Earth and Life Institute, Université Catholique de Louvain, 1348, Louvain la Neuve, Belgium.
Agronomy Faculty, Vietnam National University of Agriculture, Hanoi, Vietnam.
J Appl Genet. 2023 Dec;64(4):603-614. doi: 10.1007/s13353-023-00775-7. Epub 2023 Aug 9.
Salt threatens rice cultivation in many countries. Hence, breeding new varieties with high salt tolerance is important.A panel of 2,391 rice accessions from the 3 K Rice Genome Project was selected to evaluate salt tolerance via the standard evaluation score (SES) in hydroponics under 60 mM NaCl at the seedling stage. Three sub-population panels including 1,332, 628, and 386 accessions from the original 2,391 ones were constructed based on low relatedness revealed by a phylogenetic tree generated by Archaeopteryx Tree. A genome-wide association study (GWAS) was conducted on the entire and sub-population panels using SES data and a selection of 5, 10, 20, and 40% of SNPs selected from the original 1,011,601 SNPs by filtering minor allele frequency > 5% and missing rate < 5%. To perform GWAS, three methods implemented in three different software packages were utilized.Using the integration of GWAS programs, a total of four QTLs associated with SES scores were identified in different panels. Some QTLs co-located with previously detected QTL-related traits. qSES1.1 was detected in three panels, qSES1.3 and qSES2.1 in two panels, and qSES3.1 in one panel through GWAS by all three methods used and selected SNPs. These four QTLs were selected to detect candidate genes. Combining gene-based association study plus haplotype analysis in the entire population and the three sub-populations let us shortlist three candidate genes, viz. LOC_Os01g23640 and LOC_Os01g23680 for qSES1.1, and LOC_Os01g71240 for qSES1.3 region affecting salt tolerance. The identified QTLs and candidate genes provided useful materials and genetic information for future functional characterization and genetic improvement of salt tolerance in rice.
盐威胁着许多国家的水稻种植。因此，培育具有高耐盐性的新品种非常重要。本研究从 3K 水稻基因组计划中选择了 2391 份水稻种质资源，在水培条件下用 SES 方法，在幼苗期用 60mM NaCl 进行耐盐性评价。根据由 Archaeopteryx Tree 生成的系统发育树揭示的低相关性，从最初的 2391 个材料中构建了三个亚群panel，包括 1332、628 和 386 个材料。使用 SES 数据和从最初的 1011601 个 SNP 中选择的 5%、10%、20%和 40%的 SNP 子集，在整个panel 和亚群panel 上进行了全基因组关联分析（GWAS）。通过过滤最小等位基因频率>5%和缺失率<5%，选择了 5%、10%、20%和 40%的 SNP。为了进行 GWAS，使用了三个不同软件包中的三种方法。通过整合 GWAS 程序，在不同的panel 中总共鉴定到与 SES 评分相关的 4 个 QTL。一些 QTL 与之前检测到的与 QTL 相关的性状共定位。通过三种方法和选定的 SNP，在三个 panel 中检测到 qSES1.1，在两个 panel 中检测到 qSES1.3 和 qSES2.1，在一个 panel 中检测到 qSES3.1。选择这四个 QTL 来检测候选基因。在整个群体和三个亚群中，结合基于基因的关联研究和单倍型分析，我们将三个候选基因，即 LOC_Os01g23640 和 LOC_Os01g23680 定位到 qSES1.1 区域，LOC_Os01g71240 定位到 qSES1.3 区域，影响耐盐性。鉴定的 QTL 和候选基因为水稻耐盐性的未来功能特征和遗传改良提供了有用的材料和遗传信息。
