Avignon France, pp 239–242Google Scholar
  42. Nunome T, Ishiguro K, Yoshida T, Hirai M (2001) Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers. Breed Sci 51:19–26CrossRefGoogle Scholar
  43. Paran I, Goldman I, Zamir D (1997) QTL analysis of morphological traits in a tomato recombinant inbred line population. Genome 40:242–248Google Scholar
  44. Powell ALT, Nguyen CV, Hill T, Cheng KL, Figueroa-Balderas R, Aktas H, Ashrafi H, Pons C, Fernandez-Muñoz R, Vicente A, Lopez-Baltazar J, Barry CS, Liu Y, Chetelat R, Granell A, van Deynze A, Giovannoni JJ, Bennett AB (2012) Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336:1711–1715PubMedCrossRefGoogle Scholar
  45. Schreiber G, Reuveni M, Evenor D, Oren-Shamir M, Ovadia R, Sapir-Mir M, Bootbool-Man A, Nahon S, Shlomo H, Chen L, Levin I (2012) ANTHOCYANIN1 from Solanum chilense is more efficient in accumulating anthocyanin metabolites than its Solanum lycopersicum counterpart in association with the ANTHOCYANIN FRUIT phenotype of tomato. Theor Appl Genet 124:295–307PubMedCrossRefGoogle Scholar
  46. Tanksley SD, Ganal MW, de Prince JP, Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Roder S, Wing RA, Wu W, Young ND (1992) High-density linkage maps of the tomato and potato genomes. Genetics 132:1141–1160PubMedCentralPubMedGoogle Scholar
  47. Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  48. Vales MI, Schon CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM (2005) Effect of population size on the estimation of QTL: a test using resistance to barley rust stripe. Theor Appl Genet 111:1260–1270PubMedCrossRefGoogle Scholar
  49. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78PubMedCrossRefGoogle Scholar
  50. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733PubMedCentralPubMedCrossRefGoogle Scholar
  51. Yates HE, Frary A, Doganlar S, Frampton A, Eannetta N, Uhlig J, Tanksley SD (2004) Comparative fine mapping of fruit quality QTLs on chromosome 4 introgressions derived from two wild tomato species. Euphytica 135:283–296CrossRefGoogle Scholar
  52. Zheng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468Google Scholar
  53. Zygier S, Chaim A-B, Efrati A, Kaluzky G, Borovsky Y, Paran I (2005) QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato. Theor Appl Genet 111:437–445PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Amy Frary
    • 1
  • Anne Frary
    • 2
  • Marie-Christine Daunay
    • 3
  • Koen Huvenaars
    • 4
  • Rolf Mank
    • 4
  • Sami Doğanlar
    • 2
  1. 1.Department of Biological SciencesMount Holyoke CollegeSouth HadleyUSA
  2. 2.Plant Molecular Genetics Laboratory, Department of Molecular Biology and GeneticsIzmir Institute of TechnologyUrlaTurkey
  3. 3.Unité de Génétique et Amélioration des Fruits et LégumesINRAMontfaved CedexFrance
  4. 4.Keygene N.V.WageningenThe Netherlands

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