Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm
Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through m...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Public Library of Science
2015
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/165327 |
| _version_ | 1855537674033561600 |
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| author | Qiu, Xianjin Pang, Yunlong Yuan, Zhihua Xing, Danying Xu, Jianlong Dingkuhn, Michael Li, Zhikang Ye, Guoyou |
| author_browse | Dingkuhn, Michael Li, Zhikang Pang, Yunlong Qiu, Xianjin Xing, Danying Xu, Jianlong Ye, Guoyou Yuan, Zhihua |
| author_facet | Qiu, Xianjin Pang, Yunlong Yuan, Zhihua Xing, Danying Xu, Jianlong Dingkuhn, Michael Li, Zhikang Ye, Guoyou |
| author_sort | Qiu, Xianjin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding. |
| format | Journal Article |
| id | CGSpace165327 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2015 |
| publishDateRange | 2015 |
| publishDateSort | 2015 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1653272025-01-24T14:20:33Z Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm Qiu, Xianjin Pang, Yunlong Yuan, Zhihua Xing, Danying Xu, Jianlong Dingkuhn, Michael Li, Zhikang Ye, Guoyou breeding genomes grain quality indica rice marker-assisted selection milling quality quantitative trait loci Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding. 2015-12-29 2024-12-19T12:54:56Z 2024-12-19T12:54:56Z Journal Article https://hdl.handle.net/10568/165327 en Open Access Public Library of Science Qiu, Xianjin; Pang, Yunlong; Yuan, Zhihua; Xing, Danying; Xu, Jianlong; Dingkuhn, Michael; Li, Zhikang and Ye, Guoyou. 2015. Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm. PLoS ONE, Volume 10 no. 12 p. e0145577 |
| spellingShingle | breeding genomes grain quality indica rice marker-assisted selection milling quality quantitative trait loci Qiu, Xianjin Pang, Yunlong Yuan, Zhihua Xing, Danying Xu, Jianlong Dingkuhn, Michael Li, Zhikang Ye, Guoyou Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title | Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title_full | Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title_fullStr | Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title_full_unstemmed | Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title_short | Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| title_sort | genome wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm |
| topic | breeding genomes grain quality indica rice marker-assisted selection milling quality quantitative trait loci |
| url | https://hdl.handle.net/10568/165327 |
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