Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice
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...
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MDPI AG
2022-12-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/13/1/118 |
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| author | Bin Yang Jiali Zeng Shaona Chen Shengyu Li Longmei Wu Xiaorong Wan |
| author_facet | Bin Yang Jiali Zeng Shaona Chen Shengyu Li Longmei Wu Xiaorong Wan |
| author_sort | Bin Yang |
| collection | DOAJ |
| description | 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 <i>Japonica</i> rice accessions. We identified six stable loci (<i>qGR1.1</i>, <i>qGR2.1</i>, <i>qGR3.1</i>, <i>qGR7.1</i>, <i>qGR8.1</i> and <i>qGR9</i>) associated with seed germination in two consecutive years, all of which were co-localized with previously reported quantitative trait loci (QTLs). <i>OsGA2ox5</i>, encoding a gibberellin 2-oxidase, was identified as the most plausible candidate gene of the major locus <i>qGR7.1</i>. Knockout of <i>OsGA2ox5</i> led to delayed seed germination and retarded seedling growth. A non-synonymous variant (Chr7-218,245) within the coding region of <i>OsGA2ox5</i> might be closely associated with variation in seed germination among <i>Japonica</i> accessions. Low nucleotide diversity at the <i>OsGA2ox5</i> locus in <i>Japonica</i> 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. |
| first_indexed | 2024-03-09T13:53:43Z |
| format | Article |
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| language | English |
| last_indexed | 2024-03-09T13:53:43Z |
| publishDate | 2022-12-01 |
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| series | Agriculture |
| spelling | doaj.art-06349621f70048ddb60e29ef7c4dbc2b2023-11-30T20:46:01ZengMDPI AGAgriculture2077-04722022-12-0113111810.3390/agriculture13010118Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> RiceBin Yang0Jiali Zeng1Shaona Chen2Shengyu Li3Longmei Wu4Xiaorong Wan5Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaGuangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaGuangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaGuangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaRice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, ChinaGuangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaSeed 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 <i>Japonica</i> rice accessions. We identified six stable loci (<i>qGR1.1</i>, <i>qGR2.1</i>, <i>qGR3.1</i>, <i>qGR7.1</i>, <i>qGR8.1</i> and <i>qGR9</i>) associated with seed germination in two consecutive years, all of which were co-localized with previously reported quantitative trait loci (QTLs). <i>OsGA2ox5</i>, encoding a gibberellin 2-oxidase, was identified as the most plausible candidate gene of the major locus <i>qGR7.1</i>. Knockout of <i>OsGA2ox5</i> led to delayed seed germination and retarded seedling growth. A non-synonymous variant (Chr7-218,245) within the coding region of <i>OsGA2ox5</i> might be closely associated with variation in seed germination among <i>Japonica</i> accessions. Low nucleotide diversity at the <i>OsGA2ox5</i> locus in <i>Japonica</i> 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.https://www.mdpi.com/2077-0472/13/1/118riceseed germinationGWASloci |
| spellingShingle | Bin Yang Jiali Zeng Shaona Chen Shengyu Li Longmei Wu Xiaorong Wan Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice Agriculture rice seed germination GWAS loci |
| title | Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice |
| title_full | Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice |
| title_fullStr | Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice |
| title_full_unstemmed | Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice |
| title_short | Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in <i>Japonica</i> Rice |
| title_sort | genome wide association study reveals the genetic basis of seed germination in i japonica i rice |
| topic | rice seed germination GWAS loci |
| url | https://www.mdpi.com/2077-0472/13/1/118 |
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