Three-step Bayesian factor analysis applied to QTL detection in crosses between outbred pig populations

AbstractMarker assisted selection (MAS) can be used to improve the efficiency of genetic selection of traits for which phenotypic measurements are expensive or cannot be obtained on selection candidates, such as carcass traits. Marker information required for MAS may be acquired through the identification of QTLs. Generally, univariate models are used for QTL detection, although multiple-trait models (MTM) may enhance QTL detection and breeding value estimation. In MTM, however, the number of parameters can be large and, if traits are highly correlated, such as carcass traits, estimates of (co)variance matrices may be close to singular. Because of this, dimension reduction techniques such as Factor Analysis (FA) may be useful. The aim of our project is to evaluate the use of FA for structuring (co)variance matrices in the context of Bayesian models for QTL detection in crosses between outbred populations. In our method, QTL effects are postulated at the level of common factors (CF) rather than the original traits, using a three-step approach. In a first step, a MTM is fitted to arrive at estimates of systematic effects and prediction of breeding values (procedure A) and only systematic effect (procedure B). These estimates/predictions are then used to generate an adjusted phenotype that is further analyzed with a Bayesian FA model. This step yields estimates of factor scores for each animal and CF. In the last step, the scores relative to each CF are analyzed independently using probabilities for the line of origin combination. To illustrate the methodology, data on 416 F2 pigs (Brazilian Piau X commercial) with ten traits (5 fat-related, 2 loin measurements, and 3 carcass classification systems) were analyzed. For each of the three resulting CFs, an independent QTL scan was performed on chromosome 7 considering three models: I) null (i.e., absence of QTL); II) additive effect QTL, and III) additive and dominance effect QTL. The posterior probability (PP) of each model was calculated from Bayes factor for each considered procedures (A and B). A Three-step Bayesian factor analysis allowed us to calculate the probability of QTLs that simultaneously affect a group of carcass traits for each position of SSC 7. The removal of systematic effects in the first step of the evaluation (procedure B) allowed that the factor analysis, which was performed in the second step, identify three distinct factors that explained 85% of the total traits variation. For the common factor that represented fat-related traits (bacon depth, midline lower backfat thickness, higher backfat thickness on the shoulder; midline backfat thickness after the last rib; midline backfat thickness on the last lumbar vertebrae) the third step of the analysis showed that the highest probability of an additive QTL effect at the 65cM position was 86%

Genomic selection for boar taint compounds and carcass traits in a commercial pig population

AbstractThis study aimed to compare two different Genome-Wide Selection (GWS) methods (Ridge Regression BLUP − RR-BLUP and Bayesian LASSO − BL) to predict the genomic estimated breeding values (GEBV) of four phenotypes, including two boar taint compounds, i.e., the concentrations of androstenone (andro) and skatole (ska), and two carcass traits, i.e., backfat thickness (fat) and loin depth (loin), which were measured in a commercial male pig line. Six hundred twenty-two boars were genotyped for 2,500 previously selected single nucleotide polymorphisms (SNPs). The accuracies of the GEBV using both methods were estimated based on Jack-knife cross-validation. The BL showed the best performance for the andro, ska and loin traits, which had accuracy values of 0.65, 0.58 and 0.33, respectively; for the fat trait, the RR-BLUP accuracy of 0.61 outperformed the BL accuracy of 0.56. Considering that BL was more accurate for the majority of the traits, this method is the most favoured for GWS under the conditions of this study. The most relevant SNPs for each trait were located in the chromosome regions that were previously indicated as QTL regions in other studies, i.e., SSC6 for andro and ska, SSC2 for fat, and SSC11, SSC15 and SSC17 for loin

Inclusão de animais oriundos da técnica de transferência de embriões, na estimação de parâmetros genéticos de bovinos da raça Simental

peer reviewedWeight records from Simmental cattle provided by the Associação Brasileira dos Criadores das Raças Simental e Simbrasil (ABCRSS) were used in genetic parameters estimation by with (MTM2) or without (MTM1) inclusion of animals from the embryo transfer technique (ET). The genetic parameters were estimated by restrict maximum likelihood (REML). The direct heritabilities (h2d) in MTM1 were 0.04, 0.11, 0.20, 0.27, 0.31, 0.42, and in MTM2 were 0.11, 0.11, 0.17, 0.21, 0.22 and 0.26, respectively, for ages at 100, 205, 365, 450, 550 and 730 days. The inclusion of animals from the technique of embryo transfer can result in potential accuracy gains in genetic evaluations and more genetic gains because of the reduction of the generation interva

Toll-Like Receptor 6 differential expression in two pig genetic groups vaccinated against Mycoplasma hyopneumoniae

<p>Abstract</p> <p>Background</p> <p><it>Mycoplasma hyopneumoniae</it> is the etiologic agent of enzootic pneumonia, which causes important economic losses to swine industry. The Toll-like receptors (TLRs) are pattern-recognition receptors which detect microbial presence and initiate the innate as well as the adaptative immune defense. Toll-like receptor 6 is a type I transmembrane protein that recognizes bacterial components. The aim of this study was to compare mRNA expression pattern of TLR6 gene in two genetically distinct groups of pigs vaccinated against <it>Mycoplasma hyopneumoniae.</it></p> <p>Methods</p> <p>For each genetic group, peripheral blood was collected just before and 10 days after vaccination from 10 Naturalized Brazilian Piau breed and 10 Commercial White Line serum-negative female piglets. RNA was extracted from peripheral blood mononuclear cells (PBMCs), reverse transcripted and the qRT-PCR performed using SYBR green fluorescence system, using GAPDH gene as endogenous control. Analyses were performed by UNIVARIATE (Shapiro-Wilk test) and MIXED procedures of SAS software (version 9.0).</p> <p>Results</p> <p>It was observed significant interaction between breed and vaccination, being the TLR6 mRNA expression higher in the Commercial White line than in the Piau breed after vaccination. Furthermore, there was differential expression before and after vaccination in the Commercial White line.</p> <p>Conclusions</p> <p>Analysis of in TLR6 gene expression showed difference between the two distinct genetic groups, however, other TLRs gene expression must be evaluated for a better understanding of innate resistance in the pig concerning <it>Mycoplasma hyopneumoniae</it> infection.</p

Análise bayesiana univariada e bivariada para a conversão alimentar de suínos da raça Piau

The objective of this work was to present alternative uni‑ and bivariate modeling procedures for the evaluation of feed conversion (FC) of the Piau swine breed, using Bayesian inference. The effects of sex and genotype on animal FC were evaluated by the Markov chain Monte Carlo (MCMC) and the integrated nested Laplace approximation (INLA) procedures. The univariate model was evaluated using different distributions for the error – normal (Gaussian), t‑Student, gamma, log‑normal, and skew‑normal –, whereas, for the bivariate model, the normal error was considered. The skew‑normal distribution was the most parsimonious model to infer on the direct response (univariate) of FC to the effects of sex and genotype, which were nonsignificant. The bivariate model was capable to identify significant differences on weight gain and feed intake in significance levels not detected by the univariate model. Moreover, it was also able to detect differences between sexes, when grouped by NN (male, 2.73±0.04; female, 2.68±0.04) and Nn (male, 2.70±0.07; female, 2.64±0.07) genotypes, and revealed greater accuracy and precision for nutritional inferences. In both approaches, the Bayesian method proves flexible and efficient for assessing animal nutritional performance.O objetivo deste trabalho foi apresentar modelagens alternativas, uni e bivariadas, para avaliação da conversão alimentar (CA) de suínos da raça Piau, com uso de inferência bayesiana. Os efeitos de sexo e genótipo sobre a CA dos animais foram avaliados por meio de procedimentos de simulação de Monte Carlo via cadeias de Markov (MCMC) e de integração aproximada aninhada de Laplace (INLA). O modelo univariado foi avaliado com diferentes distribuições para o erro – normal (gaussiana), t de Student, gama, log‑normal e skew‑normal –, enquanto, para o modelo bivariado, considerou-se o erro normal. A distribuição skew‑normal foi o modelo mais parcimonioso para inferir sobre a resposta direta (univariada) da CA aos efeitos de sexo e genótipo, os quais não foram significativos. O modelo bivariado foi capaz de identificar diferenças significativas no ganho de peso e no consumo de ração em níveis de significância não detectados pelo modelo univariado. Além disso, ele também foi capaz de detectar diferenças entre sexos, quando agrupados por genótipos NN (machos, 2,73±0,04; fêmeas, 2,68±0,04) e Nn (machos, 2,70±0,07; fêmeas, 2,64±0,07), e revelou maior acurácia e precisão nas inferências nutricionais. Em ambas as abordagens, o método bayesiano mostra-se flexível e eficiente para a avaliação do desempenho nutricional dos animais

Mapping quantitative trait loci for performance traits on pig chromosome 6 (SSC6)

The objective of this study was to perform QTL mapping associated to performance traits on swine chromosome 6 (SSC6). The F2 population was produced by an outbred crossing using two native Brazilian breed Piau sires and 18 commercial dams. A total of 617 F2 animals were genotyped for 13 microsatellite markers. The traits evaluated on the F2 population were teat number (TN), birth weight (BW), weight at 21, 42, 63, 77 and 105 days of age (W21, W42, W63, W77, W105), weight at slaughter (WS), and average daily gain (ADG), feed intake (FI) and feed-gain ratio (FG) from 77 to 105 days of age. Data were analyzed by multiple regression developed for analysis of crosses between outbred lines, using the QTL Express software. A significant QTL was detected for FI at 99 cM. A suggestive QTL was detected for W42 located at 55 cM. A locus located at 100 cM seems to affect the traits FI and ADG. Evidence for loci affecting weight at different ages not was found

Independent component regression applied to genomic selection for carcass traits in pigs

O objetivo deste trabalho foi avaliar a eficiência do método de regressão via componentes independentes (ICR) na estimação de valores genéticos genômicos e dos efeitos de marcadores SNP para características de carcaça de uma população F2 de suínos (Piau x linhagem comercial). Os métodos foram avaliados por meio da concordância entre os valores genéticos preditos e os fenótipos corrigidos, observados por validação cruzada, e também foram comparados com outros métodos geralmente utilizados para os mesmos propósitos, tais como RR‑BLUP, PCR e PLS. Os métodos ICR e PCR apresentam resultados similares, mas o método ICR apresenta maiores valores de acurácia.The objective of this work was to evaluate the efficiency of the independent component regression (ICR) method for the estimation of genomic values and of SNP marker effects for carcass traits in a F2 pig population (Piau x commercial line). The methods were evaluated by the agreement between the genetic predicted values and the corrected phenotypes observed by cross‑validation, and they were also compared with other methods generally used for the same purposes, such as RR‑BLUP, PCR, and PLS. The ICR and PCR methods show similar results, but ICR has the highest accuracy prediction values