Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants

BMC Genomics

Shoya Komura¹  Shigeo Takumi¹  Kentaro Yoshida²  Hironobu Jinno³  Tatsuya Sonoda³  Fuminori Kobayashi⁴  Youko Oono⁴  Hirokazu Handa⁵ 

[1] Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, 657-8501, Nada, Kobe, Japan;Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, 657-8501, Nada, Kobe, Japan;Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, 606-8502, Kyoto, Japan;Hokkaido Research Organization, Kitami Agricultural Experiment Station, Yayoi 52, 099-1496, Kunneppucho, Tokorogun, Hokkaido, Japan;National Agriculture and Food Research Organization, Institute of Crop Science, Kannondai 2-1-2, 305-8518, Tsukuba, Japan;National Agriculture and Food Research Organization, Institute of Crop Science, Kannondai 2-1-2, 305-8518, Tsukuba, Japan;Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, 606-8522, Kyoto, Japan;

关键词: Hexaploid wheat;    Gamma-irradiated mutant;    Whole-genome sequencing;    Grain hardness;    Pre-harvest sprouting tolerance;   

DOI  :  10.1186/s12864-022-08344-8

来源: Springer

【 摘 要 】

BackgroundGamma-irradiated mutants of Triticum aestivum L., hexaploid wheat, provide novel and agriculturally important traits and are used as breeding materials. However, the identification of causative genomic regions of mutant phenotypes is challenging because of the large and complicated genome of hexaploid wheat. Recently, the combined use of high-quality reference genome sequences of common wheat and cost-effective resequencing technologies has made it possible to evaluate genome-wide polymorphisms, even in complex genomes.ResultsTo investigate whether the genome sequencing approach can effectively detect structural variations, such as deletions, frequently caused by gamma irradiation, we selected a grain-hardness mutant from the gamma-irradiated population of Japanese elite wheat cultivar “Kitahonami.” The Hardness (Ha) locus, including the puroindoline protein-encoding genes Pina-D1 and Pinb-D1 on the short arm of chromosome 5D, primarily regulates the grain hardness variation in common wheat. We performed short-read genome sequencing of wild-type and grain-hardness mutant plants, and subsequently aligned their short reads to the reference genome of the wheat cultivar “Chinese Spring.” Genome-wide comparisons of depth-of-coverage between wild-type and mutant strains detected ~ 130 Mbp deletion on the short arm of chromosome 5D in the mutant genome. Molecular markers for this deletion were applied to the progeny populations generated by a cross between the wild-type and the mutant. A large deletion in the region including the Ha locus was associated with the mutant phenotype, indicating that the genome sequencing is a powerful and efficient approach for detecting a deletion marker of a gamma-irradiated mutant phenotype. In addition, we investigated a pre-harvest sprouting tolerance mutant and identified a 67.8 Mbp deletion on chromosome 3B where Viviparous-B1 and GRAS family transcription factors are located. Co-dominant markers designed to detect the deletion-polymorphism confirmed the association with low germination rate, leading to pre-harvest sprouting tolerance.ConclusionsShort read-based genome sequencing of gamma-irradiated mutants facilitates the identification of large deletions linked to mutant phenotypes when combined with segregation analyses in progeny populations. This method allows effective application of mutants with agriculturally important traits in breeding using marker-assisted selection.

【 授权许可】

CC BY