Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers’ preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP mark...
| Autores principales: | , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2017
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| Acceso en línea: | https://hdl.handle.net/10568/164935 |
| _version_ | 1855537883070332928 |
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| author | Wang, Xiaoqian Pang, Yunlong Zhang, Jian Wu, Zhichao Chen, Kai Ali, Jauhar Ye, Guoyou Xu, Jianlong Li, Zhikang |
| author_browse | Ali, Jauhar Chen, Kai Li, Zhikang Pang, Yunlong Wang, Xiaoqian Wu, Zhichao Xu, Jianlong Ye, Guoyou Zhang, Jian |
| author_facet | Wang, Xiaoqian Pang, Yunlong Zhang, Jian Wu, Zhichao Chen, Kai Ali, Jauhar Ye, Guoyou Xu, Jianlong Li, Zhikang |
| author_sort | Wang, Xiaoqian |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice eating and cooking quality and protein content (PC) are important properties affecting consumers’ preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC. |
| format | Journal Article |
| id | CGSpace164935 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1649352024-12-19T14:13:28Z Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content Wang, Xiaoqian Pang, Yunlong Zhang, Jian Wu, Zhichao Chen, Kai Ali, Jauhar Ye, Guoyou Xu, Jianlong Li, Zhikang Rice eating and cooking quality and protein content (PC) are important properties affecting consumers’ preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC. 2017-12-08 2024-12-19T12:54:28Z 2024-12-19T12:54:28Z Journal Article https://hdl.handle.net/10568/164935 en Open Access Springer Wang, Xiaoqian; Pang, Yunlong; Zhang, Jian; Wu, Zhichao; Chen, Kai; Ali, Jauhar; Ye, Guoyou; Xu, Jianlong and Li, Zhikang. 2017. Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content. Sci Rep, Volume 7, no. 1 |
| spellingShingle | Wang, Xiaoqian Pang, Yunlong Zhang, Jian Wu, Zhichao Chen, Kai Ali, Jauhar Ye, Guoyou Xu, Jianlong Li, Zhikang Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title | Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title_full | Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title_fullStr | Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title_full_unstemmed | Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title_short | Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content |
| title_sort | genome wide and gene based association mapping for rice eating and cooking characteristics and protein content |
| url | https://hdl.handle.net/10568/164935 |
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