气候变化领域集成服务门户(CCPortal): Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

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DOI	10.1016/j.jare.2022.07.005
	Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments
	Shi, Shourong; Shao, Dan; Yang, Lingyun; Liang, Qiqi; Han, Wei; Xue, Qian; Qu, Liang; Leng, Li; Li, Yishu; Zhao, Xiaogang; Dong, Ping; Walugembe, Muhammed; Kayang, Boniface B.; Muhairwa, Amandus P.; Zhou, Huaijun; Tong, Haibing
发表日期	2023
ISSN	2090-1232
EISSN	2090-1224
起始页码	13
结束页码	25
卷号	47
英文摘要	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 domestica-tion track related to human activity with the most diversified varieties. Yet, few studies have demon-strated 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 includ-ing 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 anal-yses 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 fre-quency 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.(c) 2023 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
英文关键词	Chicken; Extreme environment; Whole-genome sequence; Genetic adaption
语种	英语
WOS研究方向	Multidisciplinary Sciences
WOS类目	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000987456200001
来源期刊	JOURNAL OF ADVANCED RESEARCH
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/281330
作者单位	Chinese Academy of Agricultural Sciences; Northeast Agricultural University - China; Iowa State University; Sokoine University of Agriculture; University of California System; University of California Davis
推荐引用方式 GB/T 7714	Shi, Shourong,Shao, Dan,Yang, Lingyun,et al. Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments[J],2023,47.
APA	Shi, Shourong.,Shao, Dan.,Yang, Lingyun.,Liang, Qiqi.,Han, Wei.,...&Tong, Haibing.(2023).Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments.JOURNAL OF ADVANCED RESEARCH,47.
MLA	Shi, Shourong,et al."Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments".JOURNAL OF ADVANCED RESEARCH 47(2023).