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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doaj-48aae18398ba439fa4a3520d8eba0f1d2020-11-25T00:02:57ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-07-01910.3389/fgene.2018.00229358380Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken BreedsYangyang Yuan0Dezhi Peng1Dezhi Peng2Xiaorong Gu3Xiaorong Gu4Yanzhang Gong5Zheya Sheng6Xiaoxiang Hu7Xiaoxiang Hu8Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaState Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, ChinaNational Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, ChinaState Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, ChinaNational Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, ChinaState Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, ChinaNational Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, ChinaBody 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.https://www.frontiersin.org/article/10.3389/fgene.2018.00229/fullgenome-wide association studyhaplotype-based association studygenetic architecturebody weightpolygenic basisChinese indigenous chicken |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yangyang Yuan Dezhi Peng Dezhi Peng Xiaorong Gu Xiaorong Gu Yanzhang Gong Zheya Sheng Xiaoxiang Hu Xiaoxiang Hu |
spellingShingle |
Yangyang Yuan Dezhi Peng Dezhi Peng Xiaorong Gu Xiaorong Gu Yanzhang Gong Zheya Sheng Xiaoxiang Hu Xiaoxiang Hu Polygenic Basis and Variable Genetic Architectures Contribute to the Complex Nature of Body Weight —A Genome-Wide Study in Four Chinese Indigenous Chicken Breeds Frontiers in Genetics genome-wide association study haplotype-based association study genetic architecture body weight polygenic basis Chinese indigenous chicken |
author_facet |
Yangyang Yuan Dezhi Peng Dezhi Peng Xiaorong Gu Xiaorong Gu Yanzhang Gong Zheya Sheng Xiaoxiang Hu Xiaoxiang Hu |
author_sort |
Yangyang Yuan |
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_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_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_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 |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2018-07-01 |
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. |
topic |
genome-wide association study haplotype-based association study genetic architecture body weight polygenic basis Chinese indigenous chicken |
url |
https://www.frontiersin.org/article/10.3389/fgene.2018.00229/full |
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