Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens

Xiurong Zhao; Jinxin Zhang; Huie Wang; Haiying Li; Changqing Qu; Junhui Wen; Xinye Zhang; Tao Zhu; Changsheng Nie; Xinghua Li; Gemingguli Muhatai; Liang Wang; XueZe Lv; Weifang Yang; Chunjiang Zhao; Haigang Bao; Junying Li; Bo Zhu; Guomin Cao; Wenjie Xiong; Zhonghua Ning; Lujiang Qu

doi:10.1016/j.ygeno.2022.110485

Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens

Genomics. 2022 Nov;114(6):110485. doi: 10.1016/j.ygeno.2022.110485. Epub 2022 Sep 17.

Authors

Xiurong Zhao¹, Jinxin Zhang², Huie Wang³, Haiying Li⁴, Changqing Qu⁵, Junhui Wen⁶, Xinye Zhang⁷, Tao Zhu⁸, Changsheng Nie⁹, Xinghua Li¹⁰, Gemingguli Muhatai¹¹, Liang Wang¹², XueZe Lv¹³, Weifang Yang¹⁴, Chunjiang Zhao¹⁵, Haigang Bao¹⁶, Junying Li¹⁷, Bo Zhu¹⁸, Guomin Cao¹⁹, Wenjie Xiong²⁰, Zhonghua Ning²¹, Lujiang Qu²²

Affiliations

¹ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: 1602978784@qq.com.
² State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: 1599436449@qq.com.
³ Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China. Electronic address: whedky@126.com.
⁴ College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China. Electronic address: lhy-3@163.com.
⁵ Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui 236037, China. Electronic address: qucq518@163.com.
⁶ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: wjh8545@qq.com.
⁷ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: xinye_leaf@163.com.
⁸ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: zhutao@cau.edu.cn.
⁹ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: changshengnie@cau.edu.cn.
¹⁰ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: 920230688@qq.com.
¹¹ Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China. Electronic address: gmgl-113@foxmail.com.
¹² Beijing Municipal General Station of Animal Science, Beijing 100107, China. Electronic address: wangliangcau@139.com.
¹³ Beijing Municipal General Station of Animal Science, Beijing 100107, China. Electronic address: lvxueze0310@163.com.
¹⁴ Beijing Municipal General Station of Animal Science, Beijing 100107, China. Electronic address: carspstp@126.com.
¹⁵ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: cjzhao@cau.edu.cn.
¹⁶ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: baohaigang@cau.edu.cn.
¹⁷ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: lijunying@cau.edu.cn.
¹⁸ Animal Health Supervision Institute of Zhuozhou, Hebei Province 072750, China. Electronic address: 13931368862@163.com.
¹⁹ Animal husbandry station of Fangchenggang, Guangxi Province 538001, China. Electronic address: caoguomin2003@163.com.
²⁰ Animal Disease Prevention and Control Center of Fangchenggang, Guangxi Province 538001, China. Electronic address: 269696329@qq.com.
²¹ State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: ningzhh@cau.edu.cn.
²² State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China. Electronic address: quluj@163.com.

PMID: 36126832
DOI: 10.1016/j.ygeno.2022.110485

Abstract

Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.

Keywords: Adaptation; Chicken; Cold tolerance; dnah5; ptgs2.

Publication types

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

MeSH terms

Animals
Chickens* / genetics
Genomics*