Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

Abstract Gamma-rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in development of more than 60% of global cowpea mutant varieties. Nevertheless, the characteristics of genome wide mutations induced by gamma-rays has not been studied in cowpea (Vigna unguiculata (L.) Walp.). In the present investigation, mutations elicited by gamma-rays in three cowpea mutant lines in M6 generation were characterized through whole-genome sequencing. Gamma-rays induced a relatively higher frequency (91.1%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 2.82. A > G transitions including its complementary T > C transitions predominated the transition mutations, while all the four types of transversion mutations were detected with almost equal frequencies (5.6–7.4%). Indels constituted about 9% of the total induced variation wherein small insertions (5.3%) were relatively more prominent than small deletions (3.7%). Among the indels, single base indels and in particular those involving A/T bases showed preponderance, albeit indels of up to five bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.3%) and indels (12.7%) potentially altered the encoded amino-acids/peptides. The inherent mutation rate induced by gamma-rays in cowpea was observed to be in the order of 1.76 x 10− 6 per base pair. Therefore, gamma-rays with greater tendency to induce SBSs and to a lesser extent indels could be efficiently and effectively exploited in cowpea mutation breeding.