GWAS & Selection signatures
Authors: Mahesh Neupane (USDA-ARS) , Hafedh Ben Zaabza (University of Georgia) , Sajjad Toghiani (USDA-ARS) , H.D. Norman (Technical Advisor) , John B. Cole (Council on Dairy Cattle Breeding) , Curt Van Tassell (USDA-ARS)
Holstein (HO) x 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 x 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 HOxJE 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 HOxJE 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). doi: https://doi.org/10.31274/wcgalp.24306