Abstract
BackgroundSoil 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.ResultsLarge 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.ConclusionsUsing 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.
Highlights
Soil salinity is one of the main environmental conditions that affects rice production
The goals of this study were to: 1) identify genes associated with rice salt tolerance (ST) at the seedling stage, 2) detect genes associated with yield and its related traits under saline field conditions, and 3) analyze promising gene candidates that are potentially involved in tolerance to salt stress and identify favorable haplotypes
The performance in Y16 was slightly worse than it was in Y17, suggesting that salt stress experienced in Y16 was more severe (Fig. 1 b)
Summary
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. Soil salinity is a common abiotic stress in many rice production areas that causes serious reductions in productivity. Due to current salinity levels and other soil-related problems, millions of hectares in the humid regions of South and Southeast Asia where rice is the main food crop are either left uncultivated, or rice is grown with extremely low yields. Increasing soil salinization is one of the main obstacles affecting rice production. Developing rice varieties with good salt tolerance (ST) and high yield is considered to be one of the most economic options to utilize salinized soil for rice production (Blumwald and Grover 2006)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
