Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.)

Chickpea genetic mapping has been hampered by insufficient amplicon length polymorphism for sequence based markers. To develop an alternative source of polymorphic markers, we determined naturally abundant single nucleotide polymorphism (SNP) in coding and genomic regions between FLIP 84-92C (C. arietinum) and PI 599072 (C. reticulatum) and identified an inexpensive method to detect SNP for mapping. In coding sequences, 110 single base changes or substitutions (47% transitions and 53% transversions) and 18 indels were found; while 50 single base changes (68% transitions and 33% transversions) and eight indels were observed in genomic sequences. SNP frequency in coding and genomic regions was 1 in 66 bp and 1 in 71 bp, respectively. In order to effectively use this high frequency of polymorphism, we used Cleaved Amplified Polymorphic Site (CAPS) and derived CAPS (dCAPS) marker systems to identify a restriction site at SNP loci. In this study, we developed six CAPS and dCAPS markers and fine mapped QTL1, a region previously identified as important for ascochyta blight resistance. One of the CAPS markers from a BAC end was identified to account for 56% of the variation for ascochyta blight resistance in chickpea. Conversion of naturally abundant SNPs to CAPS and dCAPS for chickpea mapping, where absence of amplicon length polymorphism is a constraint, has potential to generate high-density maps necessary for map-based cloning and integration of physical and genetic maps.