Dairy cattle

Breed-of-Origin Genetic Parameters and Genome-Wide Association Study for Milk Yield in Tanzanian Crossbred Dairy Cattle

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Abstract

Improving dairy productivity in East African smallholder systems requires genomic tools adapted to deeply admixed populations lacking pedigree records. This study estimated genetic parameters using breed-of-origin genomic prediction and conducted a genome-wide association study (GWAS) for milk yield in Tanzanian crossbred dairy cattle.A total of 2,601 Holstein-Friesian à— East African Zebu crossbreds, genotyped and imputed to 676K SNPs, were used. Exotic and indigenous ancestry proportions (mean exotic=0.76, range 0.25-0.85) were estimated using ADMIXTURE (K=2). Breed-of-origin genomic relationship matrices (G_ind, G_exo) were constructed by weighting centred genotypes by the square root of ancestry proportions, ensuring diagonal additivity with G_total (r=1.000).Genetic parameters were estimated on averaged test-day records per animal (mean 18.9, range 3-70) in sommer, with ward and season as fixed effects and farm as a random effect. Standard GBLUP estimated h²=0.145±0.047. Farm environment explained 38% of phenotypic variance - the dominant source of variation in these smallholder systems - yet genetic variance is real and estimable from SNPs alone without pedigree. BOA-GBLUP partitioned variance into indigenous (σ²_ind=0.000, boundary) and exotic (σ²_exo=0.808±0.266) components. The likelihood ratio test favoured standard GBLUP (LRT p=1.000, ns), consistent with limited power to resolve the two components when exotic ancestry strongly predominates. Larger and more ancestrally diverse cohorts are needed to fully exploit the BOA framework.For GWAS, phenotypes were pre-adjusted for fixed and farm effects using the same mixed model, then analysed using GCTA MLMA with a GRM controlling for ancestry and relatedness. The genomic inflation factor (λ=0.985) confirmed a well-calibrated scan with no inflation from population structure. No SNP reached the Bonferroni threshold (pThis study demonstrates that BOA-GBLUP is feasible in smallholder systems using imputed genotypes alone - no pedigree, phasing, or reference panels required. Standard GBLUP is the preferred model at current sample size; BOA will gain power as cohorts grow and ancestry spread widens. The GWAS provides the first genomic dissection of milk yield in East African crossbreds, with the casein gene region as a priority for validation in larger cohorts.

Keywords: 2026

How to Cite:

Alemu, s., Ojango, J., Gebreyohanes, G., Ekine, C. & Mrode, R., (2026) “Breed-of-Origin Genetic Parameters and Genome-Wide Association Study for Milk Yield in Tanzanian Crossbred Dairy Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283079. doi: https://doi.org/10.31274/wcgalp.23477

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