Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

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.

Dwarfism in beef cattle, a literature review.

Includes bibliography.

Determination of breeding strategies for beef cattle bull breeders selling bulls into two competing markets on a non-linear price grid

Computer simulation was used to suggest potential selection strategies for beef cattle breeders with different mixes of clients between two potential markets. The traditional market paid on the basis of carcass weight (CWT), while a new market considered marbling grade in addition to CWT as a basis for payment. Both markets instituted discounts for CWT in excess of 340 kg and light carcasses below 300 kg. Herds were simulated for each price category on the carcass weight grid for the new market. This enabled the establishment of phenotypic relationships among the traits examined [CWT, percent intramuscular fat (IMF), carcass value in the traditional market, carcass value in the new market, and the expected proportion of progeny in elite price cells in the new market pricing grid]. The appropriateness of breeding goals was assessed on the basis of client satisfaction. Satisfaction was determined by the equitable distribution of available stock between markets combined with the assessment of the utility of the animal within the market to which it was assigned. The best goal for breeders with predominantly traditional clients was a CWT in excess of 330 kg, while that for breeders with predominantly new market clients was a CWT of between 310 and 329 kg and with a marbling grade of AAA in the Ontario carcass pricing system. For breeders who wished to satisfy both new and traditional clients, the optimal CWT was 310-329 kg and the optimal marbling grade was AA-AAA. This combination resulted in satisfaction levels of greater than 75% among clients, regardless of the distribution of the clients between the traditional and new marketplaces.

USE OF PROGENY TESTING IN BEEF-CATTLE - PREDICTION OF GENETIC GAIN IN A NELORE CATTLE-BREEDING PROGRAM

Genetic gains predicted for selection, based on both individual performance and progeny testing, were compared to provide information to be used in implementation of progeny testing for a Nelore cattle breeding program. The prediction of genetic gain based on progeny testing was obtained from a formula, derived from methodology of Young and weller (J. Genetics 57: 329-338, 1960) for two-stage selection, which allows prediction of genetic gain per generation when the individuals under test have been pre-selected on the basis of their own performance. The application of this formula also allowed determination of the number of progeny per tested bull needed to maximize genetic gain, when the total number of tested progeny is limited.

Use of progeny testing in beef cattle: Prediction of genetic gain in a Nelore Cattle Breeding Program

Genetic gains predicted for selection, based on both individual performance and progeny testing, were compared to provide information to be used in implementation of progeny testing for a Nelore cattle breeding program. The prediction of genetic gain based on progeny testing was obtained from a formula, derived from methodology of Young and Weiler (J. Genetics 57: 329-338, 1960) for two-stage selection, which allows prediction of genetic gain per generation when the individuals under test have been pre-selected on the basis of their own performance. The application of this formula also allowed determination of the number of progeny per tested bull needed to maximize genetic gain, when the total number of tested progeny is limited.

Prospecting candidate SNPs for backfat in Canchim beef cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effects of sex and age on genotype x environment interaction for beef cattle body weight studied using reaction norm models

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Trends of the genetic connectedness measures among Nelore beef cattle herds

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic and environmental heterogeneity of residual variance of weight traits in Nellore beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Breed and selection line differences in the temperament of beef cattle

O temperamento de quatro raças bovinas foi avaliado utilizando-se o teste de velocidade de fuga (FT) e o escore de comportamento (BST). FT foi definida como o tempo necessário para animais percorrerem uma distância de 2 m após a pesagem. BST foi baseada no comportamento dos animais na balança, amostrando-se quatro categorias de comportamento: movimentos, intensidade de respiração, vocalizações e coices. Os coeficientes de herdabilidade de FT e BST foram estimados com uso de um modelo de máxima verossimilhança restrita, considerando meio irmãos paternos. Caracu apresentou menores médias para BST do que as demais raças. Nelore apresentou resultados intermediários, seguida por Guzerat e Gyr com médias mais elevadas (p < 0,05). Resultados similares foram observados para FT, mas as médias de Caracu e Nelore não diferiram entre si. Observou-se baixa associação entre FT e BST (r p= -0,36; p < 0,01). A correlação entre rank de touros ordenados pelos seus valores preditos (p) para FT e BST foi moderada e negativa (r s = -0,63; p < 0,001). A herdabilidade de FT e BST foi de 0,35 e 0,34, respectivamente. A comparação de rebanhos Nelore com diferentes critérios de seleção para peso corporal mostrou que linhas de seleção podem modular positivamente o temperamento de Bos indicus.

Assessment of GH1, CAPN1 and CAST polymorphisms as markers of carcass and meat traits in Bos indicus and Bos taurus-Bos indicus cross beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Growth hormone 1 gene (GH1) polymorphisms as possible markers of the production potential of beef cattle using the Brazilian Canchim breed as a model

The growth hormone 1 gene (GH1) is a candidate gene for body weight and weight gain in cattle since it plays a fundamental role in growth regulation. We investigated the GH1 gene AluI and DdeI restriction enzyme polymorphisms, located 149 bp apart in the cattle genome, as possible markers of the production potential of Canchim crossbreed cattle, a 5/8 Charolais (Bos taurus) and 3/8 Nelore (Bos indicus) breed developed in Brazil, by evaluating the birth weight, weaning weight, yearling weight and plasma insulin-like growth factor-1 (IGF-1) concentration of 7 month to 10 months old Canchim calves (n = 204) of known genealogy and which had been genotyped for the AluI and DdeI markers. Our results showed significant effect (p < 0.05) between the homozygous DdeI+/DdeI+ polymorphism and the estimated breeding value for weaning weight (ESB-WW), while the AluI leucine homozygous (L/L) and leucine/valine (L/V) heterozygous polymorphisms showed no significant effect on the traits studied. The restriction sites of the two enzymes led to the formation of haplotypes which also exerted a significant effect (p < 0.05) on the ESB-WW, with the largest difference being 8.5 kg in favor of the homozygous L plus DdeI+/L plus DdeI+ genotype over the heterozygous L plus DdeI-/V plus DdeI+ genotype.

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore (Bos indicus) beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)