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

Autor: Jhingan S; Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany., Kumar A; Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany., Harloff HJ; Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany., Dreyer F; NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany., Abbadi A; NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany., Beckmann K; NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany., Obermeier C; Department of Plant Breeding, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany., Jung C; Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany.
Jazyk: angličtina
Zdroj: The Plant journal : for cell and molecular biology [Plant J] 2023 Feb; Vol. 113 (4), pp. 866-880. Date of Electronic Publication: 2023 Jan 19.
DOI: 10.1111/tpj.16079
Abstrakt: 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 (4×) 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' (http://www.emsbrassica.plantbreeding.uni-kiel.de), 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.
(© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
Databáze: MEDLINE
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