Sustainability & efficiency

Genome-wide runs of homozygosity islands reveal genes linked with feed efficiency in South African Holstein cows

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Abstract

A genome-wide runs of homozygosity (ROH) scan was conducted to identify ROH islands, estimate genomic inbreeding, and detect selection signatures linked to feed efficiency in South African Holstein cows. The analysis was based on genotypic data of 592 Holstein cows, comprising 47,296 quality-filtered SNPs. Sampled animals were from ten herds participating in the South African National Milk Recording and Improvement Scheme. The ROH and genomic inbreeding coefficient (FROH) were determined using the "detectRUNS" package in R. Gene annotation of ROH islands was performed using Ensembl BioMart, and functional enrichment analysis was conducted using the DAVID Functional Annotation Tool. A total of 15,290 ROH were identified, with an average length of 7.04±5.01 Mb and 25.8±12.4 ROH per animal. The ROH landscape was dominated by ROH ranging from 4 to 8 Mb in length (45.8%). Chromosome-level ROH density ranged from 0.029 (BTA18) to 0.237 (BTA10), with high-density values also observed on BTA20, BTA4, and BTA7. A weak association with chromosome size (r=0.24) was observed, reflecting that ROH islands are largely determined by localized genomic regions under selection rather than overall chromosome size. Genomic inbreeding was moderate (FROH = 0.073±0.040), consistent with typical commercial Holstein populations shaped by historical selection and limited sire diversity. The top 1% SNPs-in-ROH clustered within a broad 31.5 to 69.0 Mb region on BTA10, containing several sub-islands of intense homozygosity. The strongest peak (51.6-60.4 Mb) occurred in 23.65% of the animals, representing the core selection sweep. Functional enrichment analysis indicated involvement of biological processes related to growth, cellular signalling, and metabolic regulation. The major sweep contained genes such as ADAM10, LIPC, AQP9, and CYP19A1, which are involved in lipid metabolism, cellular signalling, and endocrine regulation, while secondary sub-islands on BTA7 and BTA20 encompassed genes including NLRP3, COX7B, ABCA7, STK11, RICTOR, LIFR, and IL7R. Additional sub-islands harboured genes involved in mitochondrial function, immune response, and metabolic regulation. These signatures confirm a multi-gene architecture for feed efficiency, reflecting recent strong selection on energy metabolism in South African Holsteins. Therefore, the identified genes may be useful for improving feed efficiency through advanced breeding strategies in this population.

Keywords: 2026

How to Cite:

Banga, C., Lashmar, S., Madilindi, M., Scholtz, M. & Zishiri, O., (2026) “Genome-wide runs of homozygosity islands reveal genes linked with feed efficiency in South African Holstein cows”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286444. doi: https://doi.org/10.31274/wcgalp.24008

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