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

Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central, [2000-

Genome-Wide Association Study*; Genes, Plant/*genetics ; Seeds/*growth & development ; Glycine max/*genetics ; Glycine max/*growth & development; Polymorphism, Single Nucleotide

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.

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Keywords: Candidate genes; Genome-wide association analysis; Hundred seed weight; Single nucleotide polymorphism

Date Created: 20190816 Date Completed: 20200103 Latest Revision: 20231213

20250114

PMC6693149

10.1186/s12864-019-6009-2

31412769