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Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins

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Abstract

The eggplant (Solanum melongena L.) genome is the least investigated among the economically most important solanaceous crops. Extensive use of molecular markers will improve eggplant germplasm enhancement and breeding. Microsatellites, or simple sequence repeats, have proved to be very useful for eggplant germplasm management and breeding, but there is limited availability of these polymorphic, codominant, and highly repeatable markers in eggplant. We developed a genomic DNA library enriched with AG/CT, which allowed the identification of 55 new genomic microsatellites. Variation parameters of microsatellite loci analyzed showed high average values. The potential of these markers for fingerprinting was assessed in a collection of 24 accessions, of which 22 correspond to S. melongena from different types (landraces, heirlooms, modern F1 hybrids, and obsolete cultivars) and origins, and two to each of the cultivated relatives S. aethiopicum and S. macrocarpon. The multivariate (cluster and PCoA) analyses clearly differentiated four main clusters: (a) two outgroups formed by S. aethiopicum and S. macrocarpon accessions, (b) S. melongena accessions derived mostly from the Mediterranean basin, Central Europe, Africa, and America (‘occidental’ eggplants), and (c) S. melongena accessions derived mostly from Eastern and Southeastern Asia (‘oriental’ eggplants). However, no apparent association pattern was found for accessions of the different types. Observed heterozygosity (H o) values were low, although hybrid cultivars had higher values (H o = 0.12) than non-hybrid materials (H o = 0.02). The new set of eggplant microsatellite markers has proved highly informative and useful for studying the diversity, relationships, and genetic characteristics of an eggplant collection. These markers will be useful for germplasm management and breeding in eggplant.

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References

  • Barone A, Di Matteo A, Carputo D, Frusciante L (2009) High-throughput genomics enhances tomato breeding efficiency. Curr Genomics 10:1–9

    Article  PubMed  CAS  Google Scholar 

  • Behera TK, Sharma P, Singh BK, Kumar G, Kumar R, Mohapatra T, Singh NK (2006) Assessment of genetic diversity and species relationships in eggplant (Solanum melongena L.) using STMS markers. Sci Hortic 107:352–357

    Article  CAS  Google Scholar 

  • Bohme M, Pinker I, Pietzsch R, Zude M (2008) Growing and fruiting of eggplant genotypes (Solanum melongena L.) under greenhouse conditions in Europe. Acta Hortic 769:69–76

    Google Scholar 

  • Botstein D, White RI, Skolnich M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:324–331

    Google Scholar 

  • Buntjer JB (1997) Phylogenetic computer tools (PhylTools), version 1.32 for Windows. Laboratory of Plant Breeding, Wageningen University, Wageningen

  • Chadha ML (1993) Improvement of brinjal. In: Chadha KL, Kalloo G (eds) Advances in horticulture vol. 5—vegetable crops: part 1. Malholtra Publishing House, New Delhi, pp 105–135

    Google Scholar 

  • Chakraborty R, Kimmel M, Strivers DN, Davison LJ, Deka R (1997) Relative mutation rates at di- tri- and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 94:1041–1046

    Article  PubMed  CAS  Google Scholar 

  • 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):557–572

    Article  CAS  Google Scholar 

  • Danan S, Veyrieras JB, Lefebvre V (2011) Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol 11:16

    Article  PubMed  Google Scholar 

  • Daunay MC (2008) Eggplant. In: Prohens J, Nuez F (eds) Handbook of plant breeding: vegetables II. Springer, New York, pp 163–220

    Google Scholar 

  • Daunay MC, Janick J (2007) History and iconography of eggplant. Chron Hortic 47(3):16–22

    Google Scholar 

  • Dekkers JCM, Hospital F (2002) The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3(1):22–32

    Article  PubMed  CAS  Google Scholar 

  • Demir K, Bakir M, Sarıkamış G, Acunalp S (2010) Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers. Genet Mol Res 9(3):1568–1576

    Article  PubMed  CAS  Google Scholar 

  • Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:6

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Felsenstein J (1989) PHYLIP: phylogeny inference package (version 3.2). Cladistics 5:164–166

    Google Scholar 

  • Frary A, Xu Y, Liu J, Mitchell S, Tedeschi E, Tanksley S (2005) Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theor Appl Genet 111:291–312

    Article  PubMed  CAS  Google Scholar 

  • Furini A, Wunder J (2004) Analysis of eggplant (Solanum melongena)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization. Theor Appl Genet 108:197–208

    Article  PubMed  CAS  Google Scholar 

  • Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–328

    Google Scholar 

  • Hallard J (1996) L’aubergine au Japon. PHM Rev Hortic 374:55–56

    Google Scholar 

  • Isshiki S, Iwata N, Khan MR (2008) ISSR variations in eggplant (Solanum melongena L.) and related Solanum species. Sci Hortic 117:186–190

    Article  CAS  Google Scholar 

  • Jo YD, Kim YM, Park MN, Yoo JH, Park M, Kim BD, Kang BC (2010) Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper. Mol Breed 25:187–201

    Article  CAS  Google Scholar 

  • Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  • Karihaloo JL, Brauner S, Gottlieb LD (1995) Random amplified polymorphic DNA variation in the eggplant, Solanum melongena L. (Solanaceae). Theor Appl Genet 90:767–770

    CAS  Google Scholar 

  • Koundal M, Sharma DR, Mohapatra T, Koundal KR (2006) Comparative evaluation of RAPD and AFLP based genetic diversity in brinjal (Solanum melongena L.). J Plant Biochem Biotechnol 15:15–19

    CAS  Google Scholar 

  • Lester RN, Hasan SMZ (1991) Origin and domestication of the brinjal eggplant, Solanum melongena, from S. incanum in Africa and Asia. In: Hawkes JG, Lester RN, Nee M, Estrada N (eds) Solanaceae III: taxonomy, chemistry, evolution. The Linnean Society of London, London, pp 369–387

    Google Scholar 

  • Lester RN, Thitai GNW (1989) Inheritance in Solanum aethiopicum, the scarlet eggplant. Euphytica 40:67–74

    Google Scholar 

  • Liu K, Muse S (2005) Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    Article  PubMed  CAS  Google Scholar 

  • Mace ES, Lester RN, Gebhardt CG (1999) AFLP analysis of genetic relationships among the cultivated eggplant Solanum melongena L., and wild relatives (Solanaceae). Theor Appl Genet 99:626–633

    Article  PubMed  CAS  Google Scholar 

  • Martins WS, Lucas DCS, Neves KFS, Bertioli DJ (2009) WebSat—a web software for microsatellite marker development. Bioinformation 3(6):282–283

    Article  PubMed  Google Scholar 

  • Mennella G, Rotino GL, Fibiani M, D’Alessandro A, Francese G, Toppino L, Cavallanti F, Acciarri N, Lo Scalzo R (2010) Characterization of health-related compounds in eggplant (Solanum melongena L.) lines derived from introgression lines of allied species. J Food Agric Chem 58:7597–7603

    Article  CAS  Google Scholar 

  • Muñoz-Falcón JE, Prohens J, Rodríguez-Burruezo A, Nuez F (2008a) Potential of local varieties and their hybrids for the improvement of eggplant production in the open field and greenhouse cultivation. J Food Agric Environ 6(1):83–88

    Google Scholar 

  • Muñoz-Falcón J, Prohens J, Vilanova S, Nuez F (2008b) Characterization, diversity, and relationships of the Spanish striped (Listada) eggplants: a model for the enhancement and protection of local heirlooms. Euphytica 164:405–419

    Article  Google Scholar 

  • Muñoz-Falcón JE, Prohens J, Vilanova S, Nuez F (2009a) Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders gene pool. Ann Appl Biol 154:453–465

    Article  Google Scholar 

  • Muñoz-Falcón JE, Prohens J, Vilanova S, Ribas F, Castro A, Nuez F (2009b) Distinguishing a protected geographical indication vegetable (Almagro eggplant) from closely related materials with selected morphological traits and molecular markers. J Sci Food Agric 89:320–328

    Article  Google Scholar 

  • Muñoz-Falcón JE, Vilanova S, Plazas M, Prohens J (2011) Diversity, relationships and genetic fingerprinting of the Listada de Gandía eggplant landrace using genomic SSRs and EST-SSRs. Sci Hortic 129(2):238–246

    Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  PubMed  CAS  Google Scholar 

  • 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 51:19–26

    Article  CAS  Google Scholar 

  • Nunome T, Suwabe K, Ohyama A, Fukuoka H (2003a) Identification and characterization of microsatellites in eggplant. Plant Breed 122:256–262

    Article  CAS  Google Scholar 

  • Nunome T, Suwabe K, Ohyama A, Fukuoka H (2003b) Characterization of trinucleotide microsatellites in eggplant. Breed Sci 53:77–83

    Article  CAS  Google Scholar 

  • Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet 119:1143–1153

    Article  PubMed  Google Scholar 

  • Pessarakli MM, Dris R (2004) Pollination and breeding of eggplants. J New Seeds 2(1):218–219

    Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 7:215–222

    Google Scholar 

  • Prohens J, Blanca JM, Nuez F (2005) Morphological and molecular variation in a collection of eggplant from a secondary center of diversity: implications for conservation and breeding. J Am Soc Hortic Sci 130:54–63

    CAS  Google Scholar 

  • Prohens J, Rodríguez-Burruezo A, Raigón MD, Nuez F (2007) Total phenolics concentration and browning susceptibility in a collection of different varietal types and hybrids of eggplant: implications for breeding for higher nutritional quality and reduced browning. J Am Soc Hortic Sci 132:638–646

    CAS  Google Scholar 

  • Quagliotti L (1979) Floral biology of Capsicum and Solanum melongena. In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of the Solanaceae. Academic Press, New York, pp 399–419

    Google Scholar 

  • Rodríguez-Burruezo A, Prohens J, Nuez F (2008) Performance of hybrids between local varieties of eggplant (Solanum melongena) and its relation to the mean of parents and to morphological and genetics distances among parents. Eur J Hortic Sci 73:76–83

    Google Scholar 

  • Rohlf FJ (1993) NTSYS-pc numerical taxonomy and multivariate analysis system. version 1.8. Exeter Software, Setauket, New York

    Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    PubMed  CAS  Google Scholar 

  • Schippers RR (2000) African indigenous vegetables. An overview of the cultivated species. CAB International, Wallingford

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  • Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TFC, Aquadro CF (1998) The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol Biol Evol 5:1751–1760

    Article  Google Scholar 

  • Seck A (2000) Breeding procedures and results of indigenous vegetables: examples of African eggplant Solanum aethiopicum and okra Abelmoschus spp. Acta Hortic 522:195–208

    Google Scholar 

  • Sidhu AS, Bal SS, Behera TK, Rani M (2004) An outlook in hybrid eggplant breeding. J New Seeds 6(2/3):15–29

    Google Scholar 

  • Singh AK, Singh M, Singh AK, Singh R, Kumar S, Kalloo G (2006) Genetic diversity within the genus Solanum (Solanaceae) as revealed by RAPD markers. Curr Sci 90(5):711–716

    CAS  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical taxonomy. W.H. Freeman, San Francisco

    Google Scholar 

  • Squirrel J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants. Mol Ecol 12:1339–1348

    Article  Google Scholar 

  • Stàgel A, Portis E, Toppino L, Rotino GL, Lanteri S (2008) Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 9:357

    Article  PubMed  Google Scholar 

  • Staub JE, Serquen FC, Gupta M (1996) Genetic markers, map construction and their application in plant breeding. HortScience 31:729–741

    CAS  Google Scholar 

  • Stommel JR, Whitaker BD (2003) Phenolic acid content and composition of eggplant fruit in a germplasm core subset. J Am Soc Hortic Sci 128:704–710

    CAS  Google Scholar 

  • Varshney RK, Graner A, Sorrels ME (2005) Genetic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    Article  PubMed  CAS  Google Scholar 

  • Weese TL, Bohs L (2010) Eggplant origins: out of Africa, into the Orient. Taxon 59:49–56

    Google Scholar 

  • Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395–420

    Article  Google Scholar 

  • Xu YB, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48(2):391–407

    Article  Google Scholar 

Download references

Acknowledgments

This work was funded by the Ministerio de Ciencia y Tecnología (AGL2009-07257 and RF-2008-00008-00-00), Generalitat Valenciana (ACOMP/2011/032) and Universitat Politècnica de València (PAID-05-10-2318).

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  1. Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain

    Santiago Vilanova, Juan Pablo Manzur & Jaime Prohens

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  1. Santiago Vilanova
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  2. Juan Pablo Manzur
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Correspondence to Santiago Vilanova.

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Vilanova, S., Manzur, J.P. & Prohens, J. Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Mol Breeding 30, 647–660 (2012). https://doi.org/10.1007/s11032-011-9650-2

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