Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis

• Published in: Plants (Basel) Vol. 12; no. 11; p. 2163
• Main Authors: Wang, Rui, Zhou, Zhenzhen, Xiong, Mengyuan, Du, Mingyu, Lin, Xingxing, Liu, Cuiping, Lu, Mingwei, Liu, Zhengbo, Chang, Yinping, Liu, Erbao
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 30.05.2023; MDPI
• Subjects: Abiotic stress; Abscisic acid; Analysis; Association analysis; Cloning; Comparative analysis; Damage; Environmental aspects; Gene mapping; Genes; Genetic aspects; Genetic modification; Genetic research; genome-wide association analysis; Genomes; Genomics; Germination; germination stage; Germplasm; Growth; Identification and classification; Marker-assisted selection; Mediation; Mineral industry; Mining; Mining industry; Osmosis; Physiological aspects; Plant breeding; Plant resistance; Proteins; Quantitative genetics; Quantitative trait loci; Rice; Salinity; Salinity tolerance; Salt; Salt stress (Botany); Salt tolerance; Seedlings; Single nucleotide polymorphisms; Single-nucleotide polymorphism; SNP loci; Sodium; Transcription factors; China; salt tolerance; rice; SNP loci; germination stage; genome-wide association analysis
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12112163

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline-alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR ( ) and SLR ( ), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: , and . At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.