Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct s...
| Autores principales: | , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Frontiers Media
2021
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164224 |
| _version_ | 1855534106152009728 |
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| author | Wang, Yamei Liu, Jindong Meng, Yun Liu, Hongyan Liu, Chang Ye, Guoyou |
| author_browse | Liu, Chang Liu, Hongyan Liu, Jindong Meng, Yun Wang, Yamei Ye, Guoyou |
| author_facet | Wang, Yamei Liu, Jindong Meng, Yun Liu, Hongyan Liu, Chang Ye, Guoyou |
| author_sort | Wang, Yamei |
| 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 direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding. |
| format | Journal Article |
| id | CGSpace164224 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1642242024-12-19T14:13:12Z Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis Wang, Yamei Liu, Jindong Meng, Yun Liu, Hongyan Liu, Chang Ye, Guoyou genetics medical sciences Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding. 2021-07-19 2024-12-19T12:53:37Z 2024-12-19T12:53:37Z Journal Article https://hdl.handle.net/10568/164224 en Open Access Frontiers Media Wang, Yamei; Liu, Jindong; Meng, Yun; Liu, Hongyan; Liu, Chang and Ye, Guoyou. 2021. Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis. Front. Genet., Volume 12 |
| spellingShingle | genetics medical sciences Wang, Yamei Liu, Jindong Meng, Yun Liu, Hongyan Liu, Chang Ye, Guoyou Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title | Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title_full | Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title_fullStr | Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title_full_unstemmed | Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title_short | Rapid identification of qtl for mesocotyl length in rice through combining QTL-seq and genome-wide association analysis |
| title_sort | rapid identification of qtl for mesocotyl length in rice through combining qtl seq and genome wide association analysis |
| topic | genetics medical sciences |
| url | https://hdl.handle.net/10568/164224 |
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