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Shiotsuki L.,Embrapa Goats and Sheep | Cardoso F.F.,Embrapa Southern Region Animal Husbandry | Silva II J.A.V.,Sao Paulo State University | Albuquerque L.G.,Sao Paulo State University
Journal of Animal Science

The aim of the present study was to compare a model assuming unknown paternity and a model using genetic grouping to indicate the most adequate statistical procedure for the estimation of breeding values for animals with uncertain paternity. After data consistency, 62,212 Nellore animals, offspring of 581 bulls and 27,743 cows, were used in the analyses. The pedigree file contained 75,088 animals, including 22,810 (30.18%) offspring of multiple sires and 12,876 animals belonging to the base population with unknown parents. Three different approaches were adopted to deal with uncertain paternity of multiple-sire (MS) offspring. In the model of unknown paternity, the MS groups were ignored, and the sires of MS offspring were considered to be unknown and to belong to a single base population. In the genetic group approach, 2 definitions were used. In the first definition (GGa), "phantom parents" for animals with uncertain paternity were attributed, defining the genetic group as the MS group. In the other approach, GGb, phantom parents for animals with uncertain paternity were also attributed; however, MS offspring were clustered in genetic groups according to their year of birth, every 3 yr, on the basis of the average of male generation interval. Univariate analyses were performed under the Bayesian approach via Markov chain Monte Carlo methods. Models were compared by deviance information criteria and the conditional predictive ordinate. According to the choice criteria results, the genetic group model defined by the generation interval of males was more appropriate for predicting the genetic merit of animals with uncertain paternity. Therefore, the use of this model is recommended for the prediction of genetic merit and classification of offspring of multiple sires. © 2013 American Society of Animal Science. All rights reserved. Source

Mokry F.B.,Federal University of Sao Carlos | Higa R.H.,Embrapa Agricultural Informatics | de Alvarenga Mudadu M.,Embrapa Southeast Livestock | Oliveira de Lima A.,Federal University of Sao Carlos | And 9 more authors.
BMC Genetics

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd. Source

Bremm C.,Federal University of Rio Grande do Sul | Carvalho P.C.F.,Federal University of Rio Grande do Sul | Fonseca L.,Federal University of Rio Grande do Sul | Amaral G.A.,Federal University of Rio Grande do Sul | And 4 more authors.

Invasion by exotic grasses is a severe threat to the integrity of grassland ecosystems all over the world. Because grasslands are typically grazed by livestock and wildlife, the invasion is a community process modulated by herbivory. We hypothesized that the invasion of native South American grasslands by Eragrostis plana Nees, an exotic tussock-forming grass from Africa, could be deterred by grazing if grazers switched dietary preferences and included the invasive grass as a large proportion of their diets. Bos taurus (heifers) and Ovis aries (ewes) grazed plots with varying degrees of invasion by E. plana in a replicated manipulative experiment. Animal positions and species grazed were observed every minute in 45- min grazing session. Proportion of bites and steps in and out of E. plana tussocks were measured and used to calculate several indices of selectivity. Both heifers and ewes exhibited increasing probability of grazing E. plana as the proportion of area covered by tussocks increased, but they behaved differently. In agreement with expectations based on the allometry of dietary preferences and morphology, ewes consumed a low proportion of E. plana, except in areas that had more than 90% E. plana cover. Heifers consumed proportionally more E. plana than ewes. Contrary to our hypothesis, herbivores did not exhibit dietary switching towards the invasive grass. Moreover, they exhibited avoidance of the invasive grass and preference for short-statured native species, both of which should tend to enhance invasion. Unless invasive plants are highly palatable to livestock, the effect of grazing to deter the invasion is limited, due to the inherent avoidance of the invasive grass by the main grazers in the ecosystem, particularly sheep. © 2016 Bremm et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

Carvalho P.C.F.,Federal University of Rio Grande do Sul | Bremm C.,Agricultural and Livestock Research Foundation | Mezzalira J.C.,Federal University of Rio Grande do Sul | Fonseca L.,Federal University of Rio Grande do Sul | And 6 more authors.
Animal Production Science

Despite all the biotic and abiotic factors affecting foraging by ruminants, there is a common and fundamental process, which is bite gathering. We hypothesised that because the mechanics of bite formation dominate the foraging process, changes in short-term bite mass are reflected in longer-term animal performance across a wide range of sward conditions. We focus at the meal level of foraging, using experiments in which the effect of abiotic factors and digestive constrains are minimised, making intake rate the main currency. We estimated bite mass across a wide range of structural challenges to large-herbivore foraging in a long-term experiment with heterogeneous native grasslands. A conceptual model was developed for average daily gain, where energy gain and energy costs were proximate causal variables. Energy gain was a function of diet quality and components of daily intake rate, where bite mass was the main component estimated. In turn, components of intake rate were determined by sward structure and bodyweight. Energy costs were a function of bodyweight and abiotic conditions. Finally, sward structure, bodyweight and abiotic conditions were determined by experimental treatments, seasons and years. Then, the conceptual model was translated into statistical models that included variables measured or estimated, and coefficients representing all links in the conceptual model. Weight gain was a function of bite mass, forage characteristics, and animal and abiotic conditions. Models were set up to test whether forage and stocking conditions affected monthly gain beyond the effects through bite mass, after correcting for abiotic factors. Forage mass, height and disappearance did help predict monthly gain after bite mass was included in the model, which supported our hypothesis. However, stocking treatments and season had significant effects not incorporated in bite mass. Although the model explained 77.9% of liveweight gain variation, only 35.2% was due to fixed effects, with 10.8% accounted by bite mass and its interactions. Concomitant experiments showed that sward structure (first with sward height and the second with tussock cover) does determine bite mass and short-term intake rate in the complex native grasslands we studied. Yet, other temporal varying components of monthly gain not correlated with bite mass, temperature or wind, added most of the observed variation in monthly animal performance. Part of the model failure to account for variation in performance may be related to a significant and temporally variable grazing of tussocks. We used a bite mass model that assumed no tussock grazing. In light of these results and a parallel experiment, we conclude that tussock grazing must be incorporated in future versions of the model. © CSIRO 2015. Source

Cardoso F.F.,Embrapa Southern Region Animal Husbandry | Tempelman R.J.,Michigan State University
Journal of Animal Science

The objectives of this work were to assess alternative linear reaction norm (RN) models for genetic evaluation of Angus cattle in Brazil. That is, we investigated the interaction between genotypes and continuous descriptors of the environmental variation to examine evidence of genotype by environment interaction (G×E) in post-weaning BW gain (PWG) and to compare the environmental sensitivity of national and imported Angus sires. Data were collected by the Brazilian Angus Improvement Program from 1974 to 2005 and consisted of 63,098 records and a pedigree file with 95,896 animals. Six models were implemented using Bayesian inference and compared using the Deviance Information Criterion (DIC). The simplest model was M1, a traditional animal model, which showed the largest DIC and hence the poorest fit when compared with the 4 alternative RN specifications accounting for G×E. In M2, a 2-step procedure was implemented using the contemporary group posterior means of M1 as the environmental gradient, ranging from -92.6 to +265.5 kg. Moreover, the benefits of jointly estimating all parameters in a 1-step approach were demonstrated by M3. Additionally, we extended M3 to allow for residual heteroskedasticity using an exponential function (M4) and the best fitting (smallest DIC) environmental classification model (M5) specification. Finally, M6 added just heteroskedastic residual variance to M1. Heritabilities were less at harsh environments and increased with the improvement of production conditions for all RN models. Rank correlations among genetic merit predictions obtained by M1 and by the best fitting RN models M3 (homoskedastic) and M5 (heteroskedastic) at different environmental levels ranged from 0.79 and 0.81, suggesting biological importance of G×E in Brazilian Angus PWG. These results suggest that selection progress could be optimized by adopting environment-specific genetic merit predictions. The PWG environmental sensitivity of imported North American origin bulls (0.046 ± 0.009) was significantly larger (P < 0.05) than that of local sires (0.012 ± 0.013). Moreover, PWG of progeny of imported sires exceeded that of native sires in medium and superior production levels. On the other hand, Angus cattle locally selected in Brazil tended to be more robust to environmental changes and hence be more suitable when production environments for potential progeny is uncertain. © 2012 American Society of Animal Science. All rights reserved. Source

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