Comparison of methods for predicting genomic breeding values for growth traits in Nellore cattle.

The objective of this study was to evaluate the accuracy of genomic predictions of growth traits in Nellore cattle. Data from 5064 animals belonging to farms that participate in the Conexão DeltaGen and PAINT breeding programs were used. Genotyping was performed with the Illumina BovineHD BeadChip (777,962 SNPs). After quality control of the genomic data, 412,993 SNPs were used. Deregressed EBVs (DEBVs) were calculated using the estimated breeding values (EBVs) and accuracies of birth weight (BW), weight gain from birth to weaning (GBW), postweaning weight gain (PWG), yearling height (YH), and cow weight (CW) provided by GenSys. Three models were used to estimate marker effects: genomic best linear unbiased prediction (GBLUP), BayesCπ, and improved Bayesian least absolute shrinkage and selection operator (IBLASSO). The prediction ability of genomic estimated breeding value (GEBVs) was estimated by the average Pearson correlation between DEBVs and GEBVs, predicted with the different methodologies in the validation populations. The regression coefficients of DEBVs on GEBVs in the validation population were calculated and used as indicators of prediction bias of GEBV. In general, the Bayesian methods provided slightly more accurate predictions of genomic breeding values than GBLUP. The BayesCπ and IBLASSO were similar for all traits (BW, GBW, PWG, and YH), except for CW. Thus, there does not seem to be a more suitable method for the estimation of SNP effects and genomic breeding values. Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions.

Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle.

The objective of this study was to perform a genome-wide association study (GWAS) to detect chromosome regions associated with indicator traits of sexual precocity in Nellore cattle. Data from Nellore animals belonging to farms which participate in the DeltaGen® and Paint® animal breeding programs, were used. The traits used in this study were the occurrence of early pregnancy (EP) and scrotal circumference (SC). Data from 72,675 females and 83,911 males with phenotypes were used; of these, 1,770 females and 1,680 males were genotyped. The SNP effects were estimated with a single-step procedure (WssGBLUP) and the observed phenotypes were used as dependent variables. All animals with available genotypes and phenotypes, in addition to those with only phenotypic information, were used. A single-trait animal model was applied to predict breeding values and the solutions of SNP effects were obtained from these breeding values. The results of GWAS are reported as the proportion of variance explained by windows with 150 adjacent SNPs. The 10 windows that explained the highest proportion of variance were identified. The results of this study indicate the polygenic nature of EP and SC, demonstrating that the indicator traits of sexual precocity studied here are probably controlled by many genes, including some of moderate effect. The 10 windows with large effects obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27, and together explained 7.91% of the total genetic variance. For SC, these windows are located on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of total variance. GWAS permitted to identify chromosome regions associated with EP and SC. The identification of these regions contributes to a better understanding and evaluation of these traits, and permits to indicate candidate genes for future investigation of causal mutations.