Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice
Alkaline soil is characterized by high soluble salt content, elevated pH levels, and ionic imbalance, all of which collectively intensify the harmful effects of alkaline stress on plants. To gain molecular insights into alkaline tolerance (AT), we evaluated 13 AT-related traits in 508 diverse rice a...
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| Language: | English |
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Elsevier
2025-07-01
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| Series: | Rice Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672630825000459 |
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| author | Ratan Kumar Ganapati Kai Chen Xiuqin Zhao Tianqing Zheng Fan Zhang Laiyuan Zhai Jianlong Xu |
| author_facet | Ratan Kumar Ganapati Kai Chen Xiuqin Zhao Tianqing Zheng Fan Zhang Laiyuan Zhai Jianlong Xu |
| author_sort | Ratan Kumar Ganapati |
| collection | DOAJ |
| description | Alkaline soil is characterized by high soluble salt content, elevated pH levels, and ionic imbalance, all of which collectively intensify the harmful effects of alkaline stress on plants. To gain molecular insights into alkaline tolerance (AT), we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage. A total of 2 929 764, 2 059 114, and 1 365 868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies (GWAS) in the entire population as well as in the xian and geng subpopulations, respectively. Candidate genes and their superior haplotypes were further identified through gene-based association, haplotype analysis, and gene function annotation. In total, 99 QTLs were identified for AT by GWAS, and three genes (LOC_Os03g49050 for qSSD3.1, LOC_Os05g48760 for qSKC5, and LOC_Os12g01922 for qSNC12) were selected as the most promising candidate genes. Furthermore, we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits. This study identified crucial candidate genes and their favorable alleles for AT traits, laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection. |
| format | Article |
| id | doaj-art-caa2f74c4acf4a37bd238d5698907c5f |
| institution | Kabale University |
| issn | 1672-6308 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Rice Science |
| spelling | doaj-art-caa2f74c4acf4a37bd238d5698907c5f2025-08-20T05:06:05ZengElsevierRice Science1672-63082025-07-0132453754810.1016/j.rsci.2025.04.006Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in RiceRatan Kumar Ganapati0Kai Chen1Xiuqin Zhao2Tianqing Zheng3Fan Zhang4Laiyuan Zhai5Jianlong Xu6State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Bangladesh Sugarcrop Research Institute, Ishwardi, Pabna-6620, BangladeshShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs / Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinaState Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaState Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaState Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs / Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Corresponding author.State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs / Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; Corresponding author.Alkaline soil is characterized by high soluble salt content, elevated pH levels, and ionic imbalance, all of which collectively intensify the harmful effects of alkaline stress on plants. To gain molecular insights into alkaline tolerance (AT), we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage. A total of 2 929 764, 2 059 114, and 1 365 868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies (GWAS) in the entire population as well as in the xian and geng subpopulations, respectively. Candidate genes and their superior haplotypes were further identified through gene-based association, haplotype analysis, and gene function annotation. In total, 99 QTLs were identified for AT by GWAS, and three genes (LOC_Os03g49050 for qSSD3.1, LOC_Os05g48760 for qSKC5, and LOC_Os12g01922 for qSNC12) were selected as the most promising candidate genes. Furthermore, we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits. This study identified crucial candidate genes and their favorable alleles for AT traits, laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.http://www.sciencedirect.com/science/article/pii/S1672630825000459ricealkaline tolerancegenome-wide association studyhaplotype analysiscandidate gene |
| spellingShingle | Ratan Kumar Ganapati Kai Chen Xiuqin Zhao Tianqing Zheng Fan Zhang Laiyuan Zhai Jianlong Xu Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice Rice Science rice alkaline tolerance genome-wide association study haplotype analysis candidate gene |
| title | Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice |
| title_full | Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice |
| title_fullStr | Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice |
| title_full_unstemmed | Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice |
| title_short | Genome-Wide Association Study and Haplotype Analysis Jointly Identify New Candidate Genes for Alkaline Tolerance at Seedling Stage in Rice |
| title_sort | genome wide association study and haplotype analysis jointly identify new candidate genes for alkaline tolerance at seedling stage in rice |
| topic | rice alkaline tolerance genome-wide association study haplotype analysis candidate gene |
| url | http://www.sciencedirect.com/science/article/pii/S1672630825000459 |
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