Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds
Xunhe Huang,
Newton O. Otecko,
Minsheng Peng,
Zhuoxian Weng,
Weina Li,
Jiebo Chen,
Ming Zhong,
Fusheng Zhong,
Sihua Jin,
Zhaoyu Geng,
Wei Luo,
Danlin He,
Cheng Ma,
Jianlin Han,
Sheila C. Ommeh,
Yaping Zhang,
Xiquan Zhang,
Bingwang Du
Affiliations
Xunhe Huang
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
Newton O. Otecko
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
Minsheng Peng
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
Zhuoxian Weng
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
Weina Li
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
Jiebo Chen
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
Ming Zhong
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
Fusheng Zhong
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
Sihua Jin
College of Animal Science and Technology, Anhui Agricultural University
Zhaoyu Geng
College of Animal Science and Technology, Anhui Agricultural University
Wei Luo
College of Animal Sciences, South China Agricultural University
Danlin He
College of Animal Sciences, South China Agricultural University
Cheng Ma
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
Jianlin Han
CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS)
Sheila C. Ommeh
Animal Biotechnology Group, Institute For Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology
Yaping Zhang
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
Xiquan Zhang
College of Animal Sciences, South China Agricultural University
Bingwang Du
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
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.
