Dataset Information

Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill].

ABSTRACT: BACKGROUND: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. 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). RESULT:A 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. CONCLUSIONS:The identified loci with beneficial alleles and candidate genes might be valuable for the molecular network and MAS of HSW.

SUBMITTER: Zhao X

PROVIDER: S-EPMC6693149 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill].

Zhao Xue X Dong Hairan H Chang Hong H Zhao Jingyun J Teng Weili W Qiu Lijuan L Li Wenbin W Han Yingpeng Y

BMC genomics 20190814 1

<h4>Background</h4>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. 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).<h4>Result</h4>A total of 24,180 single nucleotide polymorphisms (SNPs) ...[more]

PMID: 31412769

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Project description:BackgroundSeed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability.ResultsA total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in "QTL hotspot A" (Chr17) and "QTL hotspot B" (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in "QTL hotspot B" were found in both RIL populations and aging conditions, and also QTLs underlying "QTL hotspot A" are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders.ConclusionThis study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.

Project description:Seed-flooding stress is one of the major abiotic constraints severely affecting soybean yield and quality. Understanding the molecular mechanism and genetic basis underlying seed-flooding tolerance will be of greatly importance in soybean breeding. However, very limited information is available about the genetic basis of seed-flooding tolerance in soybean. The present study performed Genome-Wide Association Study (GWAS) to identify the quantitative trait nucleotides (QTNs) associated with three seed-flooding tolerance related traits, viz., germination rate (GR), normal seedling rate (NSR) and electric conductivity (EC), using a panel of 347 soybean lines and the genotypic data of 60,109 SNPs with MAF > 0.05. A total of 25 and 21 QTNs associated with all three traits were identified via mixed linear model (MLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) in three different environments (JP14, HY15, and Combined). Among these QTNs, three major QTNs, viz., QTN13, qNSR-10 and qEC-7-2, were identified through both methods MLM and mrMLM. Interestingly, QTN13 located on Chr.13 has been consistently identified to be associated with all three studied traits in both methods and multiple environments. Within the 1.0 Mb physical interval surrounding the QTN13, nine candidate genes were screened for their involvement in seed-flooding tolerance based on gene annotation information and available literature. Based on the qRT-PCR and sequence analysis, only one gene designated as GmSFT (Glyma.13g248000) displayed significantly higher expression level in all tolerant genotypes compared to sensitive ones under flooding treatment, as well as revealed nonsynonymous mutation in tolerant genotypes, leading to amino acid change in the protein. Additionally, subcellular localization showed that GmSFT was localized in the nucleus and cell membrane. Hence, GmSFT was considered as the most likely candidate gene for seed-flooding tolerance in soybean. In conclusion, the findings of the present study not only increase our knowledge of the genetic control of seed-flooding tolerance in soybean, but will also be of great utility in marker-assisted selection and gene cloning to elucidate the mechanisms of seed-flooding tolerance.

Dataset Information

Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill].

Publications

Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill].

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