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Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice

Author

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  • Bin Yang

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Jiali Zeng

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Shaona Chen

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Shengyu Li

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Longmei Wu

    (Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China)

  • Xiaorong Wan

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

Abstract

Seed germination is a key contributing factor to the yield of direct seeding cultivation in rice. Unraveling the genetic architecture underlying rice seed germination is pivotal for breeding elite direct-seeded rice varieties. However, only a limited number of genes regulating seed germination have been characterized in rice. In this study, we implemented a genome-wide association study (GWAS) to dissect the genetic structure of seed germination by using 131 Japonica rice accessions. We identified six stable loci ( qGR1.1 , qGR2.1 , qGR3.1 , qGR7.1 , qGR8.1 and qGR9 ) associated with seed germination in two consecutive years, all of which were co-localized with previously reported quantitative trait loci (QTLs). OsGA2ox5 , encoding a gibberellin 2-oxidase, was identified as the most plausible candidate gene of the major locus qGR7.1 . Knockout of OsGA2ox5 led to delayed seed germination and retarded seedling growth. A non-synonymous variant (Chr7-218,245) within the coding region of OsGA2ox5 might be closely associated with variation in seed germination among Japonica accessions. Low nucleotide diversity at the OsGA2ox5 locus in Japonica could be a result of selection during rice improvement. Taken together, our results provide an important foundation for elucidating the molecular mechanism underlying seed germination and genetic improvement of rice seed vigor in the future.

Suggested Citation

  • Bin Yang & Jiali Zeng & Shaona Chen & Shengyu Li & Longmei Wu & Xiaorong Wan, 2022. "Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice," Agriculture, MDPI, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:gam:jagris:v:13:y:2022:i:1:p:118-:d:1021843
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    References listed on IDEAS

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    1. Xuehui Huang & Nori Kurata & Xinghua Wei & Zi-Xuan Wang & Ahong Wang & Qiang Zhao & Yan Zhao & Kunyan Liu & Hengyun Lu & Wenjun Li & Yunli Guo & Yiqi Lu & Congcong Zhou & Danlin Fan & Qijun Weng & Chu, 2012. "A map of rice genome variation reveals the origin of cultivated rice," Nature, Nature, vol. 490(7421), pages 497-501, October.
    2. Shengyu Li & Jiali Zeng & Zhao Zheng & Qi Zhou & Shaona Chen & Yixiong Zheng & Xiaorong Wan & Bin Yang, 2022. "Comparative Transcriptome Analysis Reveals the Mechanisms Underlying Differential Seed Vigor in Two Contrasting Peanut Genotypes," Agriculture, MDPI, vol. 12(9), pages 1-15, September.
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    Keywords

    rice; seed germination; GWAS; loci;
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