Table1.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，水稻的干式直接播种技术正迅速推广，然而，与机械播种相关的种植深度不一往往会导致幼苗出土率低下。对621个水稻品种的表型分析表明，胚芽鞘长度（ML）受到深层土壤覆盖的诱导，并在田间深播耐受性方面具有重要意义。在本研究中，我们采用三种类型的单核苷酸多态性（非同义SNP、非同义SNP以及启动子内的SNP以及从整个SNP集合中随机选取的300万个SNP）进行了全基因组关联分析（GWAS），并发现相较于随机选取SNP的GWAS，非同义SNP GWAS（使用非同义SNP进行的GWAS）能够缩短计算时间并消除其他位点的混杂效应。最终检测到13个QTL位点，并通过综合分析鉴定出两个具有新功能的主要效应基因，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的优良单倍型组合使得胚芽鞘长度增加可达4厘米，在土壤覆盖10厘米的条件下，田间出苗率高达85%，这代表着对干式直接播种的耐受性得到了显著提升。本研究揭示了胚芽鞘长度关键位点及其天然存在的等位基因，这些均可用于提高水稻对干式直接播种的耐受性。