Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions
A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehe...
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Public Library of Science
2018
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| Acceso en línea: | https://hdl.handle.net/10568/164819 |
| _version_ | 1855515157719941120 |
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| author | Zhao, Yan Zhang, Hongliang Xu, Jianlong Jiang, Conghui Yin, Zhigang Xiong, Haiyan Xie, Jianyin Wang, Xueqiang Zhu, Xiaoyang Li, Yang Zhao, Weipeng Rashid, Muhammad Abdul Rehman Li, Jinjie Wang, Wensheng Fu, Binying Ye, Guoyou Guo, Yan Hu, Zhiqiang Li, Zhikang Li, Zichao |
| author_browse | Fu, Binying Guo, Yan Hu, Zhiqiang Jiang, Conghui Li, Jinjie Li, Yang Li, Zhikang Li, Zichao Rashid, Muhammad Abdul Rehman Wang, Wensheng Wang, Xueqiang Xie, Jianyin Xiong, Haiyan Xu, Jianlong Ye, Guoyou Yin, Zhigang Zhang, Hongliang Zhao, Weipeng Zhao, Yan Zhu, Xiaoyang |
| author_facet | Zhao, Yan Zhang, Hongliang Xu, Jianlong Jiang, Conghui Yin, Zhigang Xiong, Haiyan Xie, Jianyin Wang, Xueqiang Zhu, Xiaoyang Li, Yang Zhao, Weipeng Rashid, Muhammad Abdul Rehman Li, Jinjie Wang, Wensheng Fu, Binying Ye, Guoyou Guo, Yan Hu, Zhiqiang Li, Zhikang Li, Zichao |
| author_sort | Zhao, Yan |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions |
| format | Journal Article |
| id | CGSpace164819 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1648192024-12-19T14:11:52Z Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions Zhao, Yan Zhang, Hongliang Xu, Jianlong Jiang, Conghui Yin, Zhigang Xiong, Haiyan Xie, Jianyin Wang, Xueqiang Zhu, Xiaoyang Li, Yang Zhao, Weipeng Rashid, Muhammad Abdul Rehman Li, Jinjie Wang, Wensheng Fu, Binying Ye, Guoyou Guo, Yan Hu, Zhiqiang Li, Zhikang Li, Zichao aerobiosis alleles cloning domestication loci quantitative trait loci A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions 2018-08-10 2024-12-19T12:54:20Z 2024-12-19T12:54:20Z Journal Article https://hdl.handle.net/10568/164819 en Open Access Public Library of Science Zhao, Yan; Zhang, Hongliang; Xu, Jianlong; Jiang, Conghui; Yin, Zhigang; Xiong, Haiyan; Xie, Jianyin; Wang, Xueqiang; Zhu, Xiaoyang; Li, Yang; Zhao, Weipeng; Rashid, Muhammad Abdul Rehman; Li, Jinjie; Wang, Wensheng; Fu, Binying; Ye, Guoyou; Guo, Yan; Hu, Zhiqiang; Li, Zhikang and Li, Zichao. 2018. Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions. PLoS Genet, Volume 14 no. 8 p. e1007521 |
| spellingShingle | aerobiosis alleles cloning domestication loci quantitative trait loci Zhao, Yan Zhang, Hongliang Xu, Jianlong Jiang, Conghui Yin, Zhigang Xiong, Haiyan Xie, Jianyin Wang, Xueqiang Zhu, Xiaoyang Li, Yang Zhao, Weipeng Rashid, Muhammad Abdul Rehman Li, Jinjie Wang, Wensheng Fu, Binying Ye, Guoyou Guo, Yan Hu, Zhiqiang Li, Zhikang Li, Zichao Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title | Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title_full | Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title_fullStr | Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title_full_unstemmed | Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title_short | Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| title_sort | loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions |
| topic | aerobiosis alleles cloning domestication loci quantitative trait loci |
| url | https://hdl.handle.net/10568/164819 |
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