Assessment of genetic variation and relationships in a chickpea variety set using SSR markers

In this study, nine new SSR markers were developed from gene bank chickpea sequences, together with an additional nine SSR markers selected from Winter et al. (1999), allelic variation and genetic relationships were evaluated at 21 SSR loci in an accession set consisting of three desi lines and 28 kabuli type registered Turkish chickpea varieties. Except for three, a specific microsatellite locus was amplified by the rest of the primer pairs, and a total of 172 alleles were detected with an average of 8 alleles per locus. As an indication of low levels of heterozygosity in varieties, only three heterozygotes were observed. Allelic variation within and among varieties was found to be common, and no variety specific allele was detected while some varieties were monomorphic at a few marker loci. Nei?s standard genetic distance coefficients were computed from allele frequencies for all pair-wise combinations of varieties, and a UPGMA dendrogram was developed. Cluster analysis displayed all varieties as separate units in the dendrogram and grouped desi types together as an outer branch in the dendrogram. Besides the addition of 9 new SSR markers to chickpea marker collection, the study reports the successful survey of genetic variation with a highly polymorphic marker system and reveals a relatively high allelic variation in Turkish chickpea varieties.