Comparison of the Sequence Simple Repeats (SSR) Fragments Between the Genetic Maps and the Physical Map in Chickpea (Cicer arietinum)

Microsatellites or simple sequence repeats (SSRs) markers are short (2-5 nucleotides) tandemly repeated DNA sequences. They occur frequently and almost randomly in most eukaryotic genomes. Each SSR locus supposed to be unique, so the primers targeting these flanking regions can be designed to produce a specific band. Several hundreds of SSR markers were developed in chickpea genome but very little have been mapped because they show monomorphic PCR products. However, after the chickpea full genome sequence is being published, it becomes possible to look at these SSR loci and identify their physical positions across the genome. In this study we identified 33,920, 21,004 and 2,807 dinucleotide trinucleotide and tetranucleotide repeats respectively through the chickpea genome. A total of 713 SSR primer pairs developed previously in chickpea have been used in this study. The results indicated only 563 (79%) SSR primer pairs showed unique location while the remaining (21%) SSRs located within repetitive DNA through the genome. For example primer “CaM0139” was found on the eight chromosomes can produce 953 different PCR product size. Out of the unique 563 primer pairs 16.2% were on chromosome 6 and the least (3.2%) were located at chromosome 8. However, this study could help to discard the useless SSR primers in chickpea.