Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

Shourong Shi; Dan Shao; Lingyun Yang; Qiqi Liang; Wei Han; Qian Xue; Liang Qu; Li Leng; Yishu Li; Xiaogang Zhao; Ping Dong; Muhammed Walugembe; Boniface B Kayang; Amandus P Muhairwa; Huaijun Zhou; Haibing Tong

doi:10.1016/j.jare.2022.07.005

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

J Adv Res. 2023 May:47:13-25. doi: 10.1016/j.jare.2022.07.005. Epub 2022 Jul 27.

Authors

Shourong Shi¹, Dan Shao¹, Lingyun Yang², Qiqi Liang², Wei Han¹, Qian Xue¹, Liang Qu¹, Li Leng³, Yishu Li⁴, Xiaogang Zhao⁵, Ping Dong⁵, Muhammed Walugembe⁶, Boniface B Kayang⁷, Amandus P Muhairwa⁸, Huaijun Zhou⁹, Haibing Tong¹⁰

Affiliations

¹ Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China.
² Novogene Bioinformatics Institute, Beijing 10089, China.
³ College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, 150038, China.
⁴ Tropical Crop Germplasm Research Institute, Haikou, Hainan 571101, China.
⁵ Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan 626000, China.
⁶ Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA.
⁷ Department of Animal Science, University of Ghana, Legon, Accra 233, Ghana.
⁸ Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania.
⁹ Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA.
¹⁰ Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China. Electronic address: tonghb@163.com.

Abstract

Introduction: Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics.

Object: Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments.

Method: Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC).

Results: Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation.

Conclusion: Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.

Keywords: Chicken; Extreme environment; Genetic adaption; Whole-genome sequence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adaptation, Physiological / genetics
Animals
Chickens* / genetics
Gene Frequency
Genome* / genetics
Genotype
Humans