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

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.