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.

中文翻译：

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通过全基因组关联研究鉴定水培和盐田条件下水稻植株的耐盐性和与产量相关的性状基因。

背景

土壤盐分是影响水稻生产的主要环境条件之一。识别在幼苗期，特别是在盐田条件下影响水稻耐盐性（ST）相关性状的遗传位点，是通过金字塔作用于不同发育阶段的ST基因来育种ST水稻的关键。

结果

在708份水稻中观察到较大的表型变异，当暴露于盐胁迫下，产量及其相关性状受到很大限制。在全基因组关联研究（GWAS）中，检测到2255个标记-性状关联信号用于所有测得的性状，并且重要的SNP分布在903个基因中。在这些基因中，有43个基因处理了相同的功能注释，并且基因本体将“生物过程”和“分子功能”与已知对水稻盐胁迫有响应的基因结合起来。进一步的单倍型分析检测到与目标性状显着相关的15个有前途的候选基因，包括5个已知基因和10个新基因。我们确定了七个带有四个基因的有利单倍型的材料，这些基因与在盐胁迫条件下表现良好的谷物产量显着相关。

结论

利用基因中的高密度SNP进行GWAS是鉴定水稻耐盐候选基因的有效方法。确定了五个已知基因（OsMYB6，OsGAMYB，OsHKT1; 4，OsCTR3和OsSUT1）和两个新近鉴定的基因（LOC_Os02g49700，LOC_Os03g28300）与盐胁迫下的谷物产量及其相关性状显着相关。这些有前途的候选人为验证潜在的ST相关基因提供了宝贵的资源，并将通过标记辅助选择促进水稻育种的耐盐性。