Genomic Insights Into Genetic Diversity and Population Structure of Pastoral ‘Belahi’ Cattle of North Himalayan (Shivalik) Foothills

Abstract

Pastoral cattle breeding sustains nomadic communities by conserving local and non-commercial but valuable genetic resources. The aim of this study was to understand the genetic structure and diversity of newly registered pastoral Belahi cattle using genome-wide SNP data (Illumina BovineSNP50 v3.0 Array). After quality control, nearly 47% of SNPs were removed due to low minor allele frequency (< 0.05), yet the retained markers indicated well-distributed genetic variation across the genome, demonstrating substantial genetic diversity. Observed and expected heterozygosity were relatively high and nearly equal, suggesting adequate genetic variation and genomic inbreeding estimates indicated low inbreeding in Belahi cattle, although F_ROH analysis of longer runs of homozygosity revealed signs of recent inbreeding. The recent effective population size suggested a moderate risk of losing genetic diversity, which warrants attention for conservation management. The pattern of linkage disequilibrium decay showed relatively strong genetic linkage over short genomic distances, gradually decreasing over longer distances, indicating moderate recombination. Genetic diversity in Belahi cattle has been preserved, likely due to weaker artificial selection and higher historical effective population sizes. This study revealed that Belahi cattle had no evidence of recent admixture with taurine breeds. The breed exhibits a distinct genetic identity, clustering closely with other indigenous zebu breeds yet standing apart as a unique population. The findings suggest that historical management under low selection intensity and maintenance of sizable effective population size have helped preserve genetic variation in Belahi cattle.