Molecular characterisation of CGMS, maintainer and inbred lines and diversity analysis in pigeonpea [Cajanus cajan (L.) Millsp.]

The present study was initiated with forty microsatellite markers for studying the molecular genetic diversity in 28 pigeonpea genotypes(6 CGMSlinesofA₁, A₂and A₄ sources, their maintainer linesand16 inbredlines) utilisedas theparental material for the synthesis of F₁ hybrids. The level of polymorphism was too low and only 45 per cent markers were polymorphic. A total of 65 alleles were produced and the number of alleles produced ranged from two to six. The mean PIC value of 40 SSR primers was 0.147 and the primer CcM2977 produced the highest PIC value of 0.787 followed by CcM1770 (0.565). The primers viz., CcM0039 and CcM2463 were polymorphic between CGMS and inbred lines and the primer CcM2977 was polymorphic among the different sources of CGMS lines. The UPGMA clustering and Neighbour-joining analyses grouped all the CGMS lines and respective maintainer lines in a single cluster and the inbred lines as two separate clusters. Among the inbred lines ICPL 11966, ICPL11947 and ICPL11950 were distinctly grouped in one cluster and other 13 inbred lines were clustered separately. Polymorphic markers viz., CcM2977 and CcM1770 were used to confirm the hybrids of the crosses viz., ICPA 2043 x LRG 41 and ICPA 2043 x IC 33725. The present study revealed that SSR markers are highly informative for exploiting the molecular diversity prevailing among the parental lines and could be utilized for further pigeonpea improvement at genomic level.