Genome‐wide association and selection studies reveal genomic insight into saline‐alkali tolerance in rice
Saline-alkali stress has detrimental effects on growth and development of rice (Oryza sativa L.). Domesticated rice cultivars with high saline-alkali tolerance (SAT) are essential for sustainable agriculture. To explore the genomic basis underlying SAT in rice, we integrate genome-wide association study (GWAS) with selective sweep analysis using a core population consisting of 234 cultivars grown in the saline and normal fields across three consecutive years and identify 70 genes associated with SAT with signals of selection and evolution between subpopulations of tolerance and sensitivity. We detected and subsequently characterized GATA19 trans-regulated SAT1/OsCYL4 that regulated SAT through reactive oxygen species (ROS) scavenging pathway. Our results provide a comprehensive insight into genome-wide natural variants and selection sweep underlying saline-alkali tolerance and pave avenues for SAT breeding through genome editing and genomic selection in rice.
Authors
- Wenchao Chi
- Gaoming Chen (ORCID: https://orcid.org/0000-0002-1010-6461)
- Zhaoyang Dai
- Chunming Wang (ORCID: https://orcid.org/0000-0003-3780-8065)
- Hui Zhang (ORCID: https://orcid.org/0000-0003-2613-2960)
- Jianmin Wan (ORCID: https://orcid.org/0000-0002-0017-8760)
- Chengsong Zhu
- Jing Li (ORCID: https://orcid.org/0000-0002-6945-9851)
- Yan Liu (ORCID: https://orcid.org/0000-0001-5683-8695)
- Xu Chen (ORCID: https://orcid.org/0000-0003-4303-8116)
- Jin Li (ORCID: https://orcid.org/0000-0002-0567-6910)
- Zhiguang Sun
- Dayong Xu (ORCID: https://orcid.org/0000-0002-9702-7028)
- Jingfang Li (ORCID: https://orcid.org/0000-0001-7884-5810)
- Chun-Yuan Wang (ORCID: https://orcid.org/0000-0003-0983-8240)
- Xianjun Sun
- Yunlu Tian
- Xinran Cheng (ORCID: https://orcid.org/0009-0009-4781-8778)
- Baoxiang Wang
Institutions
- Nanjing Agricultural University (CN)
- Liaoning Academy of Agricultural Sciences (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Institute of Crop Sciences (CN)
- The University of Texas Southwestern Medical Center (US)
Publication Details
- Journal
- The Plant Journal
- Published
- 2025-03-01
- DOI
- https://doi.org/10.1111/tpj.70056
- Citations
- 8
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 14.54
Funders
- National Natural Science Foundation of China
- China Postdoctoral Science Foundation
- Natural Science Foundation of Jiangsu Province
- National Key Research and Development Program of China