Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice
The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eig...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Springer
2020
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| Online Access: | https://hdl.handle.net/10568/164546 |
| _version_ | 1855521627552350208 |
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| author | Qu, Pingping Shi, Jinhui Chen, Tianxiao Chen, Kai Shen, Congcong Wang, Jiankang Zhao, Xiangqian Ye, Guoyou Xu, Jianlong Zhang, Luyan |
| author_browse | Chen, Kai Chen, Tianxiao Qu, Pingping Shen, Congcong Shi, Jinhui Wang, Jiankang Xu, Jianlong Ye, Guoyou Zhang, Luyan Zhao, Xiangqian |
| author_facet | Qu, Pingping Shi, Jinhui Chen, Tianxiao Chen, Kai Shen, Congcong Wang, Jiankang Zhao, Xiangqian Ye, Guoyou Xu, Jianlong Zhang, Luyan |
| author_sort | Qu, Pingping |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygousindicavarieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.ResultsWe constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.ConclusionsIn this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding. |
| format | Journal Article |
| id | CGSpace164546 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1645462025-04-23T18:55:58Z Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice Qu, Pingping Shi, Jinhui Chen, Tianxiao Chen, Kai Shen, Congcong Wang, Jiankang Zhao, Xiangqian Ye, Guoyou Xu, Jianlong Zhang, Luyan agronomy crop science plant science soil science rice maps plant breeding genetic linkage diversification recombinant dna The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygousindicavarieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.ResultsWe constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.ConclusionsIn this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding. 2020-12 2024-12-19T12:54:01Z 2024-12-19T12:54:01Z Journal Article https://hdl.handle.net/10568/164546 en Open Access Springer Qu, Pingping; Shi, Jinhui; Chen, Tianxiao; Chen, Kai; Shen, Congcong; Wang, Jiankang; Zhao, Xiangqian; Ye, Guoyou; Xu, Jianlong and Zhang, Luyan. 2020. Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice. Rice, Volume 13, no. 1 https://doi.org/10.1186/s12284-020-0373-z |
| spellingShingle | agronomy crop science plant science soil science rice maps plant breeding genetic linkage diversification recombinant dna Qu, Pingping Shi, Jinhui Chen, Tianxiao Chen, Kai Shen, Congcong Wang, Jiankang Zhao, Xiangqian Ye, Guoyou Xu, Jianlong Zhang, Luyan Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title | Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title_full | Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title_fullStr | Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title_full_unstemmed | Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title_short | Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice |
| title_sort | construction and integration of genetic linkage maps from three multi parent advanced generation inter cross populations in rice |
| topic | agronomy crop science plant science soil science rice maps plant breeding genetic linkage diversification recombinant dna |
| url | https://hdl.handle.net/10568/164546 |
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