Local Climate Adaptation in Chinese Indigenous Pig Genomes

Area of Science:

• Genomics
• Animal Science
• Evolutionary Biology

Background:

• Local adaptation is crucial for livestock survival in diverse environments, but its genetic basis is often unclear.
• Chinese indigenous pigs possess rich genetic diversity, making them an ideal model for studying environmental adaptation.
• Understanding the genomic architecture of adaptation is vital for livestock conservation and sustainable breeding programs.

Purpose of the Study:

• To investigate the genomic basis of local adaptation in Chinese indigenous pigs.
• To identify genetic variants and pathways associated with environmental factors, especially precipitation.
• To inform climate-resilient breeding and conservation strategies for livestock.

Main Methods:

• Whole-genome resequencing of 578 individuals from 46 native pig breeds.
• Genome-wide genotype-environment association (GEA) analyses using latent factor mixed models (LFMMs).
• Redundancy analysis (RDA), gradient forest modeling, and functional annotation of significant SNPs.

Main Results:

• Identified 8644 SNPs associated with environmental factors, with 310 linked to precipitation in the wettest quarter (BIO16).
• BIO16 emerged as a significant environmental driver of genomic variation in pig populations.
• Functional analysis highlighted enrichment in regulatory elements and genes related to immune and metabolic pathways (lung, spleen, hypothalamus, intestine).
• The MS4A7 locus showed strong signals of adaptation related to precipitation.

Conclusions:

• Local adaptation in Chinese pigs is shaped by environmental factors, with precipitation playing a key role.
• Immune and metabolic pathways are implicated in the adaptation of pigs to varying climatic conditions.
• The findings provide insights into livestock adaptation and support the development of climate-resilient breeding and conservation strategies.