Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significant...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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MDPI
2019
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| Online Access: | https://hdl.handle.net/10568/164582 |
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| author | Liu, Hongyan Zhan, Junhui Li, Jiaolong Lu, Xiang Liu, Jindong Wang, Yamei Zhao, Quanzhi Ye, Guoyou |
| author_browse | Li, Jiaolong Liu, Hongyan Liu, Jindong Lu, Xiang Wang, Yamei Ye, Guoyou Zhan, Junhui Zhao, Quanzhi |
| author_facet | Liu, Hongyan Zhan, Junhui Li, Jiaolong Lu, Xiang Liu, Jindong Wang, Yamei Zhao, Quanzhi Ye, Guoyou |
| author_sort | Liu, Hongyan |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice. |
| format | Journal Article |
| id | CGSpace164582 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1645822024-12-22T05:44:55Z Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions Liu, Hongyan Zhan, Junhui Li, Jiaolong Lu, Xiang Liu, Jindong Wang, Yamei Zhao, Quanzhi Ye, Guoyou genetics genetics(clinical) Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice. 2019-12-31 2024-12-19T12:54:05Z 2024-12-19T12:54:05Z Journal Article https://hdl.handle.net/10568/164582 en Open Access MDPI Liu, Hongyan; Zhan, Junhui; Li, Jiaolong; Lu, Xiang; Liu, Jindong; Wang, Yamei; Zhao, Quanzhi and Ye, Guoyou. 2019. Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions. Genes, Volume 11 no. 1 p. 49 |
| spellingShingle | genetics genetics(clinical) Liu, Hongyan Zhan, Junhui Li, Jiaolong Lu, Xiang Liu, Jindong Wang, Yamei Zhao, Quanzhi Ye, Guoyou Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title | Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title_full | Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title_fullStr | Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title_full_unstemmed | Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title_short | Genome-wide Association Study (GWAS) for mesocotyl elongation in rice (Oryza sativa L.) under multiple culture conditions |
| title_sort | genome wide association study gwas for mesocotyl elongation in rice oryza sativa l under multiple culture conditions |
| topic | genetics genetics(clinical) |
| url | https://hdl.handle.net/10568/164582 |
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