Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-dose Ultraviolet Radiation in High-altitude Environments

Tibetan chickens exhibit specific adaptations to high-altitude conditions compared with their lowland counterparts. To illustrate the genetic mechanisms of such adaptations in highland chickens, the genomes of four highland and four lowland chicken populations were resequenced. Our results showed that genes under positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune response, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of non-synonymous single nucleotide polymorphisms between highland and lowland populations was also analyzed by chi-square test. The results showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development, which were related to adaptations to hypoxia and intense radiation. RNA sequencing also revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Additionally, an evident admixture found in Tibetan chickens suggested a history of introgression from lowland gene pools. Overall, our data provided new insights into the unique adaptation of highland animals to extreme environments. Overall design: The genomes from eight chicken populations were resequenced by Illumina Hiseq 2000 to identify positively selected genes in highland populations and RNA-Seq of four chicken populations was also performed for differential expressed genes analysis. This series contains only the RNA-seq data.