Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens
Shilin Tian,
Xuming Zhou,
Tashi Phuntsok,
Ning Zhao,
Dejing Zhang,
Chunyou Ning,
Diyan Li,
Huabin Zhao
Affiliations
Shilin Tian
Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
Xuming Zhou
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
Tashi Phuntsok
Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
Ning Zhao
Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
Dejing Zhang
Novogene Bioinformatics Institute, Beijing 100015, China
Chunyou Ning
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
Diyan Li
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Corresponding author
Huabin Zhao
Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China; Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China; Corresponding author
Summary: The genetic footprints of adaptations to naturally occurring tropical stress along with domestication are poorly reported in chickens. Here, by conducting population genomic analyses of 67 chickens inhabiting distinct climates, we found signals of gene flow from Tibetan chickens to Sri Lankan and Saudi Arabian breeds and identified 12 positively selected genes that are likely involved in genetic adaptations to both tropical desert and tropical monsoon island climates. Notably, in tropical desert climate, advantageous alleles of TLR7 and ZC3HAV1, which could inhibit replication of viruses in cells, suggest immune adaptation to the defense against zoonotic diseases in chickens. Furthermore, comparative genomic analysis showed that four genes (OC90, PLA2G12B, GPR17 and TNFRSF11A) involved in arachidonic acid metabolism have undergone convergent adaptation to tropical desert climate between birds and mammals. Our study offers insights into the genetic mechanisms of adaptations to tropical climates in birds and other animals and provides practical value for breeding design and medical research on avian viruses.
