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Global Chicken Genome Project

During the past two decades, Kunming Institute of Zoology, Chinese Academy of Sciences (KIZ-CAS) has performed series of studies about chicken genetic diversity and domestication history (see Publications and Presentations). Now, KIZ-CAS is leading a two-phase international collaborative project to improve our current knowledge on chicken genomics.

In the phase one project, we have completed analyses 863 genomes of chickens and wild jungle fowls mostly sampled from East Eurasia, that is, the putative center of chicken domestication. The results revealed a remarkably complex picture of the early domestication and subsequent dispersal of chickens in this region (Wang et al. 2020. Cell Res).

In the phase two project, we will focus on the genomic changes of chickens during their global dispersal out of the East Eurasia. We generate additional genomes of different indigenous breeds/ecotypes as well as improved/admixed lines from Asia, Africa and Europe. The final dataset of around 2,000 genomes will be important resources for depth studies on chicken demographic trajectory, dating and wide geographic spread, as well as the genetic mechanisms underlying their breeding and response to natural/artificial selection for rapid adaptation to diversified environmental, climatic and management conditions.

Funding

National Natural Science Foundation of China: 31771405, 31621062, 31771415, 31801054, 91731304, and 31822048.

Chinese Academy of Sciences: Strategic Priority Research Program (XDA2004010301), Sino-Africa Joint Research Center (SAJC201611), President’s International Fellowship Initiative (2018FYB0003, 2016VBA050, and 2016VBC051), Youth Innovation Promotion Association, and the Animal Branch of the Germplasm Bank of Wild Species (the Large Research Infrastructure Funding).

Yunnan Provincial Science and Technology Department: Yunnan Provincial Key Programs of Yunnan Eco-friendly Food International Cooperation Research Center Project (2019ZG00908).

Contract us

Group: Molecular Evolution and Genome Diversity
Laboratory: State Key Laboratory of Genetic Resources and Evolution
Institute: Kunming Institute of Zoology, Chinese Academy of Sciences
Address: No. 21 Qingsong Road, Ciba, Kunming 650204, Yunnan Province, China
E-mail: chicken@mail.kiz.ac.cn

Chicken2K Team

Principal Investigators


Major Participants

Sheila Cecily Ommeh

Ali Esmailizadeh

Nalini Yasoda Hirimuthugoda

Xunhe Huang

Jomo Kenyatta University of Agriculture and Technology, Kenya

Shahid Bahonar University of Kerman, Iran

University of Ruhuna, Sri Lanka

Jiaying University, China

Chatmongkon Suwannapoom

Moch Syamsul Arifin Zein

University of Phayao, Thailand

Research Center for Biology, Indonesian Institute of Science, Indonesia


Team Members for Database

Min-Sheng Peng

Cheng Ma

Xuzhen Li

Kunming Institute of Zoology, Chinese Academy of Sciences

Kunming Institute of Zoology, Chinese Academy of Sciences

Yunnan Agricultural University

Publications and Presentations

Early Publications

Mitochondrial DNA Variation
Multiple maternal origins of chickens: out of the Asian jungles (Molecular Phylogenetics and Evolution, 2006). Reported in Science (2012, DOI: 10.1126/science.338.6110.1020)
Chicken domestication: an updated perspective based on mitochondrial genomes (Heredity, 2013).
Caveats about interpretation of ancient chicken mtDNAs from northern China (Proceedings of the National Academy of Sciences of the United States of America, 2015).
Was chicken domesticated in northern China? New evidence from mitochondrial genomes (Science Bulletin, 2018).

Population Genomics
Genomic analyses reveal potential independent adaptation to high altitude in Tibetan chickens (Molecular Biology and Evolution, 2015).
Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication (Cell Research, 2016)
Comparative population genomics reveals genetic basis underlying body size of domestic chickens (Journal of Molecular Cell Biology, 2016).
An evolutionary genomic perspective on the breeding of dwarf chickens (Molecular Biology and Evolution, 2017).
A parallel mechanism underlying frizzle in domestic chickens (Journal of Molecular Cell Biology, 2018).


Phase One Project

863 genomes reveal the origin and domestication of chicken (Cell Research, 2020, DOI: 10.1038/s41422-020-0349-y). Reported in Science (2020, DOI: 10.1126/science.368.6498.1411)


Phase Two Project

Initiative for Global Chicken Genome Project (GCGP). 37th International Society for Animal Genetics Conference, 2019, Lleida. (ISAG 2019 Abstract Book, OP59, 16-17)


Satellite Papers

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds (BMC Genomics, 2020).

Update

2020.03.25

Chicken2K is available now. V. 1.0
Breeds:169 breeds were included.
Analysis: Breed information, Variants Annotation & Density, Genetic affinities, Population structure, Admixture analysis, Runs of Homozygosity (ROH) , Nature selection signals and Phylogenetic of population were added for each population.
deBug: Fixed some display errors

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