Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice
Abstract Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitat...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-01-01
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| Series: | Rice |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12284-022-00550-y |
| _version_ | 1798026434248179712 |
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| author | Jiongjiong Fan Hua Hua Zhaowei Luo Qi Zhang Mengjiao Chen Junyi Gong Xin Wei Zonghua Huang Xuehui Huang Qin Wang |
| author_facet | Jiongjiong Fan Hua Hua Zhaowei Luo Qi Zhang Mengjiao Chen Junyi Gong Xin Wei Zonghua Huang Xuehui Huang Qin Wang |
| author_sort | Jiongjiong Fan |
| collection | DOAJ |
| description | Abstract Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient ‘Huanghuazhan’ (HHZ) and the donor ‘Basmati Surkb 89–15’ (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes. |
| first_indexed | 2024-04-11T18:35:30Z |
| format | Article |
| id | doaj.art-6506e313f42d47ce9adc4b63b6dbb75d |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-11T18:35:30Z |
| publishDate | 2022-01-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-6506e313f42d47ce9adc4b63b6dbb75d2022-12-22T04:09:17ZengSpringerOpenRice1939-84251939-84332022-01-0115111110.1186/s12284-022-00550-yWhole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in RiceJiongjiong Fan0Hua Hua1Zhaowei Luo2Qi Zhang3Mengjiao Chen4Junyi Gong5Xin Wei6Zonghua Huang7Xuehui Huang8Qin Wang9Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityState Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural SciencesShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityShanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal UniversityAbstract Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient ‘Huanghuazhan’ (HHZ) and the donor ‘Basmati Surkb 89–15’ (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.https://doi.org/10.1186/s12284-022-00550-yRiceChromosome segment substitution lines (CSSLs)QTL mappingHeading dateRFT1 |
| spellingShingle | Jiongjiong Fan Hua Hua Zhaowei Luo Qi Zhang Mengjiao Chen Junyi Gong Xin Wei Zonghua Huang Xuehui Huang Qin Wang Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice Rice Rice Chromosome segment substitution lines (CSSLs) QTL mapping Heading date RFT1 |
| title | Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice |
| title_full | Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice |
| title_fullStr | Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice |
| title_full_unstemmed | Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice |
| title_short | Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice |
| title_sort | whole genome sequencing of 117 chromosome segment substitution lines for genetic analyses of complex traits in rice |
| topic | Rice Chromosome segment substitution lines (CSSLs) QTL mapping Heading date RFT1 |
| url | https://doi.org/10.1186/s12284-022-00550-y |
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