Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Abstract Chinese indigenous chickens (CICs) constitute world‐renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had...
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doaj-420e43b69ba143009aebdc04f580b5a92020-11-25T01:29:41ZengWileyEvolutionary Applications1752-45712019-03-0112361062110.1111/eva.12742Widespread introgression in Chinese indigenous chicken breeds from commercial broilerChunyuan Zhang0Deng Lin1Yuzhe Wang2Dezhi Peng3Huifang Li4Jing Fei5Kuanwei Chen6Ning Yang7Xiaoxiang Hu8Yiqiang Zhao9Ning Li10Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing ChinaBeijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing ChinaState Key Laboratory for Agrobiotechnology, College of Biological Sciences China Agricultural University Beijing ChinaState Key Laboratory for Agrobiotechnology, College of Biological Sciences China Agricultural University Beijing ChinaInstitute of Poultry Science Chinese Academy of Agricultural Sciences Yangzhou ChinaState Key Laboratory for Agrobiotechnology, College of Biological Sciences China Agricultural University Beijing ChinaInstitute of Poultry Science Chinese Academy of Agricultural Sciences Yangzhou ChinaNational Engineering Laboratory for Animal Breeding China Agricultural University Beijing ChinaState Key Laboratory for Agrobiotechnology, College of Biological Sciences China Agricultural University Beijing ChinaBeijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing ChinaState Key Laboratory for Agrobiotechnology, College of Biological Sciences China Agricultural University Beijing ChinaAbstract Chinese indigenous chickens (CICs) constitute world‐renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs.https://doi.org/10.1111/eva.12742Chinese indigenous chickenshaplotype similarityIntrogression |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chunyuan Zhang Deng Lin Yuzhe Wang Dezhi Peng Huifang Li Jing Fei Kuanwei Chen Ning Yang Xiaoxiang Hu Yiqiang Zhao Ning Li |
spellingShingle |
Chunyuan Zhang Deng Lin Yuzhe Wang Dezhi Peng Huifang Li Jing Fei Kuanwei Chen Ning Yang Xiaoxiang Hu Yiqiang Zhao Ning Li Widespread introgression in Chinese indigenous chicken breeds from commercial broiler Evolutionary Applications Chinese indigenous chickens haplotype similarity Introgression |
author_facet |
Chunyuan Zhang Deng Lin Yuzhe Wang Dezhi Peng Huifang Li Jing Fei Kuanwei Chen Ning Yang Xiaoxiang Hu Yiqiang Zhao Ning Li |
author_sort |
Chunyuan Zhang |
title |
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler |
title_short |
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler |
title_full |
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler |
title_fullStr |
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler |
title_full_unstemmed |
Widespread introgression in Chinese indigenous chicken breeds from commercial broiler |
title_sort |
widespread introgression in chinese indigenous chicken breeds from commercial broiler |
publisher |
Wiley |
series |
Evolutionary Applications |
issn |
1752-4571 |
publishDate |
2019-03-01 |
description |
Abstract Chinese indigenous chickens (CICs) constitute world‐renowned genetic resources due to their excellent traits, including early puberty, good meat quality and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on CICs. Using the chicken 60 K single nucleotide polymorphism chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all CICs. Approximately 15% of the genome, on average, of CICs was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to CICs at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of CICs. |
topic |
Chinese indigenous chickens haplotype similarity Introgression |
url |
https://doi.org/10.1111/eva.12742 |
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