Abstract
Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (Os01g0269800, Os01g0731100, Os08g0136700, Os08g0137800, and Os08g0137900) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs.
Highlights
IntroductionRice cultivation based on transplanted seedlings sown on puddled soil is a process that requires a uniform and precise seeding rate
Rice (Oryza sativa L.) is one of the most important staple food crops grown worldwide.Rice cultivation based on transplanted seedlings sown on puddled soil is a process that requires a uniform and precise seeding rate
Direct seeding is an attractive method for reducing water use and labor costs in rice cultivation, because, generally, rice cultivation is based on transplanting to a puddled field but requires a large 3'untranslated region (UTR)
Summary
Rice cultivation based on transplanted seedlings sown on puddled soil is a process that requires a uniform and precise seeding rate. One of the other methods, direct seeding, involves sowing seeds directly on puddled or submerged soil [1]. The difference between the two rice cultivation methods is that the latter is a water efficient and labor-saving approach; direct seeding can reduce the cost of production by 50% [2,3]. In direct seeding the seeds are exposed on the surface of a field without the seedling process that depends on difference traits. Faster and uniform germination has been reported to affect plant growth and development; rice that is suitable for direct seeding should be applied with high germination ability, seedling vigor, fast root growth, early tillering ability, and lodging resistance [1,4,5]
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