Genetic parameters for tonic immobility, body weight, and morphological traits of the red-winged tinamou (Rhynchotus rufescens).

This study was carried out to estimate genetic parameters for morphology, body weight, and tonic immobility traits in the red-winged tinamou (Rhynchotus rufescens). Information on 690 birds was used and genetic parameters were estimated using Bayesian methods under a multi-trait animal model. The following traits were considered in this study: tarsal length (TL), bill length (BL), wing length (WL), head width (HW), bill width (BW), mature weight (MW), weight at 90 days (W90), and tonic immobility (TI). The heritability showed estimates between 0.15 for wing length and 0.56 for bill length. Positive and negative genetic correlations were estimated, ranging from - 0.33 to 0.81. All the morphological, production, and behavioral traits studied will have moderate to high response to selection. The body weight at 90 days is a better alternative for use in breeding programs and its selection would not lead to an increase in the time of tonic immobility. Both the selection for weight gain and for reduction of tonic immobility time would lead to an increase in the size of the legs of the red-winged tinamou, which could be advantageous for thermal control of these birds in tropical systems.

Trait-specific long-term consequences of genomic selection in beef cattle.

Simulation studies allow addressing consequences of selection schemes, helping to identify effective strategies to enable genetic gain and maintain genetic diversity. The aim of this study was to evaluate the long-term impact of genomic selection (GS) in genetic progress and genetic diversity of beef cattle. Forward-in-time simulation generated a population with pattern of linkage disequilibrium close to that previously reported for real beef cattle populations. Different scenarios of GS and traditional pedigree-based BLUP (PBLUP) selection were simulated for 15 generations, mimicking selection for female reproduction and meat quality. For GS scenarios, an alternative selection criterion was simulated (wGBLUP), intended to enhance long-term gains by attributing more weight to favorable alleles with low frequency. GS allowed genetic progress up to 40% greater than PBLUP, for female reproduction and meat quality. The alternative criterion wGBLUP did not increase long-term response, although allowed reducing inbreeding rates and loss of favorable alleles. The results suggest that GS outperforms PBLUP when the selected trait is under less polygenic background and that attributing more weight to low-frequency favorable alleles can reduce inbreeding rates and loss of favorable alleles in GS.

Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection.

The aim of this study was to compare iterative and direct solvers for estimation of marker effects in genomic selection. One iterative and two direct methods were used: Gauss-Seidel with Residual Update, Cholesky Decomposition and Gentleman-Givens rotations. For resembling different scenarios with respect to number of markers and of genotyped animals, a simulated data set divided into 25 subsets was used. Number of markers ranged from 1,200 to 5,925 and number of animals ranged from 1,200 to 5,865. Methods were also applied to real data comprising 3081 individuals genotyped for 45181 SNPs. Results from simulated data showed that the iterative solver was substantially faster than direct methods for larger numbers of markers. Use of a direct solver may allow for computing (co)variances of SNP effects. When applied to real data, performance of the iterative method varied substantially, depending on the level of ill-conditioning of the coefficient matrix. From results with real data, Gentleman-Givens rotations would be the method of choice in this particular application as it provided an exact solution within a fairly reasonable time frame (less than two hours). It would indeed be the preferred method whenever computer resources allow its use.