Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice
Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subs...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1041081/full |
| _version_ | 1797952070711508992 |
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| author | Wenjing Yin Tianqi Lu Zhengai Chen Tao Lu Hanfei Ye Yijian Mao Yiting Luo Mei Lu Xudong Zhu Xi Yuan Yuchun Rao Yuexing Wang |
| author_facet | Wenjing Yin Tianqi Lu Zhengai Chen Tao Lu Hanfei Ye Yijian Mao Yiting Luo Mei Lu Xudong Zhu Xi Yuan Yuchun Rao Yuexing Wang |
| author_sort | Wenjing Yin |
| collection | DOAJ |
| description | Soil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subsp. indica cv. ‘HZ’) and a female variety of Nekken2 (Oryza sativa L. subsp. japonica cv. ‘Nekken2’) as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 (LOC_Os12g25200) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice. |
| first_indexed | 2024-04-10T22:41:42Z |
| format | Article |
| id | doaj.art-71316db55f01404496766dc251150729 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T22:41:42Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-71316db55f01404496766dc2511507292023-01-16T04:38:42ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011310.3389/fpls.2022.10410811041081Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in riceWenjing Yin0Tianqi Lu1Zhengai Chen2Tao Lu3Hanfei Ye4Yijian Mao5Yiting Luo6Mei Lu7Xudong Zhu8Xi Yuan9Yuchun Rao10Yuexing Wang11College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaCollege of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, ChinaState Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, ChinaSoil salinization has a serious influence on rice yield and quality. How to enhance salt tolerance in rice is a topical issue. In this study, 120 recombinant inbred line populations were generated through nonstop multi-generation selfing using a male indica rice variety Huazhan (Oryza sativa L. subsp. indica cv. ‘HZ’) and a female variety of Nekken2 (Oryza sativa L. subsp. japonica cv. ‘Nekken2’) as the parents. Germination under 80 mM NaCl conditions was measured and analyzed, and quantitative trait locus (QTL) mapping was completed using a genetic map. A total of 16 salt-tolerance QTL ranges were detected at bud stage in rice, which were situated on chromosomes 3, 4, 6, 8, 9, 10, 11, and 12. The maximum limit of detection was 4.69. Moreover, the qST12.3 was narrowed to a 192 kb region on chromosome 12 using map-based cloning strategy. Statistical analysis of the expression levels of these candidate genes under different NaCl concentrations by qRT-PCR revealed that qST12.3 (LOC_Os12g25200) was significantly down-regulated with increasing NaCl concentration, and the expression level of the chlorine-transporter-encoding gene LOC_Os12g25200 in HZ was significantly higher than that of Nekken2 under 0 mM NaCl. Sequencing analysis of LOC_Os12g25200 promoter region indicated that the gene expression difference between parents may be due to eight base differences in the promoter region. Through QTL mining and analysis, a plurality of candidate genes related to salt tolerance in rice was obtained, and the results showed that LOC_Os12g25200 might negatively regulate salt tolerance in rice. The results provide the basis for further screening and cultivation of salt-tolerant rice varieties and have laid the foundation for elucidating further molecular regulation mechanisms of salt tolerance in rice.https://www.frontiersin.org/articles/10.3389/fpls.2022.1041081/fullricegermination ratesalt stressQTL mappingrecombinant inbred line population |
| spellingShingle | Wenjing Yin Tianqi Lu Zhengai Chen Tao Lu Hanfei Ye Yijian Mao Yiting Luo Mei Lu Xudong Zhu Xi Yuan Yuchun Rao Yuexing Wang Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice Frontiers in Plant Science rice germination rate salt stress QTL mapping recombinant inbred line population |
| title | Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| title_full | Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| title_fullStr | Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| title_full_unstemmed | Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| title_short | Quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| title_sort | quantitative trait locus mapping and candidate gene analysis for salt tolerance at bud stage in rice |
| topic | rice germination rate salt stress QTL mapping recombinant inbred line population |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1041081/full |
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