Abstract
Background
The hundred seed weight (HSW) was one of soybean [Glycine max (L.) Merrill] yield components, and was also especially critical for various soybean food types. In this study, a representative sample consisted of 185 accessions, selected from Northeast China, was tested under six tested environments for determination of quantitative trait nucleotide (QTN) of HSW through genome-wide association study (GWAS).
Result
A total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequency more than 0.2 and missing data less than 3% were utilized to the estimate linkage disequilibrium (LD) level in the tested association panel. Thirty-four association signals were identified to be associated with HSW via GWAS. Among them, nineteen QTN were the novel and another fifteen QTN were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTN, located near peak SNP for six tested environments, were considered as candidate genes, such as plant growing regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signaling, and TCA, some of which have been found to participant in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean.
Conclusions
The identified loci with beneficial alleles and the candidate genes might be valuable for the molecular network and MAS of HSW.
Genome-wide association mapping of resistance to Phytophthora sojae in a soybean [Glycine max (L.) Merr.] germplasm panel from maturity groups IV and V