Comparing methodologies to estimate fixed genetic effects and to predict genetic values for an Angus × Nellore cattle population.

The study assesses the need for and effectiveness of using ridge regression when estimating regression coefficients of covariates representing genetic effects due to breed proportion in a crossbreed genetic evaluation. It also compares 2 ways of selecting the ridge parameters. A large crossbred Angus × Nellore population with 294,045 records for weaning gain and 148,443 records for postweaning gain was used. Phenotypic visual scores varying from 1 to 5 for weaning and postweaning conformation, weaning and postweaning precocity, weaning and postweaning muscling, and scrotal circumference were analyzed. Three models were used to assess the need for ridge regression, having 4, 6, and 8 genetic covariates. All 3 models included the fixed contemporary group effect and random animal, maternal, and permanent environment effects. Model AH included fixed direct and maternal breed additive and the direct and maternal heterosis covariates, model AHE also included direct and maternal epistatic loss covariates, and model AHEC further included direct and maternal complementarity effects. The normal approach is to include these covariates as fixed effects in the model. However, being all derived from breed proportions, they are highly collinear and, consequently, may be poorly estimated. Ridge regression has been proposed as a method of reducing the collinearity. We found that collinearity was not a problem for models AH and AHE. We found a high variance inflation factor, >20, associated with some maternal covariates in the AHEC model reflecting instability of the regression coefficients and that this instability was well addressed by using ridge regression using a ridge parameter calculated from the variance inflation factor.

Origins and genetic diversity of British cattle breeds in Brazil assessed by pedigree analyses.

Pedigree information available for Angus (ANG), Devon (DEV), Hereford (HER), and Shorthorn (SHO) cattle in Brazil was analyzed to appraise the genetic diversity and population structure of these breeds. Pedigree records collected from the beginning of the 20th century until 2010 were used in the analyses. Over time, the number of herdbook registrations declined in HER after a peak in the 1970s, remained low in DEV and SHO, and increased steadily in ANG since the 1990s, such that it the latter is now the leading British cattle breed in Brazil. The average number of offspring registered per sire ranged from about 12 (SHO) to 20 (DEV) and the mean generation interval ranged from about 6.0 (HER and SHO) to 6.4 (ANG) years. In the reference population (calves born in 2009 and 2010, plus those born in 2008 for SHO) the mean equivalent number of generations known ranged from about 7 (SHO) to 9 (HER). In the 4 breeds studied, nearly all animals born over the last few years are inbred, even though the mean level of inbreeding in the reference population is below 4% in all breeds. The rate of inbreeding per generation, computed from the individual increase in inbreeding, ranged from about 0.2 (ANG) to 0.5% (DEV), with a corresponding effective population size of 245 and 92, respectively, which is above the recommended minimum critical threshold. The number of founders/ancestors contributing with 50% of the reference population gene pool was 211/26 for ANG, 41/14 for DEV, 164/25 for HER, and 79/10 for SHO, with effective number of founders/ancestors/founder genomes of 470/68/36, 89/33/16, 289/59/30, and 200/28/18 for ANG, DEV, HER, and SHO, respectively. The genetic contribution of different countries to the gene pool of each breed indicated that, throughout the period studied, DEV genes originated predominantly from the United Kingdom, while for the other breeds there was a changing pattern over time. Until the 1970s Argentina was the major supplier of ANG, while HER and SHO genes were mostly from Uruguay, but since then the United States took the leading role as supplier of ANG, HER, and SHO genes to Brazil. Our results reveal a mild increase in inbreeding in all breeds studied, with effective population size estimates indicating that reasonable levels of genetic diversity have been maintained in all 4 breeds. Continuous monitoring of inbreeding trends and of parameters derived from probability of gene origin should be ensured to warrant the long-term maintenance of genetic diversity.

Bioeconomic model and selection indices in Aberdeen Angus cattle.

A bioeconomic model was developed to calculate economic values for biological traits in full-cycle production systems and propose selection indices based on selection criteria used in the Brazilian Aberdeen Angus genetic breeding programme (PROMEBO). To assess the impact of changes in the performance of the traits on the profit of the production system, the initial values ​​of the traits were increased by 1%. The economic values for number of calves weaned (NCW) and slaughter weight (SW) were, respectively, R$ 6.65 and R$ 1.43/cow/year. The selection index at weaning showed a 44.77% emphasis on body weight, 14.24% for conformation, 30.36% for early maturing and 10.63% for muscle development. The eighteen-month index showed emphasis of 77.61% for body weight, 4.99% for conformation, 11.09% for early maturing, 6.10% for muscle development and 0.22% for scrotal circumference. NCW showed highest economic impact, and SW had important positive effect on the economics of the production system. The selection index proposed can be used by breeders and should contribute to greater profitability.