BACKGROUND AND AIMS The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

中文翻译：

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在水稻叶鞘中寻找与除盐相关的 SNP 的 GWAS 方法

背景和目的 在叶鞘水平去除盐分的能力被认为是水稻耐盐性的主要机制之一。因此，了解叶鞘脱盐能力的遗传控制将有助于改进耐盐水稻品种的分子育种，加快未来品种的发展，以提高盐灾地区的生产力。我们报告了一项全基因组关联研究 (GWAS)，旨在发现与水稻叶鞘中除盐相关的单核苷酸多态性 (SNP)。方法 在这项研究中，使用 296 份水稻（Oryza sativa）多样性面板来鉴定脱盐相关性状，并使用 36 901 个 SNP 进行 GWAS。Na+和Cl-浓度的鞘：叶片比用于确定叶鞘中的盐去除能力。候选基因通过基因本体论和 RNA-seq 分析进一步缩小到那些推定功能可能与盐转运相关并在盐胁迫下上调的基因。主要结果 对于 Na+ 鞘：叶片比的关联信号，仅在 5 号染色体上的籼亚群中发现了显着的 SNP。在 GWAS 研究中发现的候选基因中，5 个基因上调，8 个基因下调盐胁迫下的叶鞘组织。结论 这些 GWAS 数据意味着籼稻品种组中的水稻品种是盐胁迫下水稻叶鞘中与 Na+ 去除相关的基因和等位基因的主要来源。