Table10.DOCX

Dry direct-seeding of rice is rapidly increasing in China, but variable planting depth associated with machine sowing can lead to low seedling emergence rates. Phenotype analysis of 621 rice accessions showed that mesocotyl length (ML) was induced by deep soil covering and was important in deep-sowing tolerance in the field. Here, we performed and compared GWAS using three types of SNPs (non-synonymous SNP, non-synonymous SNPs and SNPs within promoters and 3 million randomly selected SNPs from the entire set of SNPs) and found that Non-Syn GWAS (GWAS using non-synonyomous SNP) decreased computation time and eliminated confounding by other loci relative to GWAS using randomly selected SNPs. Thirteen QTLs were finally detected, and two new major-effect genes, named OsML1 and OsML2, were identified by an integrated analysis. There were 2 and 7 non-synonymous SNPs in OsML1 and OsML2, respectively, from which 3 and 4 haplotypes were detected in cultivated rice. Combinations of superior haplotypes of OsML1 and OsML2 increased ML by up to 4 cm, representing high emergence rate (85%) in the field with 10 cm of soil cover. The studies provide key loci and naturally occurring alleles of ML that can be used in improving tolerance to dry direct-seeding.

在中国，水稻的直接干播技术正迅速推广，然而，由机械播种导致的种植深度不一可能会引起幼苗出土率较低的问题。对621个水稻品种的表型分析表明，中胚轴长度（ML）受深层土壤覆盖的影响，并在田间深播耐受性中起着至关重要的作用。本研究中，我们通过三种类型的单核苷酸多态性（非同义SNP、同义SNP以及启动子内的SNP和从整个SNP集中随机选取的300万个SNP）进行了全基因组关联分析（GWAS），并发现与非同义SNP的GWAS相比，使用随机选取的SNP进行的GWAS在降低计算时间的同时，消除了其他位点的混杂影响。最终检测到13个数量性状位点（QTL），通过综合分析，鉴定出两个具有新效力的主要基因，分别命名为OsML1和OsML2。在OsML1和OsML2中分别检测到2和7个非同义SNP，从栽培水稻中检测到3和4个单倍型。OsML1和OsML2优秀单倍型的组合使中胚轴长度增加了高达4厘米，代表在10厘米土壤覆盖下田间的高出土率（85%）。这些研究为提高水稻对直接干播耐受性的关键位点及天然存在的等位基因提供了重要参考。