Abstract
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.
Highlights
Rice is one of the most important food crops, feeding more than one-half of the world population
The Principal components (PC) analysis showed that PC1 could explain more than 90% genetic variation, suggesting the 621 accessions could be classified in two major subpopulations (Figure 1A and Figure S3)
The results showed that OsML2 was an important expressed gene in regulating mesocotyl elongation, and several non-synonymous SNPs were associated with mesocotyl length (ML)
Summary
Rice is one of the most important food crops, feeding more than one-half of the world population. Rice planting is currently carried out in two ways, namely transplanting and direct-seeding (Farooq et al, 2011). Transplanting is a traditional system based on transplanting of seedlings from seedbeds to paddy fields, and is used to ensure high seedling emergence and uniform plant density (Farooq et al, 2011; Wu et al, 2015). Direct-seeding is the major cultivation method in Europe and the United States due to mechanized farming practices, and savings in labor and time (Farooq et al, 2011). Dry direct-seeding is increasing rapidly in China, but variable planting depths associated with machine sowing cause agronomic problems that prevent the achievement of optimum plant populations (Farooq et al, 2006a,b).
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