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

Abstract

Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments.

Keywords: adaptive selection; admixture; extreme environment; gene ontology terms; highland chicken.

Fig. 1.—

Geographic distribution of highland and lowland chicken populations used for sequencing analysis. T-LZ, 2,900 m altitude; T-LS, 3,650 m altitude; T-NC, 3,250 m altitude; Lh-W, 3,650 m altitude; WL-E, 50 m altitude; WL-D, 50 m altitude; CH, 500 m altitude; LD, 150 m altitude.

Fig. 2.—

Population variation analysis. (a) Phylogenetic tree and (b) principal component analysis of highland and lowland chicken populations. T-LZ, 2,900 m altitude; T-LS, 3,650 m altitude; T-NC, 3,250 m altitude; Lh-W, 3,650 m altitude; WL-E, 50 m altitude; WL-D, 50 m altitude; CH, 500 m altitude; LD, 50 m altitude.

Fig. 3.—

Population structure analysis of highland and lowland chicken populations. T-LZ, 2,900 m altitude; T-LS, 3,650 m altitude; T-NC, 3,250 m altitude; Lh-W, 3,650 m altitude; WL-E, 50 m altitude; WL-D, 50 m altitude; CH, 500 m altitude; LD, 150 m altitude.

Fig. 4.—

Analysis of positive gene selection in the chicken genome. (a) Distribution of heterozygosity (H_p) values in highland and lowland chicken populations for 40-kb windows. (b) Distribution of corresponding Z-transformed H_p values (ZH_p) for 40-kb windows. (c) The lowest end of ZH_p distribution in chromosomes 1–28. Horizontal dashed lines indicate the threshold at ZH_p = −6.