Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle

<p>Abstract</p> <p>Background</p> <p>The success of genomic selection depends mainly on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), the number of animals in the training set (TS) and the heritability (h²) of the trait. The extent of LD depends on the genetic structure of the population and the density of markers. The aim of this study was to calculate accuracy of direct genomic estimated breeding values (DGEBV) using best linear unbiased genomic prediction (GBLUP) for different marker densities, heritabilities and sizes of the TS in simulated populations that mimicked previously reported extent and pattern of LD in beef cattle.</p> <p>Results</p> <p>The accuracy of DGEBV increased significantly (p < 0.05) with the increase in the number of bulls in the TS (480, 960 or 1920), trait h²(0.10, 0.25 or 0.40) and marker densities (40 k or 800 k). Increasing the number of animals in the TS by 4-fold and using their phenotypes to estimate marker effects was not sufficient to maintain or increase the accuracy of DGEBV obtained using estimated breeding values (EBVs) when the trait h²was lower than 0.40 for both marker densities. Comparing to expected accuracies of parent average (PA), the gains by using DGEBV would be of 27%, 13% and 10% for trait h²equal to 0.10, 0.25 and 0.40, respectively, considering the scenario with 40 k markers and 1920 bulls in TS.</p> <p>Conclusions</p> <p>As reported in dairy cattle, the size of the TS and the extent of LD have major impact on the accuracy of DGEBV. Based on the findings of this simulation study, large TS, as well as dense marker panels, aiming to increase the level of LD between markers and QTL, will likely be needed in beef cattle for successful implementation of genomic selection.</p

Genetic association between longevity and linear type traits of Holstein cows

Longevity is a desirable trait in the dairy industry because of its relationship to profitability. The aim of this study was to estimate genetic parameters for longevity measurements related to productive life, or life in the herd, and linear type traits of Brazilian Holstein cows born between the years 1990 and 2008. The (co) variance components were estimated by the restricted maximum likelihood method. The heritability for measurements of longevity and linear type traits ranged from 0.05 to 0.07 and 0.08 to 0.39, respectively. The genetic correlations between measurements of longevity and linear type traits ranged from -0.39 to 0.31. Direct selection for longevity does not necessarily lead to long-lived cows, due to low heritability. Indirect genetic selection for udder depth, bone quality, udder height, rear teat placement and conformation traits showed the highest genetic correlations with measurements of time between birth and last milk record and time from first calving to last milk record

Uso de funções ortogonais para descrever a produção de leite no dia de controle por meio de modelos de regressão aleatória Genetic modelling of daily milk yield using orthogonal polynomials in random regression

Registros de produção de leite de 68.523 controles leiteiros de 8.536 vacas da raça Holandesa, filhas de 537 reprodutores, distribuídas em 266 rebanhos, com parições nos anos de 1996 a 2001, foram utilizados na comparação de modelos de regressão aleatória, para estimação de componentes de variância. Os modelos de regressão aleatória diferiram entre si pelo grau do polinômio de Legendre utilizado para descrever a trajetória da curva de lactação dos animais. Os modelos incluíram os efeitos rebanho-mês-ano do controle, composição genética dos animais, freqüência de ordenhas diárias, regressão polinomial em cada classe de idade-estação de parto para descrever a parte fixa da lactação e regressão polinomial aleatória relacionadas aos efeitos genético direto e de ambiente permanente. As estimativas de herdabilidade obtidas oscilaram de 0,122 a 0,291. Verificou-se que o modelo de regressão aleatória que utilizou a maior ordem para os polinômios de Legendre descreveu melhor a variação genética da produção de leite, de acordo com o critério de Akaike.<br>Data comprising 68,523 test day milk yield of 8,536 cows of the Holstein breed, daughters of 537 sires, distributed in 266 herds, calving from 1996 to 2001, were used to compare random regression models, for estimating variance. Test day records (TD) were analyzed by different random regression models regarding the function used to describe the trajectory of the lactation curve of the animals. Legendre orthogonal polynomials function of second, third and fourth order were used. The random regression models included the effects of herd-month-year of the control, genetic group of the animals; the frequency of the daily milk; regression coefficients for each class of age-season (in order to describe the fixed part of the lactation curve) and random regression coefficients related to the direct genetic and the permanent environmental effects. The heritability estimates obtained using the random regression models ranged from 0.122 to 0.291. The random regression model which used the fourth order Legendre polynomials was the model which better described the genetic variation of the milk yield, according to AIC test

Genetic parameters for type traits in Holstein cows in Brazil

Data from 26,558 Holstein cows in 802 herds were used to estimate genetic, residual and phenotypic parameters for 22 type traits. The model included the fixed effects of herd-year, period of classification, classifier, stage of lactation and age of cows at calving (covariate) and random genetic and residual effects. Heritability for type traits ranged from 0.10 to 0.39. The genetic variability in these traits suggested the possibility for moderate genetic gains through selection. The phenotypic correlations were moderated, mainly in the section conformation. Genetic correlations between type traits ranged from -0.44 to 0.85. High genetic correlations indicated that breeding programs could be successful without including all type traits. The selection for the final score at the expense of other traits must be performed with restraint, because in the long term, this may promote undesirable changes in some type traits