Mitochondrial DNA Polymorphisms Revealed by RAPD Assays Distinguish the Male-sterile and Male-fertile Cytoplasms in Pearl Millet

Diversification of cytoplamic male sterile (CMS) sources is of considerable significance in pearl millet, considering that almost all the commercially cultivated hybrids, particularly in India, are based on a single CMS source, A1. We analyzed the mitochondrial DNA (mtDNA) polymorphisms among five pearl millet CMS sources (A1 to A5) and a male-fertile maintainer (B) line, all in an isonuclear background. Analysis using 21 random primers led to identification of polymorphic bands specific to the A1, A2, A3 and A5 CMS lines. Two RAPD primers, OP-G12 and OP-G19, in combination were able to distinguish all the male-sterile and male-fertile cytoplasms. Highly effective for this purpose also were four RAPD markers, OP-B7, OP-D8, OP-F10 and OP-G12. Cluster analysis, followed by bootstrap analysis, of the mtDNA dataset revealed two distinct clusters: cluster-I comprising the A1, A2, A3 CMS lines and the male-fertile line, and cluster-II comprising the A4 and A5 CMS lines.