Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jul 30;9:357.
doi: 10.1186/1471-2164-9-357.

Gene-based Microsatellite Development for Mapping and Phylogeny Studies in Eggplant

Free PMC article

Gene-based Microsatellite Development for Mapping and Phylogeny Studies in Eggplant

Anikò Stàgel et al. BMC Genomics. .
Free PMC article


Background: Eggplant (Solanum melongena L.) is a member of the Solanaceae family. In spite of its widespread cultivation and nutritional and economic importance, its genome has not as yet been extensively investigated. Few analyses have been carried out to determine the genetic diversity of eggplant at the DNA level, and linkage relationships have not been well characterised. As for the other Solanaceae crop species (potato, tomato and pepper), the level of intra-specific polymorphism appears to be rather limited, and so it is important that an effort is made to develop more informative DNA markers to make progress in understanding the genetics of eggplant and to advance its breeding. The aim of the present work was to develop a set of functional microsatellite (SSR) markers, via an in silico analysis of publicly available DNA sequence.

Results: From >3,300 genic DNA sequences, 50 SSR-containing candidates suitable for primer design were recovered. Of these, 39 were functional, and were then applied to a panel of 44 accessions, of which 38 were cultivated eggplant varieties, and six were from related Solanum species. The usefulness of the SSR assays for diversity analysis and taxonomic discrimination was demonstrated by constructing a phylogeny based on SSR polymorphisms, and by the demonstration that most were also functional when tested with template from tomato, pepper and potato. As a results of BLASTN analyses, several eggplant SSRs were found to have homologous counterparts in the phylogenetically related species, which carry microsatellite motifs in the same position.

Conclusion: The set of eggplant EST-SSR markers was informative for phylogenetic analysis and genetic mapping. Since EST-SSRs lie within expressed sequence, they have the potential to serve as perfect markers for genes determining variation in phenotype. Their high level of transferability to other Solanaceae species can be used to provide anchoring points for the integration of genetic maps across species.


Figure 1
Figure 1
UPGMA dendrogram. Analysis of the 44 genotype set, based on 116 EST-SSR alleles. Sample codes are described in Table 2.
Figure 2
Figure 2
Biplot of the Principal co-ordinates analysis. Analysis based on microsatellite data depicting the genetic relationship among the 44 Solanum genotypes.

Similar articles

See all similar articles

Cited by 22 articles

See all "Cited by" articles


    1. Daunay MC, Lester RN, Ano G. Cultivated eggplants. In: Charpier A, Jacquot M, Hamon S, Nicolas D, editor. tropical plant breeding. Oxford university press, Oxford; 2001. pp. 200–225.
    1. Hinata H. Eggplant (Solanum melongena L.) In: Bajaj YPS, editor. Biotechnology in agriculture and Forestry, Crop I. Vol. 2. Springer, Berlin; 1986. pp. 363–370.
    1. Barchi L, Bonnet J, Boudet C, Signoret P, Nagy I, Lanteri S, Palloix A, Lefebvre V. A high-resolution intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced RIL subsets for fast mapping. Genome. 2007;50:51–60. doi: 10.1139/G06-140. - DOI - PubMed
    1. Jacobs JME, Van Eck HJ, Arens P, Verkerk-Bakker B, Lintel B, Hekkert HJM, Bastiaanssen A, El-Kharbotly A, Pereira E, Jacobsen E, Stiekema WJ. A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. TAG. 2004;91:289–300. - PubMed
    1. Tanksley SD, Ganal MW, 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 MS, Wing RA, Wu W, Young ND. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992;132:1141–1160. - PMC - PubMed