Conservation & local programs

Runs of Homozygosity and Selection Signatures in Indigenous Cattle Populations of Ethiopia Using SNP Markers

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Abstract

Indigenous African cattle remain vital to food security, livelihoods, and cultural identity across the continent, particularly due to their unique adaptive traits enabling survival under heat stress, disease challenges, and low-input production systems. As climate change intensifies and demand for improved productivity increases, understanding the genomic basis of adaptation and diversity within these populations is essential for designing sustainable breeding and conservation programs. This study investigated population structure, genetic diversity, runs of homozygosity (ROH), and selection signatures in five Ethiopian indigenous cattle populations, Boran (n = 11), Arsi (n = 11), Horro (n = 6), Danakil (n = 15), and Ambo (n = 4) to characterize their genomic architecture and infer demographic history. A total of 47 animals were genotyped using the Illumina Bovine 50K SNP BeadChip, and quality control steps included minor allele frequency filtering (MAF ≤ 0.01) and linkage disequilibrium pruning using PLINK v1.9. Population structure was assessed through Principal Component Analysis and ADMIXTURE (K = 4), ROH were identified using a sliding-window approach, and selection signatures were detected using integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). Pairwise FST and identity-by-descent (IBD) analyses were further employed to quantify genetic differentiation and relatedness. Pairwise genetic differentiation (Fst) among Ethiopian cattle breeds ranged from 0.0007 to 0.0233. The lowest Fst was observed between Arsi and Horro (Fst = 0.0007), indicating minimal genetic differentiation. In contrast, the highest Fst value occurred between Boran and Ambo (Fst = 0.0233), representing the greatest genetic divergence among the breed pairs. A relatively high level of differentiation was also detected between Ambo and Danakil (Fst = 0.0174). Overall, most breed pairs showed low genetic differentiation (Fst . ADMIXTURE revealed complex ancestry patterns and historical admixture among breeds. ROH analyses indicated moderate levels of inbreeding across populations, reflecting both traditional management practices promoting broad genetic bases and possible recent bottlenecks; the distribution of ROH length classes provided insights into the timing of these events. The study underscores the importance of maintaining genetic diversity while enhancing adaptive capacity to ensure livestock resilience and food security under changing environmental and production conditions

Keywords: 2026

How to Cite:

Addisu, G., alemu, s., Edea, Z. & Ekine-Dzivenu, C., (2026) “Runs of Homozygosity and Selection Signatures in Indigenous Cattle Populations of Ethiopia Using SNP Markers”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286330. doi: https://doi.org/10.31274/wcgalp.23932

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