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Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds

Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype–genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role...

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Autores principales: Yuan, Yangyang, Peng, Dezhi, Gu, Xiaorong, Gong, Yanzhang, Sheng, Zheya, Hu, Xiaoxiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6036123/
https://www.ncbi.nlm.nih.gov/pubmed/30013594
http://dx.doi.org/10.3389/fgene.2018.00229
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author Yuan, Yangyang
Peng, Dezhi
Gu, Xiaorong
Gong, Yanzhang
Sheng, Zheya
Hu, Xiaoxiang
author_facet Yuan, Yangyang
Peng, Dezhi
Gu, Xiaorong
Gong, Yanzhang
Sheng, Zheya
Hu, Xiaoxiang
author_sort Yuan, Yangyang
collection PubMed
description Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype–genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role of other factors in its genetic architecture, including their frequencies in the population and their interactions, have been largely overlooked. To comprehensively characterized the genetic architecture of BW, we performed a genome-wide association study (GWAS) both at the single-marker and haplotype level on birds from four indigenous Chinese chicken breeds (Chahua, Silkie, Langshan, and Beard), rather than studying crosses between two founder lines. Additionally, samples from two more breeds (Red Junglefowl and Recessive White) were included to better reflect variable genetic characteristics across populations. Six loci were mapped in this study, revealing the polygenic basis underlying BW. Moreover, by further examining the frequencies of the significantly associated haplotypes in each subpopulation and their effect sizes, most of the loci were found to affect BW in the Beard chicken breed alone. Two loci in GGA9 and GGA27, however, had a common effect on BW across subpopulations, showing that different underlying genetic mechanisms contribute to the phenotypic variability. These findings, particularly the variable genetic architectures found in different loci, improve our understanding of the overall genetic contributions to the large variability in BW among Chinese indigenous chicken breeds. These findings thus will have important implications for future chicken breeding.
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spelling pubmed-60361232018-07-16 Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds Yuan, Yangyang Peng, Dezhi Gu, Xiaorong Gong, Yanzhang Sheng, Zheya Hu, Xiaoxiang Front Genet Genetics Body weight (BW) is one of the most important economic traits for animal production and breeding, and it has been studied extensively for its phenotype–genotype associations. While mapping studies have mostly aimed at finding as many loci as possible that contributed to the variation in BW, the role of other factors in its genetic architecture, including their frequencies in the population and their interactions, have been largely overlooked. To comprehensively characterized the genetic architecture of BW, we performed a genome-wide association study (GWAS) both at the single-marker and haplotype level on birds from four indigenous Chinese chicken breeds (Chahua, Silkie, Langshan, and Beard), rather than studying crosses between two founder lines. Additionally, samples from two more breeds (Red Junglefowl and Recessive White) were included to better reflect variable genetic characteristics across populations. Six loci were mapped in this study, revealing the polygenic basis underlying BW. Moreover, by further examining the frequencies of the significantly associated haplotypes in each subpopulation and their effect sizes, most of the loci were found to affect BW in the Beard chicken breed alone. Two loci in GGA9 and GGA27, however, had a common effect on BW across subpopulations, showing that different underlying genetic mechanisms contribute to the phenotypic variability. These findings, particularly the variable genetic architectures found in different loci, improve our understanding of the overall genetic contributions to the large variability in BW among Chinese indigenous chicken breeds. These findings thus will have important implications for future chicken breeding. Frontiers Media S.A. 2018-07-02 /pmc/articles/PMC6036123/ /pubmed/30013594 http://dx.doi.org/10.3389/fgene.2018.00229 Text en Copyright © 2018 Yuan, Peng, Gu, Gong, Sheng and Hu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Yuan, Yangyang
Peng, Dezhi
Gu, Xiaorong
Gong, Yanzhang
Sheng, Zheya
Hu, Xiaoxiang
Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title_full Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title_fullStr Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title_full_unstemmed Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title_short Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds
title_sort polygenic basis and variable genetic architectures contribute to the complex nature of body weight —a genome-wide study in four chinese indigenous chicken breeds
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6036123/
https://www.ncbi.nlm.nih.gov/pubmed/30013594
http://dx.doi.org/10.3389/fgene.2018.00229
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