Direct access to millions of mutations by whole genome sequencing of an oilseed rape mutant population

Induced mutations are an essential source of genetic variation in plant breeding. Ethyl methanesulfonate (EMS) mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In the present study, a rapeseed M-2 population was derived from M-1 parent cultivar 'Express' treated with EMS. Whole genomes were sequenced from fourfold (4x) pools of 1988 M-2 plants representing 497 M-2 families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284 442 single nucleotide polymorphisms (SNPs) per M-2 DNA pool were found resulting from EMS mutagenesis. 55% of the SNPs were C -> T and G -> A transitions, characteristic for EMS induced ('canonical') mutations, whereas the remaining SNPs were 'non-canonical' transitions (15%) or transversions (30%). Additionally, we detected 88 725 high confidence insertions and deletions per pool. On average, each M-2 plant carried 39 120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Approximately 82% of such mutations were located either 5 kb upstream or downstream (56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool 'EMSBrassica' (), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.

Automated summary

Induced mutations are important sources of genetic variation in plant breeding. In this study, a rapeseed M-2 population was obtained by treating the parent cultivar 'Express' with EMS, and whole genomes were sequenced from 497 M-2 families. The mutation frequencies varied across chromosomes, and the majority of detected mutations were canonical transitions characteristic of EMS mutagenesis. The sequenced resource described in this study provides valuable information for functional gene studies in rapeseed breeding.