期刊
RICE
卷 12, 期 1, 页码 -出版社
SPRINGEROPEN
DOI: 10.1186/s12284-019-0349-z
关键词
Rice; Salt tolerance; Genome-wide association study (GWAS); Candidate gene; Quantitative trait locus; loci (QTL)
类别
资金
- National Key Technology Support Program [2015BAD02B01-2-1]
- National Natural Science Foundation of China [31471429]
- Fundamental Research Funds for Science, Technology and Innovation Commission of Shenzhen Municipality [JCYJ20160530191619099]
- Agricultural Science and Technology Innovation Program [CAAS-ZDXT201800]
- Cooperation and Innovation Mission [CAAS-ZDXT201800]
- Guangdong Provincial Science and Technology Project [2017B020201003]
Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms biological processes and molecular function with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.
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