Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings
Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (<i>Gossypium hirsutum</i&g...
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2025-06-01
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| author | Xianxu Wei Siyu Yao Jiangnuo Di Jiaxin Guan Aohan Wang Jie Yang Luyao Zhang Yang Liu Mengyao Liang Zhihao Niu Xuan Zhang Jiarui Xue Mengxue Shen Lin Li Yao Su Zhengwen Sun |
| author_facet | Xianxu Wei Siyu Yao Jiangnuo Di Jiaxin Guan Aohan Wang Jie Yang Luyao Zhang Yang Liu Mengyao Liang Zhihao Niu Xuan Zhang Jiarui Xue Mengxue Shen Lin Li Yao Su Zhengwen Sun |
| author_sort | Xianxu Wei |
| collection | DOAJ |
| description | Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (<i>Gossypium hirsutum</i> L.) accessions genotyped with 2.97 million single-nucleotide polymorphisms (SNPs). Phenotypic analysis reveals substantial variation under LP stress, with LP-SDW showing the highest coefficient of variation (33.69%). The GWASs identified thousands of significant SNPs, including pleiotropic loci associated with multiple traits. Chromosomes A08, D09, and D12 harbored novel associated signals. Multi-locus models significantly enhanced detection sensitivity, identifying 123 SNPs undetected by single-locus approaches. Functional annotations prioritized six candidate genes near associated SNPs, including GhM_A08G1315 (remorin protein) and GhM_D06G1152 (carotenoid cleavage dioxygenase), whose LP-induced expression patterns were validated by qRT-PCR. These genes are implicated in membrane signaling, root architecture modulation, and hormone metabolism. Our findings provide novel genetic insights into LP tolerance and establish a foundation for breeding phosphorus-efficient varieties through marker-assisted selection in cotton. |
| format | Article |
| id | doaj-art-dfa3fa4795c8436d93bba5bf6c9e77ce |
| institution | Matheson Library |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-dfa3fa4795c8436d93bba5bf6c9e77ce2025-06-25T14:19:52ZengMDPI AGPlants2223-77472025-06-011412180310.3390/plants14121803Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton SeedlingsXianxu Wei0Siyu Yao1Jiangnuo Di2Jiaxin Guan3Aohan Wang4Jie Yang5Luyao Zhang6Yang Liu7Mengyao Liang8Zhihao Niu9Xuan Zhang10Jiarui Xue11Mengxue Shen12Lin Li13Yao Su14Zhengwen Sun15State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaState Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, ChinaPhosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (<i>Gossypium hirsutum</i> L.) accessions genotyped with 2.97 million single-nucleotide polymorphisms (SNPs). Phenotypic analysis reveals substantial variation under LP stress, with LP-SDW showing the highest coefficient of variation (33.69%). The GWASs identified thousands of significant SNPs, including pleiotropic loci associated with multiple traits. Chromosomes A08, D09, and D12 harbored novel associated signals. Multi-locus models significantly enhanced detection sensitivity, identifying 123 SNPs undetected by single-locus approaches. Functional annotations prioritized six candidate genes near associated SNPs, including GhM_A08G1315 (remorin protein) and GhM_D06G1152 (carotenoid cleavage dioxygenase), whose LP-induced expression patterns were validated by qRT-PCR. These genes are implicated in membrane signaling, root architecture modulation, and hormone metabolism. Our findings provide novel genetic insights into LP tolerance and establish a foundation for breeding phosphorus-efficient varieties through marker-assisted selection in cotton.https://www.mdpi.com/2223-7747/14/12/1803cottonlow phosphorusGWAScandidate genesmolecular breeding |
| spellingShingle | Xianxu Wei Siyu Yao Jiangnuo Di Jiaxin Guan Aohan Wang Jie Yang Luyao Zhang Yang Liu Mengyao Liang Zhihao Niu Xuan Zhang Jiarui Xue Mengxue Shen Lin Li Yao Su Zhengwen Sun Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings Plants cotton low phosphorus GWAS candidate genes molecular breeding |
| title | Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings |
| title_full | Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings |
| title_fullStr | Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings |
| title_full_unstemmed | Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings |
| title_short | Single- and Multi-Locus GWAS Unravels Novel Genomic Regions Related to Low-Phosphate Stress in Cotton Seedlings |
| title_sort | single and multi locus gwas unravels novel genomic regions related to low phosphate stress in cotton seedlings |
| topic | cotton low phosphorus GWAS candidate genes molecular breeding |
| url | https://www.mdpi.com/2223-7747/14/12/1803 |
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