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Impacts of nucleotide fixation during soybean domestication and improvement

BACKGROUND: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pre...

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Autores principales: Zhao, Shancen, Zheng, Fengya, He, Weiming, Wu, Haiyang, Pan, Shengkai, Lam, Hon-Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358728/
https://www.ncbi.nlm.nih.gov/pubmed/25849896
http://dx.doi.org/10.1186/s12870-015-0463-z
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author Zhao, Shancen
Zheng, Fengya
He, Weiming
Wu, Haiyang
Pan, Shengkai
Lam, Hon-Ming
author_facet Zhao, Shancen
Zheng, Fengya
He, Weiming
Wu, Haiyang
Pan, Shengkai
Lam, Hon-Ming
author_sort Zhao, Shancen
collection PubMed
description BACKGROUND: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time. RESULTS: Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases. CONCLUSIONS: Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0463-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-43587282015-03-14 Impacts of nucleotide fixation during soybean domestication and improvement Zhao, Shancen Zheng, Fengya He, Weiming Wu, Haiyang Pan, Shengkai Lam, Hon-Ming BMC Plant Biol Research Article BACKGROUND: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time. RESULTS: Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases. CONCLUSIONS: Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0463-z) contains supplementary material, which is available to authorized users. BioMed Central 2015-03-08 /pmc/articles/PMC4358728/ /pubmed/25849896 http://dx.doi.org/10.1186/s12870-015-0463-z Text en © Zhao et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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, Shancen
Zheng, Fengya
He, Weiming
Wu, Haiyang
Pan, Shengkai
Lam, Hon-Ming
Impacts of nucleotide fixation during soybean domestication and improvement
title Impacts of nucleotide fixation during soybean domestication and improvement
title_full Impacts of nucleotide fixation during soybean domestication and improvement
title_fullStr Impacts of nucleotide fixation during soybean domestication and improvement
title_full_unstemmed Impacts of nucleotide fixation during soybean domestication and improvement
title_short Impacts of nucleotide fixation during soybean domestication and improvement
title_sort impacts of nucleotide fixation during soybean domestication and improvement
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358728/
https://www.ncbi.nlm.nih.gov/pubmed/25849896
http://dx.doi.org/10.1186/s12870-015-0463-z
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