Summary A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost‐effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC 3 F 2 lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population ( Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG‐SNPs and 396 published markers for developing the genetic map. As a result, a second‐generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG‐SNPs and 389 published marker loci with an average inter‐marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second‐generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula , followed by Glycine max , Lotus japonicus and least with Vigna unguiculata . Development of these cost‐effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes.

Large‐scale development of cost‐effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes