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

Abstract

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
• single base substitutions
• indels
• mutation
• whole genome sequencing

Author contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Dhanasekar Punniyamoorthy and Souframanien Jegadeesan. The first draft of the manuscript was written by Dhanasekar Punniyamoorthy and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.

Notes on contributors

Dhanasekar Punniyamoorthy

Dhanasekar Punniyamoorthy is a plant breeder working on genetic improvement of cowpea and pigeonpea through mutation and conventional breeding approaches for the past two decades. His main areas of research include ideotype breeding and biotic stress resistance breeding.

Jegadeesan Souframanien

Jegadeesan Souframanien is a blackgram breeder and heading the Pulses Improvement Section, overseeing the research activities on different pulse crops like blackgram, mungbean, cowpea, pigeonpea, cluster bean and lentils. His primary areas of research include mutation and molecular breeding for resistance to yellow mosaic virus disease and Callosobruchus storage pest.