The genetic relationships among 10 species of Cajanus (Fabaceae) and 11 accessions of Cajanus cajan (pigeonpea) were assessed using RAPD and ISSR markers. All the species and accessions had an average genetic similarity of 63% and several accessions of Cajanus cajan had more than 90% similarity among themselves. In the genus Cajanus, the clustering of species in the dendrogram based on molecular data supported the sectional classification of the genus proposed by van der Maesen (1986) to a large extent. While C. cajan and its wild progenitor C. cajanifolius belonging to the sect. Cajanus came in a cluster, C. lineatus, C. sericeus and C. reticulatus of the sect. Atylia formed a separate clade. Similarly, members of the sect. Volubilis (C. crassus and C. mollis) and sect. Cantharospermum (C. scarabaeoides and C. albicans) also formed distinct groups justifying the established infra-generic classification. The pigeonpea (Cajanus cajan) accessions of Indian and African origin got separated in the dendrogram and Indian genotypes formed clusters according to their geographical area of occurrence and cultivation. The genetic diversity and molecular phylogeny of the genus Cajanus and pigeonpea cultivars have been discussed in the paper.
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