Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

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Abstract

Background

Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these iconic chickens. This study aimed to uncover the genetic structure and the molecular underpinnings of the YFCs trademark coloration.

Results

The whole-genomes of 100 YFCs from 10 major traditional breeds and 10 Huaibei partridge chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed three geographically based clusters among the YFCs. Compared to other Chinese indigenous chicken genomes incorporated from previous studies, a closer genetic proximity within YFC breeds than between YFC breeds and other chicken populations is evident. Through genome-wide scans for selective sweeps, we identified RALY heterogeneous nuclear ribonucleoprotein ( RALY), leucine rich repeat containing G protein-coupled receptor 4 ( LGR4), solute carrier family 23 member 2 ( SLC23A2), and solute carrier family 2 member 14 ( SLC2A14), besides the classical beta-carotene dioxygenase 2 ( BCDO2), as major candidates pigment determining genes in the YFCs.

Conclusion

We provide the first comprehensive genomic data of the YFCs. Our analyses show phylogeographical patterns among the YFCs and potential candidate genes giving rise to the yellow color trait of the YFCs. This study lays the foundation for further research on the genome-phenotype cross-talks that define important poultry traits and for formulating genetic breeding and conservation strategies for the YFCs.

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Author and article information

Contributors

Yaping Zhang: zhangyp@mail.kiz.ac.cn

Xiquan Zhang: xqzhang@scau.edu.cn

Bingwang Du: dudu903@163.com

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 20 April 2020

Publication date PMC-release: 20 April 2020

Publication date Collection: 2020

Volume: 21

Electronic Location Identifier: 316

Affiliations

[1 ]GRID grid.443485.a, Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, , School of Life Science of Jiaying University, ; Meizhou, 514015 China

[2 ]ISNI 0000000119573309, GRID grid.9227.e, State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, , Chinese Academy of Sciences, ; Kunming, 650223 China

[3 ]Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204 China

[4 ]GRID grid.257160.7, College of Animal Science and Technology, , Hunan Agricultural University, ; Changsha, 410128 China

[5 ]ISNI 0000 0004 1760 4804, GRID grid.411389.6, College of Animal Science and Technology, , Anhui Agricultural University, ; Hefei, 230036 China

[6 ]ISNI 0000 0000 9546 5767, GRID grid.20561.30, College of Animal Sciences, , South China Agricultural University, ; Guangzhou, 510642 China

[7 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, , Chinese Academy of Agricultural Sciences (CAAS), ; Beijing, 100193 China

[8 ]GRID grid.419369.0, International Livestock Research Institute (ILRI), ; Nairobi, 30709-00100 Kenya

[9 ]ISNI 0000 0000 9146 7108, GRID grid.411943.a, Animal Biotechnology Group, Institute For Biotechnology Research, , Jomo Kenyatta University of Agriculture and Technology, ; Nairobi, 62000-00200 Kenya

[10 ]GRID grid.440773.3, State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, , Yunnan University, ; Kunming, 650091 China

[11 ]ISNI 0000000119573309, GRID grid.9227.e, Center for Excellence in Animal Evolution and Genetics, , Chinese Academy of Sciences, ; Kunming, 650223 China

Article

Publisher ID: 6736

DOI: 10.1186/s12864-020-6736-4

PMC ID: 7171827

PubMed ID: 32312230

SO-VID: 0763df42-d837-4577-8d7f-ab1c82928bc4

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.

History

Date received : 12 December 2019

Date accepted : 15 April 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100012245, Science and Technology Planning Project of Guangdong Province;

Award ID: 2016A030303068

Award Recipient : Xunhe Huang

Funded by: FundRef http://dx.doi.org/10.13039/501100003453, Natural Science Foundation of Guangdong Province;

Award ID: 2014A030307018

Award Recipient : Xunhe Huang

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: yellow,chicken,genome,bcdo2,breeding,color,genetic diversity

Data availability:

ScienceOpen disciplines: Genetics

Keywords: yellow, chicken, genome, bcdo2, breeding, color, genetic diversity

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