Conservation & local programs

Detection of Runs of Homozygosity and Heterozygosity-Rich Regions in Brahman Cattle

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Abstract

Intensive use of reproductive and genetic technologies can reduce genetic diversity and increase inbreeding. Runs of homozygosity (ROH) quantify genomic autozygosity, whereas heterozygosity-rich regions (HRR) may reflect balancing selection or adaptation and provide complementary insights into genetic diversity and population history. This study aimed to characterize genome-wide autozygosity and HRR in Brahman cattle and to investigate ROH and HRR islands for shared gene content. The dataset included 5,468 genotyped Brahman animals raised in Bolivia, with genomic data obtained from the ANCP database (Ribeirão Preto, São Paulo, Brazil) using the 53K Bovine SNP chip. Quality control was performed in PLINK v1.9 by removing non-autosomal markers, SNPs, and individuals with a missing call rate >0.05. No filtering for allele frequency or linkage disequilibrium was applied. ROH and HRR were identified using a sliding-window approach implemented in the detectRUNS package in R. ROH were defined using windows ≥20 SNPs and ≥1 Mb, whereas HRR were defined using ≥10 SNPs and ≥250 kb. ROH and HRR islands were derived from the top 0.1% of SNPs with the highest homozygosity or heterozygosity frequency and clustered using a 250-kb gap threshold. Islands were annotated for gene content and evaluated through over-representation analysis. ROH were detected in all animals, totaling 307,764 segments. The mean genomic inbreeding coefficient (FROH) was 0.062, indicating that, on average, 6.22% (~177.7 Mb) of the autosomal genome was autozygous. Partitioning FROH by ROH length classes revealed contributions from both short and long ROH segments, reflecting the combined effects of ancient and recent inbreeding. Individuals averaged 56.28 ± 12.55 ROH segments (range: 9-137), with a mean length of ~3.16 Mb. Short ROH (1-2 Mb) were most frequent (63.8%) but accounted for 27.8% of autozygosity, whereas ROH of 2-4 Mb, 4-8 Mb, 8-16 Mb, and >16 Mb contributed 15.5%, 18.1%, 18.5%, and 20.1% of the autozygous genome, respectively. Class-specific inbreeding coefficients were FROH₁-â‚‚Mb = 0.0173,FROHâ‚‚-â‚„Mb = 0.0096,FROHâ‚„-₈Mb = 0.0113,FROH₈-₁₆Mb = 0.0115, andFROH >₁₆Mb = 0.0125. Threshold-based estimates wereFROH >â‚‚Mb = 0.0449, FROH >â‚„Mb = 0.0353, FROH >₈Mb = 0.0240, andFROH >₁₆Mb = 0.0125, highlighting the strong influence of long ROH and the presence of recent inbreeding. HRR were also widespread, with individuals showing an average of 522 segments covering ~13.7% of the genome. Overall, we identified 100 ROH islands and 239 HRR islands harboring genes related to growth, muscle development, and heat adaptation, consistent with selection for beef production and environmental adaptation in Brahman cattle.

Keywords: 2026

How to Cite:

Amorim, S., Peripolli, E., Espigolan, R., Arias, M., Camaripano, L. & Baldi, F., (2026) “Detection of Runs of Homozygosity and Heterozygosity-Rich Regions in Brahman Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286829. doi: https://doi.org/10.31274/wcgalp.24137

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