Abstract
Low levels of polymorphism and lack of sufficient numbers of microsatellite markers are factors that constrain molecular breeding in pigeonpea. BAC-end sequencing approach was used to obtain a set of BAC-associated SSRs (simple sequence repeats), providing a resource for both genetic and physical map analysis. 87,590 pigeonpea BAC end sequences, representing 56.5 Mb from genome, were surveyed for the presence of microsatellite using MIcroSAtellite (MISA). Among 18,149 pigeonpea microsatellites (1 SSR per 32.1Mbp) di-nucleotide motifs were the most abundant (41%), followed by tri-nucleotide motifs (~10%). Most di- and tri-nucleotide sequences were AT-rich (i.e., TA and TAA). With the goal of increasing genetic marker density, 6,590 oligonucleotide primers pairs were designed, 3,072 primer pairs were synthesized and tested. Amplified products were obtained for 2,946 primer pairs and were used to identify polymorphism in a set of 24 pigeonpea genotypes that are parents of different mapping populations segregating for Fusarium wilt (FW), sterility mosaic (SM) and water logging. Number of polymorphic markers identified ranged from 100-415 across different crosses. Genotyping of these polymorphic markers in the respective mapping populations is underway. Marker genotyping data along with phenotyping data obtained from these mapping populations will facilitate mapping of QTLs/genes for the traits of interest to breeders