Microevolutionary mechanism of high‐altitude adaptation in Tibetan chicken populations from an elevation gradient

Abstract

As an indigenous breed, the Tibetan chicken is found in highland regions and shows physiological adaptations to high altitude; however, the genetic changes that determine these adaptations remain elusive. We assumed that the microevolution of the Tibetan chicken occurred from lowland to highland regions with a continuous elevation range. In this study, we analyzed the genome of 188 chickens from lowland areas to the high-altitude regions of the Tibetan plateau with four altitudinal levels. Phylogenetic analysis revealed that Tibetan chickens are significantly different from other altitude chicken populations. Reconstruction of the demographic history showed that the migration and admixture events of the Tibetan chicken occurred at different times. The genome of the Tibetan chicken was also used to analyze positive selection pressure that is associated with high-altitude adaptation, revealing the wellknown candidate gene that participates in oxygen binding (HBAD), as well as other novel potential genes (e.g., HRG and ANK2) that are related to blood coagulation and cardiovascular efficiency. Our study provides novel insights regarding the evolutionary history and microevolution mechanisms of the high-altitude adaptation in the Tibetan chicken.

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

“…Notably, the oxygen transporter activity and oxygen binding pathways were significantly and specifically enriched in SM. These pathways have been identified in animals such as Tibetan sheep [ 55 ] and Tibetan chickens [ 56 ] to explain their adaptation to hypoxia. This coincides with the actual situation of this duck population.…”

Analysis of genetic variants in protein‐coding genes of Aoluguya reindeer based on the whole‐genome data

“…Among these 10 489 SNPs, only eight variants were predicted to be deleterious (Table S6). Notably, the SNP predicted to be deleterious at chr17:14370957 is within the ANK2 gene, which is associated with animal fat deposition (Zhao et al., 2023), blood coagulation and cardiovascular efficiency (Zhong et al., 2022). It was observed only in the AOL population with a derived allele frequency of 0.97, which warrants further investigation.…”

Whole-genome variants dataset of 209 local chickens from China

“…Genomic analysis can reveal the demographic history of different chicken breeds and reconstruct gene flow among them, which contributes to a better understanding of the domestic history and potential mechanisms of some economic traits, such as breast muscle yield 17 , yellow skin 4,18 . The analysis of genome-wide variants in chickens distributed in different regions can be used to investigate genetic adaptation and diversity, especially adaptation to environmental conditions, such as altitude, temperature, and anoxic environments [19][20][21][22] . Moreover, selective sweep analysis based on single nucleotide polymorphisms (SNPs) is an effective method for identifying genetic markers and mechanisms underlying chicken production performance, reproduction, immunity, etc.…”

“…Moreover, selective sweep analysis based on single nucleotide polymorphisms (SNPs) is an effective method for identifying genetic markers and mechanisms underlying chicken production performance, reproduction, immunity, etc. This approach provides important insights into modern breeding systems [20][21][22][23][24][25] . In addition to SNPs and insertion-deletions (InDels), genome-wide sequencing has also been used to identify copy number variants (CNVs) 26 and structural variants (SVs) 27 , although the detection rate and efficiency of SV calling are relatively low compared to those of PacBio sequencing 28 .…”