Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage
Abstract Cold stress has a significantly negative effect on the growth, development, and yield of rice. However, the genetic basis for the differences in the cold tolerance of Xian/indica and Geng/japonica rice seedlings is still largely unknown. In this study, an RIL population was generated by cro...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2024-11-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-024-00749-1 |
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| author | Bian Wu Minghui Fu Jinghua Du Mengjing Wang Siyue Zhang Sanhe Li Junxiao Chen Wenjun Zha Changyan Li Kai Liu Huashan Xu Huiying Wang Shaojie Shi Yan Wu Peide Li Aiqing You Lei Zhou |
| author_facet | Bian Wu Minghui Fu Jinghua Du Mengjing Wang Siyue Zhang Sanhe Li Junxiao Chen Wenjun Zha Changyan Li Kai Liu Huashan Xu Huiying Wang Shaojie Shi Yan Wu Peide Li Aiqing You Lei Zhou |
| author_sort | Bian Wu |
| collection | DOAJ |
| description | Abstract Cold stress has a significantly negative effect on the growth, development, and yield of rice. However, the genetic basis for the differences in the cold tolerance of Xian/indica and Geng/japonica rice seedlings is still largely unknown. In this study, an RIL population was generated by crossing of the cold-tolerant japonica variety Nipponbare and the cold-sensitive indica variety WD16343 for BSA-seq analysis, and a major cold tolerance QTL qCTS11 was identified on chromosome 11. This locus was narrowed to the 584 kb region through fine mapping. Sequence alignment and expression analysis identified the cloned gene COLD11 and a novel cold-related gene OsCTS11. According to the reported functional variation of COLD11, Nipponbare (TCG + 3GCG)×2 presented more GCG repeats in the 1st exon than WD16343 (TCG + 3GCG), partially explaining the difference in cold tolerance between the parents. OsCTS11, encoding a stress enhanced protein based on phylogenetic analysis, was strongly induced by cold stress and located in the chloroplast and the nucleus. oscts11-mutant lines generated via CRISPR/Cas9 system improved the cold tolerance of rice seedlings. Our study not only reveals novel genetic loci associated with cold tolerance, but also provides potentially valuable gene resources for the cultivation of cold-tolerant rice. |
| format | Article |
| id | doaj-art-4bc8eaa33f934e35b138a1bf7c637d62 |
| institution | OA Journals |
| issn | 1939-8425 1939-8433 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj-art-4bc8eaa33f934e35b138a1bf7c637d622025-08-20T02:33:04ZengSpringerOpenRice1939-84251939-84332024-11-0117111410.1186/s12284-024-00749-1Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling StageBian Wu0Minghui Fu1Jinghua Du2Mengjing Wang3Siyue Zhang4Sanhe Li5Junxiao Chen6Wenjun Zha7Changyan Li8Kai Liu9Huashan Xu10Huiying Wang11Shaojie Shi12Yan Wu13Peide Li14Aiqing You15Lei Zhou16Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural SciencesAbstract Cold stress has a significantly negative effect on the growth, development, and yield of rice. However, the genetic basis for the differences in the cold tolerance of Xian/indica and Geng/japonica rice seedlings is still largely unknown. In this study, an RIL population was generated by crossing of the cold-tolerant japonica variety Nipponbare and the cold-sensitive indica variety WD16343 for BSA-seq analysis, and a major cold tolerance QTL qCTS11 was identified on chromosome 11. This locus was narrowed to the 584 kb region through fine mapping. Sequence alignment and expression analysis identified the cloned gene COLD11 and a novel cold-related gene OsCTS11. According to the reported functional variation of COLD11, Nipponbare (TCG + 3GCG)×2 presented more GCG repeats in the 1st exon than WD16343 (TCG + 3GCG), partially explaining the difference in cold tolerance between the parents. OsCTS11, encoding a stress enhanced protein based on phylogenetic analysis, was strongly induced by cold stress and located in the chloroplast and the nucleus. oscts11-mutant lines generated via CRISPR/Cas9 system improved the cold tolerance of rice seedlings. Our study not only reveals novel genetic loci associated with cold tolerance, but also provides potentially valuable gene resources for the cultivation of cold-tolerant rice.https://doi.org/10.1186/s12284-024-00749-1RiceCold StressBSA-seqCOLD11OsCTS11 |
| spellingShingle | Bian Wu Minghui Fu Jinghua Du Mengjing Wang Siyue Zhang Sanhe Li Junxiao Chen Wenjun Zha Changyan Li Kai Liu Huashan Xu Huiying Wang Shaojie Shi Yan Wu Peide Li Aiqing You Lei Zhou Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage Rice Rice Cold Stress BSA-seq COLD11 OsCTS11 |
| title | Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage |
| title_full | Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage |
| title_fullStr | Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage |
| title_full_unstemmed | Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage |
| title_short | Identification of the Cold-Related Genes COLD11 and OsCTS11 via BSA-seq and Fine Mapping at the Rice Seedling Stage |
| title_sort | identification of the cold related genes cold11 and oscts11 via bsa seq and fine mapping at the rice seedling stage |
| topic | Rice Cold Stress BSA-seq COLD11 OsCTS11 |
| url | https://doi.org/10.1186/s12284-024-00749-1 |
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