Chickpea genetic mapping was initially hampered by insufficient polymorphism and an early reliance on dominant markers. The development of Sequence Tagged Microsattelite Sites (STMS) and other co-dominant markers has greatly improved our understanding of the chickpea genome. Development of BAC libraries and cDNA libraries has provided additional tools for genome analysis and generation of sequence based markers. Despite these advancements, insufficient polymorphism within chickpea has remained a significant obstacle to place sequence-based markers on the chickpea genetic map. Cleaved Amplified Polymorphic Site (CAPS) and derived CAPS (dCAPS) are two kinds of marker systems that identify altered and introduce, respectively, a restriction site at SNP loci. In this study, we developed six CAPS and dCAPS markers for BAC ends and a gene and fine mapped QTL1 for Ascochyta blight resistance. One of the CAPS markers for a BAC end was identified to account for 56% of the variation for Ascochyta blight resistance. Also, one Single Nucleotide Polymorphism (SNP) was observed between the mapping parents for every 52 nucleotides in this genomic region. Our ultimate goal is to determine the frequency of single nucleotide polymorphism (SNP) in the chickpea genome and to use those SNPs to develop additional markers for fine mapping of certain regions of the chickpea genome. Conversion of naturally abundant SNPs to CAPS and dCAPS in chickpea mapping, where absence of polymorphism is a constraint, has potential to generate high-density maps necessary for map-based cloning and integration of physical and genetic maps.
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