Whole Genome Analyses Reveal Novel Genes Associated with Chicken
Adaptation to Tropical and Frigid Environments
Abstract
Investigating the genetic footprints of historical temperature selection
can get insights to local adaptation and potential influences of climate
change on long-term population dynamics. 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. 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). 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
SLC33A1 and 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 SNPs in these two genes appeared strongly associated with
tropical environment adaptation. In addition, the 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. Our findings partially
unravel how selection footprints from environmental temperature stress
can lead to advantageous genomic adaptions to tropical and frigid
environments in poultry and provides a valuable resource for selective
breeding of chickens and other domestic animals.