# Genomic Signatures Underlying Environmental Adaptation and Reproductive Traits in the Tibetan Pig

## TL;DR

This study identifies genetic factors in Tibetan pigs that help them survive in high-altitude environments and affect their reproductive traits.

## Contribution

A high-quality genome assembly and resequencing data reveal genes linked to Tibetan pig adaptation and reproduction.

## Key findings

- Genes like XIRP2 and CACNA1A are linked to cold and hypoxia tolerance in Tibetan pigs.
- Reproductive traits are associated with genes involved in immune response and energy metabolism.
- Tibetan pigs have fewer and shorter runs of homozygosity compared to other breeds.

## Abstract

The Tibetan pig is a unique breed adapted to the harsh high-altitude environment of the Qinghai–Tibet Plateau, exhibiting strong tolerance to cold, hypoxia, and coarse feed, but with relatively low reproductive performance. To uncover the genetic basis of these traits, we constructed a high-quality chromosome-level genome of a male Tibetan pig and analyzed whole-genome resequencing data from 124 sows. By comparing Tibetan pigs with lowland breeds, we identified key genetic regions and genes linked to environmental adaptation—such as those involved in heart function, fat metabolism, and blood vessel regulation. We also discovered genes associated with reproductive traits like litter size and piglet weight, which are related to immune response, energy metabolism, and growth. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and offer valuable markers for breeding programs aimed at improving Tibetan pig productivity while preserving their hardy characteristics.

Background: The Tibetan pig, a highland breed with exceptional adaptability to harsh environments (cold, hypoxia, coarse feed) but poor growth/reproductive traits, was studied to uncover genetic mechanisms and support breeding improvements. Methods: We conducted de novo genome assembly of a male Tibetan pig using stLFR sequencing, supplemented with ONT data, and compared the assembly to the Duroc pig genome (v11.1). Results: The assembled genome (2.25 Gb, contig N50 = 136.5 Mb, GC content = 41.74%, 94.16× coverage) showed 96.9% BUSCO completeness. Structural variant (SV) analysis identified 22,008 insertions and 27,639 deletions, with an SV genotyping accuracy of 0.9735. Selective sweep analysis highlighted adaptive genes: XIRP2 (cardiac function), KSR2/CACNA1A (fat metabolism), COL11A1 (cartilage), and ADORA2A (vascular regulation). Tibetan pigs exhibited the fewest and shortest runs of homozygosity (ROHs) among four breeds, with ROH-linked SNPs implicating lipid catabolism genes (LIPE, PNPLA2, MGLL, DGAT1). An SNP-based GWAS revealed reproductive trait associations: immune gene IL2RB, energy metabolism genes PRKAG2, ADGRA1, and PTPRN2, and growth genes SLIT2 and BMP6. SV analysis identified additional candidates: energy metabolism genes HAO2 and NRG4, growth genes MTUS2 and FGF12, and immune genes SCGB1A1 and C8A. Conclusions: This study provides a chromosome-level genome assembly of a male Tibetan pig (generated from stLFR and ONT data), and, through whole-genome resequencing of 124 Tibetan sows, identifies key genetic factors underlying Tibetan pigs’ environmental adaptability and reproductive limitations, enabling genomic strategies to enhance breeding efficiency while preserving adaptive traits.