Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study
Autor: | Jianlong Xu, Yajun Zhu, Xiaoqian Wang, Danying Xing, Xiuqin Zhao, Liu Chen, Xianjin Qiu, Pang Yunlong, Congcong Shen, Kai Chen, Dai Mingli, Rongwei Yang |
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Rok vydání: | 2019 |
Předmět: |
0106 biological sciences
0301 basic medicine Candidate gene Soil salinity Soil Science Genome-wide association study Single-nucleotide polymorphism Plant Science lcsh:Plant culture Biology 01 natural sciences 03 medical and health sciences Salt tolerance lcsh:SB1-1110 Quantitative trait locus/loci (QTL) Gene Genetics Genome-wide association study (GWAS) Haplotype food and beverages biology.organism_classification Phenotype 030104 developmental biology Seedling Original Article Rice Agronomy and Crop Science 010606 plant biology & botany |
Zdroj: | Rice Rice, Vol 12, Iss 1, Pp 1-13 (2019) |
ISSN: | 1939-8433 1939-8425 |
Popis: | 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. |
Databáze: | OpenAIRE |
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