Genetic evaluation and genotype by environment interaction using test-day models for Portuguese and Brazilian Holstein cattle

SILVA, Delvan Alves, D.Sc., Universidade Federal de Viçosa, July, 2019. Genetic evaluation and genotype by environment interaction using test-day models for Portuguese and Brazilian Holstein cattle. Adviser: Paulo Sávio Lopes. Co-advisers: Júlio Gil Vale Carvalheira, Fabyano Fonseca e Silva and Cláudio Napolis Costa. The validation of test-day (TD) models (autoregressive, AR and random regression, RR) in Brazilian Holstein cattle via genetic evaluation is of great importance since there is an interest to change traditional by TD models for multiple lactations. In addition, the investigation of the presence of genotype by environment interaction (G x E) between Brazil and Portugal populations may be important for breeding strategies as long as breeders would be allowed to invest or not in foreign genotypes. To do so, the traits used in this study were milk, fat and protein yields, and somatic cell score (SCS), using the first three lactations. The data was provided by Portuguese and Brazilian Holstein Cattle Breeders Associations and recorded between 1994 and 2016. First, TD milk, fat and protein yields, and SCS were used to study the effect of fixed (HTDF) vs. random (HTDR) contemporary groups (herd-test-date) with or without unknown parent groups (UPG) by using AR. The recovery of information performed on the HTDR models increased the lower reliabilities from 0.50 to 0.75, 0.54 to 0.66, 0.64 to 0.71 and 0.25 to 0.67 for milk, fat and protein yields, and for SCS, respectively (for bulls with 10 or more daughters). The differences in annual genetic gains between models (HTDR vs HTDF) were for sires (cows) of 30.66 (38.59) kg, 1.18 (1.35) kg, 1.26 (1.22) kg and -0.001 (-0.03) scores for milk, fat and protein yields and SCS, respectively. The contemporary groups as a random effect in the AR model seemed to be more relevant than just the UPG effect itself. However, the combination of both may provide higher annual genetic gains. In general, the HTDR model with UPG was the procedure that best fit and should be used for genetic evaluations and genetic trend analysis of longitudinal traits in Brazilian Holstein cattle. Subsequently, TD milk yield and SCS records were fitted to AR and RR models with the objective to compare their efficiency in the Brazilian genetic evaluations. Milk yield (SCS) heritabilities were similar between both models and ranged from 0.17 to 0.23 (0.11 to 0.17). The rank correlation between estimated breeding values (EBV) obtained from AR and RR models were 0.96 and 0.94 for milk yield and 0.97 and 0.95 for SCS, respectively, for bulls (with 10 or more daughters) and cows. Annual genetic gains for bulls (cows) obtained using AR model were 46.11 (49.50) kg for milk yield and -0.019 (-0.025) score for SCS. Using RR models this gain was 47.70 (55.56) kg for milk yield and 0.022 (-0.028) score for SCS. In general, the AR models were more efficient and, given the lower number of parameters to estimate and its suitability to fit data from small herds, these models are more parsimonious and should be used in genetic evaluations of Holstein cattle in Brazil. Finally, a two-step genetic evaluation was used to verify G x E. In step 1, we performed a within-country (Portugal and Brazil separately) genetic evaluation by using AR models. Similar heritability estimates for SCS were observed for both countries, whereas for milk yield the heritability were 0.31 for Portugal and 0.23 for Brazil. The rank correlation between EBV of common bulls were 0.75 for milk yield and 0.62 for SCS. In step 2, the precorrected phenotypes from Portugal and Brazil were considered two distinct traits in bi-trait reaction norm models. For milk yield, the genetic correlation between environmental gradient (HTD levels) within countries were higher than 0.92 for Portugal and 0.98 for Brazil. For SCS, the genetic correlation between HTD levels ranged from 0.64 to 0.99 for Portugal and from 0.79 to 0.99 for Brazil. The average of genetic correlation estimates between HTD levels from Portugal and HTD levels from Brazil was 0.73 for milk yield and 0.57 for SCS. In conclusion, our results indicated the presence of G x E in Holstein cattle in different production systems and climatic conditions. The low genetic correlation in the Portuguese population indicated the presence of G x E between extreme environmental gradient for SCS.