Pattern of Runs of Homozygosity and Selection Signatures in Nili Ravi Buffalo

The present study analyzed the genomic landscape of Nili Ravi buffalo using the Axiom 90K SNP chip to assess SNP density, Runs of Homozygosity (ROH), and genomic differentiation. SNP density analysis revealed substantial variation across chromosomes, with Chromosome 1 exhibiting the highest density (>50 SNPs per 1Mb window), while Chr7, Chr13, and Chr20 had lower densities. High-density SNP regions were identified as potential genomic hotspots under selection, whereas regions with sparse SNP coverage indicated gaps in genetic diversity. ROH analysis identified four ROH length categories, with medium-length ROH (2–4 Mb and 4–8 Mb) constituting 68.9% of total ROHs, indicating a moderate inbreeding history. Chromosome 5 showed the highest short ROH occurrences (1–2 Mb), while Chromosome 3 had the longest ROHs (>16 Mb). The highest ROH coverage was observed on Chromosomes 5 (10%), 3 (9.9%), and 19 (8.8%). Eight genomic regions with high ROH frequencies on chromosomes 5, 11, and 19 contained candidate genes related to adaptability, productivity, and disease resistance. Key genes identified included COL8A1, ACACA, SREBF1, AKT3, and WNT11, linked to milk production, fat metabolism, and fertility traits. Genomic differentiation analysis using FST values (mean = 0.682) between Nili Ravi and Kundi buffalo populations identified 24 genomic regions under selection, with Chromosome 11 harboring the highest-ranked SNP (FST = 0.740787) associated with ARPP19. Other key candidate genes included CSMD1, ROR1, DNAJC15, and FBXW7, involved in disease resistance, metabolism, and reproductive traits. These findings provide crucial insights for genetic selection programs aimed at improving economically significant traits in Nili Ravi buffalo.