Development of genome-based ssr markers in chickpea (Cicer arietinum lL.) and investigation of transferability to near-relative species

Construction of a high-resolution genotyping assays is considerably important in order to identify and map useful genes or QTLs controlling important agronomic traits. In the perspective of excellent genetic attributes of SSR (Simple Sequence Repeats) markers with the basic requirement of a simple, cost-effective agarose gel-based assay for their efficient genotyping applications, to enhance the resolution of the existing genetic linkage map is always desirable. In the present study, the genome data belonging Cicer arietinum L. CA 2969 and Cicer reticulatum Ladiz. was obtained by using whole genome re-sequencing (WGRS). Totally, 1650 In/Dels were obtained from all genome reads. When the In/Del regions are compared among two genomes, 133 polymorphic SSR regions were identified and 58 primer sets were successfully designed. We tested primer sets for measures of genetic diversity in 30 genotypes including eight accesions of C. arietinum (four kabuli types and four kabuli types), eight accessions of C. reticulatum, eight accessions of C. echinospermum P.H. Davis and six accesions of C. anatolicum Alef., C. canariense A.Santos & G.P.Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum DC. The studied SSRs revealed a total of 374 alleles with an average of 2.360 alleles with mean values of observed heterozygosity (Ho: 0.080), expected heterozygosity (He: 0.345) and polymorphism information content (PIC: 0.731). Principal component analysis (PCA) revealed clearly four groups in the analyzed accessions. The SSR markers developed in this study were also tested in 30 genotypes of F6 population derived from an interspecific cross between C. arietinum (♀) × C. reticulatum (♂). According to chi-square (χ2) analysis, an expected 1:1 segregation ratio was observed in all markers except for SSR20. The results of this study will provide essential information for further studies in comparative genomic studies and gene introgressions and evolutionary analyses in wild species. Also, these markers can be useful for the marker assisted breeding research in chickpea.