Abstract
BackgroundThe hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. In this study, a representative sample consisting of 185 accessions was selected from Northeast China and analysed in three tested environments to determine the quantitative trait nucleotide (QTN) of HSW through a genome-wide association study (GWAS).ResultA total of 24,180 single nucleotide polymorphisms (SNPs) with minor allele frequencies greater than 0.2 and missing data less than 3% were utilized to estimate linkage disequilibrium (LD) levels in the tested association panel. Thirty-four association signals were identified as associated with HSW via GWAS. Among them, nineteen QTNs were novel, and another fifteen QTNs were overlapped or located near the genomic regions of known HSW QTL. A total of 237 genes, derived from 31 QTNs and located near peak SNPs from the three tested environments in 2015 and 2016, were considered candidate genes, were related to plant growth regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signalling, and the TCA cycle, some of which have been found to participate in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean.ConclusionsThe identified loci with beneficial alleles and candidate genes might be valuable for the molecular network and MAS of HSW.
Highlights
The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types
The aim of the present study is to identify quantitative trait loci (QTL) associated with HSW and to screen candidate genes located in peak single nucleotide polymorphisms (SNPs) regions
The samples from these six maturity groups were selected since the accessions from different maturity groups have special adaptability to the three tested sites of Northeast China (‘Harbin’, ‘Gongzhuling’ and ‘Shenyang’) with two degrees difference in latitude between each two sites, which could fully reflect the formation of HSW and accurately evaluate the effects of environment on HSW to effectively increase the accuracy of the phenotypic data and quantitative trait nucleotide (QTN)
Summary
The hundred seed weight (HSW) is one of the yield components of soybean [Glycine max (L.) Merrill] and is especially critical for various soybean food types. A representative sample consisting of 185 accessions was selected from Northeast China and analysed in three tested environments to determine the quantitative trait nucleotide (QTN) of HSW through a genome-wide association study (GWAS). A total of 237 genes, derived from 31 QTNs and located near peak SNPs from the three tested environments in 2015 and 2016, were considered candidate genes, were related to plant growth regulation, hormone metabolism, cell, RNA, protein metabolism, development, starch accumulation, secondary metabolism, signalling, and the TCA cycle, some of which have been found to participate in the regulation of HSW. A total of 106 SNPs from 16 candidate genes were significantly associated with HSW in soybean. As a typical quantitative trait, HSW is controlled by multiple genes with small or large genetic effects, especially additive effects [7, 8] and the heritability range is relatively high (44–94 %). The traditional selection method requires evaluation in multiple environments over several years and is expensive, time-consuming and labour-intensive
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