# Genome-environment association analysis reveals climate-driven adaptation of chickens

## TL;DR

This study explores how chickens adapt to different climates by analyzing their genomes and environmental factors.

## Contribution

The study identifies 184 genes linked to climate adaptation in chickens, including immune-related genes and SNPs with geographic patterns.

## Key findings

- 184 genes were found to be potentially associated with climate adaptation in chickens.
- Five SNPs in four genes showed distinct geographic distribution patterns linked to climate factors.
- EHH analysis suggests strong selective pressures on these loci, indicating their importance in adaptation.

## Abstract

Domestic chickens are one of the most widely raised and distributed bird species, exhibiting remarkable environmental adaptability, which makes them valuable model organisms for investigating the genetic mechanisms underlying climate adaptation. This study aimed to enhance our understanding of adaptive mechanisms in chickens by jointly analyzing genomic variations and climatic variables related to temperature and precipitation. To this end, whole-genome sequencing data were collected from 199 indigenous domestic chickens raised under diverse environmental conditions worldwide, and three genome-environment association analyses were performed.

We identified 184 genes potentially associated with climate adaptation in chickens. Among these, the TSHR gene may play multiple roles in adaptation driven by different climatic factors. Immune-related genes also appear to contribute to climate adaptation in chickens. By calculating the allele frequencies of single nucleotide polymorphisms (SNPs) within candidate genes associated with temperature and precipitation adaptation, we identified five SNPs within four genes (ZNF536, ENSGALG00000049158, PAPPA, and EHMT1) that exhibited distinct geographic distribution patterns. Extended haplotype homozygosity (EHH) analysis of these SNPs revealed that haplotypes carrying the mutant allele exhibited slower decay in EHH compared to those carrying the wild-type allele. These results further indicate that the loci have experienced strong selective pressures, suggesting that the associated genes may play crucial roles in climate adaptation in chickens.

Overall, this study provides new insights into the genetic mechanisms underlying climate adaptation in domestic chickens.

The online version contains supplementary material available at 10.1186/s12711-025-00989-9.