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

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...

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Autores principales: Zhao, Xue, Dong, Hairan, Chang, Hong, Zhao, Jingyun, Teng, Weili, Qiu, Lijuan, Li, Wenbin, Han, Yingpeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693149/
https://www.ncbi.nlm.nih.gov/pubmed/31412769
http://dx.doi.org/10.1186/s12864-019-6009-2
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author Zhao, Xue
Dong, Hairan
Chang, Hong
Zhao, Jingyun
Teng, Weili
Qiu, Lijuan
Li, Wenbin
Han, Yingpeng
author_facet Zhao, Xue
Dong, Hairan
Chang, Hong
Zhao, Jingyun
Teng, Weili
Qiu, Lijuan
Li, Wenbin
Han, Yingpeng
author_sort Zhao, Xue
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-6009-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-66931492019-08-16 Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill] Zhao, Xue Dong, Hairan Chang, Hong Zhao, Jingyun Teng, Weili Qiu, Lijuan Li, Wenbin Han, Yingpeng BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-6009-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-08-14 /pmc/articles/PMC6693149/ /pubmed/31412769 http://dx.doi.org/10.1186/s12864-019-6009-2 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Zhao, Xue
Dong, Hairan
Chang, Hong
Zhao, Jingyun
Teng, Weili
Qiu, Lijuan
Li, Wenbin
Han, Yingpeng
Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title_full Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title_fullStr Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title_full_unstemmed Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title_short Genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [Glycine max (L.) Merrill]
title_sort genome wide association mapping and candidate gene analysis for hundred seed weight in soybean [glycine max (l.) merrill]
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693149/
https://www.ncbi.nlm.nih.gov/pubmed/31412769
http://dx.doi.org/10.1186/s12864-019-6009-2
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