Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle

Area of Science:

• Genomics
• Animal Genetics
• Evolutionary Biology

Background:

• Chinese native cattle breeds exhibit adaptive evolution driven by significant temperature variations across diverse climatic regions.
• Understanding the genetic basis of temperature adaptation is crucial for cattle survival in extreme environments.

Purpose of the Study:

• To investigate the genetic differentiation among Chinese cattle breeds adapted to different temperature environments.
• To identify specific genes, variants, and genomic regions associated with cold and hot temperature adaptability.

Main Methods:

• Whole-genome sequencing of 336 individuals from 21 cattle breeds.
• Analysis of single nucleotide polymorphism (SNP), insertion-deletion (InDel), and structural variant (SV) data.
• Comparative genomics to identify selective sweeps and allele frequency differences.

Main Results:

• Clear genetic differentiation was observed among cattle breeds from cold, warm, and hot regions.
• Numerous selective genomic regions, genes, and variants/SVs linked to temperature adaptability were identified.
• Key candidate genes (e.g., KLB, HSPA4, ECSCR, DNAJC18, SLC9A1) were implicated in cold/hot adaptation based on allele frequencies, biological functions, and interaction networks.

Conclusions:

• Integrated analysis of SNP, InDel, and SV data provides a comprehensive genetic framework for environmental adaptation.
• The study enhances understanding of the molecular mechanisms of temperature adaptation in cattle.
• Findings offer a molecular basis for developing new cattle breeds with improved climate resilience.