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Emelin M, Qiu X, Fan F, Alamin M, Faruquee M, Hu H, Xu J, Yang J, Xu H, Ali J, Liu B, Shi Y, Li Z, Zhang L, Zheng T, Xu J. Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice. BMC Plant Biol 2024; 24:38. [PMID: 38191321 PMCID: PMC10775519 DOI: 10.1186/s12870-023-04707-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/26/2023] [Indexed: 01/10/2024]
Abstract
Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers' final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (composed of two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test the mapping effects of different methods by using MQ-GS correlation dissection as sample case; (3) to perform genetic and breeding simulation on pyramiding favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci on average for MQ-GS traits. Notably, 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful resources for rice molecular breeding.
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Affiliation(s)
- Mwenda Emelin
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianjin Qiu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, 210014, China
| | - Md Alamin
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhiuddin Faruquee
- International Rice Research Institute, Bangladesh Office, Dhaka, 1213, Bangladesh
| | - Hui Hu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Junying Xu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Nanjing, 210014, China
| | - Haiming Xu
- Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, 1301, Metro Manila, Philippines
| | - Bailong Liu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yumin Shi
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhikang Li
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Luyan Zhang
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tianqing Zheng
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research InstituteChinese Academy of Agricultural Sciences, Sanya, 572024, China.
| | - Jianlong Xu
- Institute of Crop Sciences/State Key Laboratory of Crop Gene Resources and Breeding/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research InstituteChinese Academy of Agricultural Sciences, Sanya, 572024, China.
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