Integrated SNP and SV Analyses Reveal Genetic Mechanisms Underlying High-Altitude Adaptation in Goats

Area of Science:

• Genomics
• Evolutionary Biology
• Animal Science

Background:

• High-altitude environments present challenges like hypoxia and UV radiation for livestock.
• Previous goat altitude adaptation studies were limited by small sample sizes and low sequencing depth.
• Understanding adaptive mechanisms is vital for livestock resilience.

Purpose of the Study:

• To comprehensively analyze goat adaptation to diverse altitudes using whole-genome resequencing.
• To identify genetic variations, including SNPs and structural variations (SVs), associated with high-altitude adaptation.
• To explore gene flow, population structure, and SV-trait associations in goats across altitudinal gradients.

Main Methods:

• Whole-genome resequencing of 151 individuals from 17 goat breeds across three altitude gradients.
• Analysis of single nucleotide polymorphisms (SNPs) and structural variations (SVs).
• Selective sweep analyses (F_ST, θπ ratio, XP-CLR, XP-EHH, LFMM) to identify candidate genes.

Main Results:

• Characterized population relationships, gene flow, and the SV landscape.
• Identified candidate genes (e.g., ABCC4, RPS6, DSG4, LY9) linked to hypoxia response, oxidative stress, metabolism, and nervous system regulation.
• ABCC4 showed consistent selection signals in both SNP and SV analyses, indicating a significant role in adaptation.

Conclusions:

• Provided multi-level genomic evidence for goat adaptation to high-altitude stress.
• Highlighted the importance of both SNPs and SVs in understanding adaptive evolution.
• Offered insights into the genetic basis of livestock resilience in extreme environments.