Genome-wide analysis reveals adaptation to high altitudes in Tibetan sheep

Abstract

Tibetan sheep have lived on the Tibetan Plateau for thousands of years; however, the process and consequences of adaptation to this extreme environment have not been elucidated for important livestock such as sheep. Here, seven sheep breeds, representing both highland and lowland breeds from different areas of China, were genotyped for a genome-wide collection of single-nucleotide polymorphisms (SNPs). The FST and XP-EHH approaches were used to identify regions harbouring local positive selection between these highland and lowland breeds, and 236 genes were identified. We detected selection events spanning genes involved in angiogenesis, energy production and erythropoiesis. In particular, several candidate genes were associated with high-altitude hypoxia, including EPAS1, CRYAA, LONP1, NF1, DPP4, SOD1, PPARG and SOCS2. EPAS1 plays a crucial role in hypoxia adaption; therefore, we investigated the exon sequences of EPAS1 and identified 12 mutations. Analysis of the relationship between blood-related phenotypes and EPAS1 genotypes in additional highland sheep revealed that a homozygous mutation at a relatively conserved site in the EPAS1 3' untranslated region was associated with increased mean corpuscular haemoglobin concentration and mean corpuscular volume. Taken together, our results provide evidence of the genetic diversity of highland sheep and indicate potential high-altitude hypoxia adaptation mechanisms, including the role of EPAS1 in adaptation.

Figure 1. Description of the location and genetic relationships of samples.

(A) Sampling and habitats of the seven Tibetan sheep breeds. The map was created using the R package ‘maptools’, version: 0.8–37, URL: http://r-forge.r-project.org/projects/maptools/. (B) Plots for the first (Component 1) and second (Component 2) dimensions revealed the clustering of all individuals. (C) Genome-wide admixtures inferred by STRUCTURE 2.3.4. The results from K = 2 are shown; (D) Neighbour-joining (NJ) phylogenetic tree for the seven breeds based on pairwise F_ST. Each population is represented by a different symbol and colour label: high-altitude breeds are indicated in red, and low-altitude breeds are indicated in blue. The abbreviations for the seven breeds are shown in Supplemental Table S1.

Figure 2. Genome-wide distribution of F_ST and XP-EHH values.

Red dots represent sites showing significant signals in both the F_ST and XP-EHH approaches; black dots represent sites showing significant signal in the F_ST approach only. The symbols for candidate genes for adaptation to high-altitude hypoxia in the map are shown in bold and italics.

Figure 3

Genotype–phenotype association with the (A) RBC, (B) MCV and (C) MCH parameters for the 11^th SNP in EPAS1 in the Tibetan breeds. *Indicates a significant difference between the genotypes; **Indicates an extremely significant difference between the genotypes.

Figure 4. Complexity of plausible pathways of positively selected genes in high-altitude adaptation in Tibetan sheep.

The symbols for candidate genes for adaptation to high-altitude in the map are shown in bold. Candidate loci marked with an asterisk (*) represent the hypoxia priority candidate genes. Candidate selected genes are associated with hypoxia, energy metabolism, angiogenesis, Ca²⁺ metabolism, generating cortisone, erythropoietin and iron homeostasis under high-altitude conditions.