GWAS & Selection signatures

Genomic Regions Associated with Heterosis in Holstein-Jersey Crossbred Dairy Cattle

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Abstract

Holstein (HO) à— Jersey (JE) crossbreeding combines complementary breed strengths and mitigate inbreeding through increased heterozygosity. This study aimed to better understand the genetics behind hybrid vigor (heterosis) in HO à— JE crossbred dairy cattle. Supervised admixture ancestry estimates, together with runs of homozygosity (ROH) and runs of heterozygosity (ROHet), were used to quantify genome-wide inbreeding and retained heterozygosity. Genotypes were obtained for 5,660 HOà—JE crossbred males from the National Cooperator Database managed by the Council on Dairy Cattle Breeding, retaining animals with 62.5%) to evaluate ancestry-dependent patterns. ROH and ROHet segments were identified using detectRUNS package in R. Hotspots were defined using 1Mb genomic bins and mapped to ARS-UCD1.2 gene annotations. Principal component analysis was highly consistent with BBR-based classification (~98% concordance). Supervised admixture with pure breeds showed a continuous gradient of intermediate ancestry among crossbreds. Agreement between admixture and BBR was strong (r ~ 0.99), with typical differences of ~2-3% and a small systematic shift (BBR slightly higher Holstein and lower Jersey on average). ROH burden and FROH showed a clear pattern across ancestry. Crossbreds with 37.5-62.5% Jersey ancestry had the lowest ROH and FROH (highest heterozygosity; most F1-like), whereas animals with low or high Jersey ancestry had more ROH and higher FROH, indicating greater autozygosity. Hotspot analyses identified a shared, gene-dense ROHet island across all three Jersey-ancestry classes at Chr14:0-1 Mb, spanning 58 genes, including DGAT1 and additional genes with diverse roles including fertility and stress/immune signaling. Together, integrating breed composition provides an interpretable framework to monitor retained heterozygosity in HOà—JE crossbreds and prioritizes candidate genomic regions for downstream trait association analysis of heterosis.

Keywords: 2026

How to Cite:

Neupane, M., Ben Zaabza, H., Toghiani, S., Norman, H., Cole, J. & Van Tassell, C., (2026) “Genomic Regions Associated with Heterosis in Holstein-Jersey Crossbred Dairy Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2291548. doi: https://doi.org/10.31274/wcgalp.24306

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