Purpose: Gamma rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in the development of more than 60% of global cowpea (Vigna unguiculata (L.) Walp.) mutant varieties. Nevertheless, the nature and type of genome-wide mutations induced by gamma rays have not been studied in cowpea and therefore, the present investigation was undertaken.
Materials and methods: Genomic DNAs from three stable gamma rays-induced mutants (large seed size, small seed size and disease resistant mutant) of cowpea cultivar 'CPD103' in M6 generation along with its progenitor were used for Illumina-based whole-genome resequencing.
Results: Gamma rays induced a relatively higher frequency (88.9%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 3.51 in M6 generation. A > G transitions, including its complementary T > C transitions, predominated the transition mutations, while all four types of transversion mutations were detected with frequencies over 6.5%. Indels (small insertions and deletions) constituted about 11% of the total induced variations, wherein small insertions (6.3%) were relatively more prominent than small deletions (4.8%). Among the indels, single-base indels and, in particular, those involving A/T bases showed a preponderance, albeit indels of up to three bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.45%) and indels (20.2%) 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 1.4 × 10-7 per base pair in M6 generation.
Conclusion: Gamma-rays with a greater tendency to induce SBSs and, to a lesser extent, indels could be efficiently and effectively exploited in cowpea mutation breeding.
Keywords: Cowpea; gamma-rays; indels; mutation; single base substitutions; whole genome sequencing.