AFLP analysis in pigeonpea (Cajanus cajan (L.) Millsp.) revealed close relationship of cultivated genotypes with some of its wild relatives

A total of 561 amplified fragment length polymorphism (AFLP) loci were generated and used to study the genetic diversity of wild and cultivated genotypes of pigeonpea. Out of 561 marker loci, 558 were polymorphic with an average of 76.12 bands. Analysis of molecular variation (AMOVA) revealed significant strong population structure when genotypes were structured according to continent of origin (FST = 0.22) also when structured into cultivated and wild genotypes (FST = 0.16). Maximum polymorphic loci were observed in cultivated species C. cajan (352) which is due to more number of genotypes used while, a minimum number of 45 polymorphic bands were obtained in C. acutifolius. Highest (0.291) average gene diversity was recorded in species C. mollis and lowest (0.079) average gene diversity was recorded in C. acutifolius. The 33 genotypes grouped into 14 clusters at 26% Jaccard’s similarity coefficients. Clustering analysis revealed most cultivated genotypes grouped into one major cluster while, the wild genotypes grouped into many clusters at 26% Jaccard’s similarity revealing greater diversity within wild species as compared to cultivated genotypes. From among the various cultivated genotypes studied, four genotypes BRG 3, ICP 7035, TTB 7 and ICP 8863 were molecularly and morphologically diverse and were used as parental genotypes to study nature of inheritance and to identify markers linked to sterility mosaic disease.