Integrative Genomic and Transcriptomic Insights into High-Altitude Adaptation in Changthangi Goats

The Changthangi goat, native to the high-altitude Ladakh Plateau in northern India, thrives in oxygen-deficient environments above 4,000 m. This study investigated the genetic basis of high-altitude adaptation in Changthangi goats by integrating comparative genomics and transcriptomics, using the tropical lowland Jamunapari goat as a comparative model. Whole-genome sequence data from 15 individuals per breed were analyzed using complementary selection sweep metrics, including nucleotide diversity, Tajima's D, iHS, CLR, XP-EHH, and FST. These analyses identified candidate genomic regions under strong selective pressure, encompassing genes involved in hypoxia sensing (HIF-1α, HIF-2α/EPAS1, EGLN1), angiogenesis (VEGFA, AGGF1, ZEB1), cardiovascular regulation (PRKCB, ESR1, RYR2), mitochondrial and energy metabolism (ACADSB, ACSS3, ACSL1), cellular stress tolerance (BCL2, ATM), and thermogenesis (UCP1, FGF21). Unlike previous caprine studies that primarily infer hypoxia adaptation from genomic signals alone, our study integrates cardiac transcriptomics to demonstrate that genomic selection in Changthangi goats is accompanied by coordinated transcriptional remodeling across interconnected physiological systems in a physiologically relevant tissue. Comparative cardiac transcriptomic profiling revealed concordant expression divergence in genes associated with oxygen transport, vascular remodeling, mitochondrial function, substrate utilization, redox balance, and genome maintenance. This integrative multi-omics framework provides a mechanistic view of caprine high-altitude adaptation and highlights the value of combining genomic selection analyses with tissue-specific transcriptional profiling to resolve complex adaptive traits.