10.3389/fpls.2018.00332.s018
Yan Zhao
Yan
Zhao
Weipeng Zhao
Weipeng
Zhao
Conghui Jiang
Conghui
Jiang
Xiaoning Wang
Xiaoning
Wang
Huaiyang Xiong
Huaiyang
Xiong
Elena G. Todorovska
Elena G.
Todorovska
Zhigang Yin
Zhigang
Yin
Yanfa Chen
Yanfa
Chen
Xin Wang
Xin
Wang
Jianyin Xie
Jianyin
Xie
Yinghua Pan
Yinghua
Pan
Muhammad A. R. Rashid
Muhammad A. R.
Rashid
Hongliang Zhang
Hongliang
Zhang
Jinjie Li
Jinjie
Li
Zichao Li
Zichao
Li
Table3.DOCX
Frontiers
2018
deep-sowing tolerance
genome-wide association study
mesocotyl length
non-synonymous SNP
Oryza sativa
2018-03-16 04:24:10
Dataset
https://frontiersin.figshare.com/articles/dataset/Table3_DOCX/5991457
<p>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.</p>