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Genomic predictions for milk yield of crossbred dairy cattle.

Y. Steyn




Genomic predictions for milk yield of crossbred dairy cattle.
Y. Steyn*1, D. Gonzalez-Pena2, N. Vukasinovic2, D. Lourenco1, I. Misztal1, S. DeNise2. 1University of Georgia Athens, GA, 2Zoetis Kalamazoo, MI.

The objective of this study was to predict genomic breeding values for milk yield of crossbred dairy cattle under different scenarios using single-step genomic BLUP (ssGBLUP). Genotypes of 89,558 Holstein, 40,769 Jersey and 22,373 crossbred animals were used, of which all Holstein, 9,313 Jersey and 1,667 crossbred animals had phenotypic records. Low density genotypes were imputed to 45k SNP markers. SNP effects were estimated from single-breed evaluations for Jersey (JE), Holstein (HO) and crossbreds (CROSS), and multi-breed evaluations including all Jersey and Holstein (JE_HO) or approximately equal proportions of Jersey, Holstein and crossbred animals (MIX). Direct genomic predictions (DGV) of the validation animals (358 crossbred animals with phenotypes excluded from evaluations) were calculated using the resulting SNP effects. Additionally, breed proportions (BP) of crossbred animals were applied to combine DGV estimated based on each pure breed. The predictivity of DGV was calculated as Pearson correlation between DGV and phenotypes of the validation animals adjusted for fixed effects in the model. Regression of adjusted phenotypes on DGV was used to assess the inflation of DGVs. The predictivity of DGV for CROSS, JE, HO, JE_HO and MIX scenario was 0.50, 0.50, 0.47, 0.50, and 0.46, respectively. Using BP was least successful, with a predictivity of 0.32. The inflation of the DGV for CROSS, JE, HO, JE_HO, MIX and BP scenarios were 1.17, 0.65, 0.55, 0.78, 1.00, and 0.85, respectively. Rather than using BP, the DGVs of crossbred animals should be predicted using ssGBLUP under a scenario that includes pure breed genotypes

Keywords: single-step GBLUP, indirect predictions, SNP effects.

Biography: I completed my masters in animal breeding and genetics at the University of Pretoria in South Africa focusing on residual feed intake in Bonsmara cattle. I worked for SA Stud Book for 5 years where I was involved in the national genetic evaluations of over 20 beef cattle, 3 dairy cattle, and over 10 sheep and goat breeds. We worked in collaboration with universities and breed associations to develop genomic selection for South African livestock. I am doing my PhD at the University of Georgia and mostly focused on multi-, across- and cross-breed evaluations.