Table4_Discovery and Validation of Grain Shape Loci in U.S. Rice Germplasm Through Haplotype Characterization.XLSX

Rice grain shape is a major determinant of rice market value and the end-use. We mapped quantitative trait loci (QTL) for grain shape traits in a bi-parental recombinant inbred line population (Trenasse/Jupiter) and discovered two major grain length QTLs—qGL3.1 and qGL7.1. Previously, a major grain shape gene GS3 was reported in the qGL3.1 region and grain length gene GL7 was reported to be encompassing qGL7.1 locus. The re-sequencing SNP data on the International Rice Research Institute (IRRI) 3K Rice Genome Project (RGP) panel were obtained from the IRRI SNP-Seek database for both genes and haplotype diversity was characterized for each gene in this diverse panel. United States rice germplasm was not well represented in the IRRI 3K RGP database. Therefore, a minimum SNP set was identified for each gene that could differentiate all the characterized haplotypes. These haplotypes in the 3K RGP panel were screened across 323 elite U.S. genotypes using the minimum SNP set. The screening of haplotypes and phenotype association confirmed the role of GS3 under qGL3.1. However, screening of the GL7 haplotypes in the U.S. germplasm panel showed that GL7 did not play a role in qGL7.1, and in addition, GL7.1 did not segregate in the Trenasse/Jupiter RIL population. This concluded that qGL7.1 is a novel QTL discovered on chr7 for grain shape in the Trenasse/Jupiter RIL population. A high-throughput KASP-based SNP marker for each locus (GS3 and qGL7.1) was identified and validated in elite U.S. rice germplasm to be used in an applied rice breeding program.

稻谷粒形是影响稻米市场价值与终端用途的核心性状。本研究在双亲本重组自交系群体（Trenasse/Jupiter）中对粒形相关性状的数量性状位点（quantitative trait loci，QTL）进行了定位，鉴定到两个控制粒长的主效QTL：qGL3.1与qGL7.1。此前已有研究表明，qGL3.1区域内存在调控粒形的主效基因GS3，而qGL7.1位点曾被认为覆盖了粒长基因GL7。本研究从国际水稻研究所（IRRI）的SNP-Seek数据库获取了IRRI 3000水稻基因组计划（RGP）群体的重测序单核苷酸多态性（single nucleotide polymorphism，SNP）数据，并对该多样性群体中各基因的单倍型多样性进行了表征分析。但IRRI 3K RGP数据库对美国水稻种质资源的代表性不足，为此，本研究为每个基因筛选出一套最小SNP标记集，可区分所有已表征的单倍型。利用这套最小SNP标记集，我们对3K RGP群体中的上述单倍型在323份美国优良水稻种质材料中进行了筛选验证。单倍型筛选与表型关联分析证实，GS3正是qGL3.1的调控基因。但对美国种质群体中GL7单倍型的筛选结果显示，GL7并非qGL7.1的调控基因；此外，GL7.1在Trenasse/Jupiter重组自交系群体中并未发生遗传分离。综上，qGL7.1是本研究在Trenasse/Jupiter重组自交系群体中鉴定到的一个位于7号染色体上的全新粒形调控QTL。本研究为GS3和qGL7.1两个位点分别开发了高通量KASP-SNP标记，并在美国优良水稻种质中完成了验证，可应用于实用水稻育种项目。