Multi-Trait analysis of growth traits: fitting reduced rank models using principal components for Simmental beef cattle / Efetividade da redução da dimensão da matriz de covariância do efeito genético direto na avaliação genética do crescimento em bovinos Simental

ABSTRACT: The aim of this research was to evaluate the dimensional reduction of additive direct genetic covariance matrices in genetic evaluations of growth traits (range 100-730 days) in Simmental cattle using principal components, as well as to estimate (co)variance components and genetic parameters. Principal component analyses were conducted for five different models-one full and four reduced-rank models. Models were compared using Akaike information (AIC) and Bayesian information (BIC) criteria. Variance components and genetic parameters were estimated by restricted maximum likelihood (REML). The AIC and BIC values were similar among models. This indicated that parsimonious models could be used in genetic evaluations in Simmental cattle. The first principal component explained more than 96% of total variance in both models. Heritability estimates were higher for advanced ages and varied from 0.05 (100 days) to 0.30 (730 days). Genetic correlation estimates were similar in both models regardless of magnitude and number of principal components. The first principal component was sufficient to explain almost all genetic variance. Furthermore, genetic parameter similarities and lower computational requirements allowed for parsimonious models in genetic evaluations of growth traits in Simmental cattle.

RESUMO: Objetivou-se estudar a efetividade da redução da dimensão da matriz de covariância do efeito genético direto na avaliação genética do crescimento (pesos dos 100 aos 730 dias de idade) de bovinos Simental, por meio da análise de componentes principais, e estimar componentes de (co)variância e parâmetros genéticos. A análise de componentes principais foi realizada ajsutando-se cinco diferentes modelos: um modelo multicaracterístico padrão, de posto completo, e quatro modelos de posto reduzido. Os modelos foram comparados via informação de Akaike (AIC) e informação Bayesiana de Schwarz (BIC). Os componentes de variância e parâmetros genéticos foram obtidos via REML. Os valores de AIC e BIC para os modelos testados foram similares, indicando a possibilidade da escolha de um modelo mais parcimonioso na avaliação genética da raça Simental. O primeiro componente principal explicou mais de 96% de toda variação genética aditiva direta em ambos os modelos. Os valores de herdabilidades foram maiores em idades mais avançadas e variaram de 0,05 (peso aos 100 dias) a 0,30 (peso aos 730 dias). As estimativas de correlações genéticas foram similares em todos os modelos e apresentaram mesma magnitude e comportamento independentemente do número de componentes principais adotado. Diante dos resultados, pode-se afirmar que apenas o primeiro componente principal foi suficiente para explicar quase que na totalidade a variação genética aditiva direta existente. Além disso, a similaridade dos parâmetros genéticos estimados e a menor demanda computacional são indicativos da possibilidade da utilização de modelos mais parcimoniosos na avaliação genética de bovinos Simental.

Estrutura populacional da raça Girolando / Population structure of Girolando breed

O objetivo neste estudo foi avaliar a estrutura genética da população de bovinos da raça Girolando no Brasil. Analisou-se o arquivo de pedigree de 26.969 animais, composto de 3.031 machos e 23.938 fêmeas. O nível de conteúdo de informação do pedigree na geração atual foi 61%, mostrando ser de qualidade moderada. O coeficiente de endogamia médio e o coeficiente de relação médio da população Girolando foram 0,11 e 0,13%, respectivamente. O tamanho efetivo da população, considerando a geração completa traçada, foi 188, acima do nível crítico. Do total de 9.457 ancestrais que contribuíram para a população de referência, 457 explicaram 50% da variabilidade genética da população. O número efetivo de fundadores foi 551 e o de ancestrais 393. O intervalo médio de geração foi de 5,26 anos, sendo ligeiramente maior nas trilhas gaméticas mãe-filho e pai-filha. A partir dos coeficientes estimados, pode-se concluir que a endogamia nos rebanhos da raça Girolando foi de pequena magnitude e que as práticas de acasalamento foram adequadas durante o período avaliado. No entanto, é importante continuar com o monitoramento desses coeficientes a fim de prevenir perda de variabilidade genética.

The aim of this study was to evaluate the population structure of Girolando cattle in Brazil. The pedigree file contained 26,969 individuals, from which 3,031 were males and 23,938 were females. The average level of completeness of the pedigree in the current generation was of reasonable quality (61%). Inbreeding and average relatedness coefficients were low: 0.11 and 0.13%, respectively. Estimates of effective population size considering the full generations traced was 188, which is above the critical level range. The number of ancestors that contributed to the reference population was 9,457 animals, from which 457 explained 50% of the genetic variability of the population. The effective number of founders and the effective number of ancestors in this population were, respectively, 551 and 393. The average generation interval was 5.26 years, slightly higher in genetic pathways dam-son and sire-daughter. The inbreeding in the Girolando breed was of small magnitude, indicating that the current practices of mating were adequate during the study period. However, it is important to continue monitoring these coefficients in order to prevent loss of genetic variability.

Modelagem hierárquica Bayesiana na avaliação de curvas de crescimento de suínos genotipados para o gene halotano / Hierarchical Bayesian modeling for the evaluation of growth curves of pigs genotyped for the halothane gene

Para avaliar a influência do gene halotano sobre a curva de crescimento de suínos, bem como sua interação com o sexo do animal, foi proposta uma modelagem hierárquica Bayesiana. Nesta abordagem, os parâmetros dos modelos não-lineares de crescimento (Logístico, Gompertz e von Bertalanffy) foram estimados conjuntamente com os efeitos de sexo e genótipos do gene halotano. Foram utilizados 344 animais F2(Comercial x Piau) pesados ao nascer, aos 21, 42, 63, 77, 105 e 150 dias. O modelo Logístico foi aquele que apresentou melhor qualidade de ajuste por apresentar menor DIC (Deviance Information Criterion) que os demais. As amostras das distribuições marginais a posteriori para as diferenças entre as estimativas dos parâmetros do modelo Logístico indicaram que o peso dos machos à idade adulta com genótipo heterozigoto (HalNn) foi superior ao dos homozigotos (HalNN). A título de comparação, também foi considerada a abordagem frequentista tradicional, baseada em dois passos distintos, a qual, por apresentar um menor poder de discernimento estatístico, não mostrou diferenças significativas.

A hierarchical Bayesian modeling was used to evaluate the influence of halothane gene and its interaction with sex on pig´s growth curves. Under this approach, the parameters from growth models (Logistic, Gompertz and von Bertalanffy) were estimated jointly with the effects of halothane gene and sex. A total of 344 F2 (Commercial x Piau) animals were weighted at birth, 21, 42, 63, 77, 105 and 150 days in life. The Logistic model has presented the best fit based on DIC (Deviance Information Criterion). Thus, the samples from marginal posterior distributions for the differences between the parameters estimates of Logistic model have indicated that the maturity weight of males with heterozygous genotypes (HalNn) was superior to males with homozygous genotypes (HalNN). In order to realize a comparison with the traditional methodology, the frequentist approach based on two distinct steps also was used, but there was not identified significant differences between growth curve parameter estimates from each group (combinations of halothane genotypes and sex).

Quadrados mínimos parciais uni e multivariado aplicados na seleção genômica para características de carcaça em suínos / Uni and multivariate partial least squares applied to genomic selection for carcass traits in pigs

A principal contribuição da genética molecular é a utilização direta das informações de DNA no processo de identificação de indivíduos geneticamente superiores. Sob esse enfoque, idealizou-se a seleção genômica ampla (Genome Wide Selection - GWS), a qual consiste na análise de marcadores SNPs (Single Nucleotide Polymorphisms) amplamente distribuídos no genoma. Devido a esse grande número de SNPs, geralmente maior que o número de indivíduos genotipados, e à alta colinearidade entre eles, métodos de redução de dimensionalidade são requeridos. Dentre estes, destaca-se o método de regressão via Quadrados Mínimos Parciais (Partial Least Squares - PLS), que além de solucionar tais problemas, permite uma abordagem multivariada, considerando múltiplos fenótipos. Diante do exposto, objetivou-se aplicar e comparar a regressão PLS univariada (UPLS) e multivariada (MPLS) na GWS para características de carcaça em uma população F2 de suínos Piau×Comercial. Os resultados evidenciaram a superioridade do método MPLS, uma vez que este proporcionou maiores valores de acurácia em relação à abordagem univariada.

The main contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. Under this approach, genome-wide selection (GWS) can be used with this purpose. GWS consists in analyzing of a large number of SNP markers widely distributed in the genome, and due to the fact that the number of markers is much larger than the number of genotyped individuals and also to the fact that such markers are highly correlated special statistical methods, like Partial Least Squares (PLS), are widely required. Thus, the aim of this paper was to propose an application of Uni (UPLS) and Multivariate (MPLS) Partial Least Squares regression to GWS of carcass traits in an F2 (Piau × commercial) pig population. The results showed that MPLS method provided most accurate genomic breeding values estimates than univariate method.

Expression profile of genes associated with mastitis in dairy cattle

In order to characterize the expression of genes associated with immune response mechanisms to mastitis, we quantified the relative expression of the IL-2, IL-4, IL-6, IL-8, IL-10, IFN-γ and TNF-α genes in milk cells of healthy cows and cows with clinical mastitis. Total RNA was extracted from milk cells of six Black and White Holstein (BW) cows and six Gyr cows, including three animals with and three without mastitis per breed. Gene expression was analyzed by real-time PCR. IL-10 gene expression was higher in the group of BW and Gyr cows with mastitis compared to animals free of infection from both breeds (p < 0.05). It was also higher in BW Holstein animals with clinical mastitis (p < 0.001), but it was not significant when Gyr cows with and without mastitis were compared (0.05 < p < 0.10). Among healthy cows, BW Holstein animals tended to present a higher expression of all genes studied, with a significant difference for the IL-2 and IFN-γ genes (p < 0.001). For animals with mastitis no significant difference in gene expression was observed between the two breeds. These findings suggest that animals with mastitis develop a preferentially cell-mediated immune response. Further studies including larger samples are necessary to better characterize the gene expression profile in cows with mastitis.

Modelagem da dinâmica de rebanho de bovino de corte por meio de cadeia de Markov / Modeling dynamics of the beef cattle herd through Markov chain

A estrutura etária do rebanho e a estratégia de descarte de matrizes são pontos importantes na avaliação da eficiência do sistema de produção de gado de corte. Neste trabalho foi monitorado o rebanho de cria, cujas matrizes eram mantidas ou descartadas com base em critério técnico, conforme a avaliação do desempenho reprodutivo. Para tanto, foi utilizada a cadeia de Markov com o objetivo de simular a probabilidade de descarte por idade, ao longo da vida, e de calcular a expectativa de vida da matriz no rebanho. Após a introdução da estação de monta, a pressão de descarte foi maior, com aumento da probabilidade de descarte e da diminuição da probabilidade de permanência da matriz no rebanho nas idades mais avançadas. Com a introdução de tecnologias e especialmente da monta controlada, o processo torna-se mais dinâmico com a identificação e descarte de novilhas e matrizes improdutivas, diminuindo a idade média das vacas no rebanho e de descarte das mesmas.

The determination of age structure in a herd and the culling strategy in dams are important points to evaluate efficiency of a beef cattle production system. A breeding herd was monitored, where cows were maintained or discard according to technical criterion. Using the Markov chain the culling probability due to age throughout the life time of the cow was simulated. Life expectancy of the dam in the herd was also calculated. After the breeding season, culling pressure was higher and culling probability increased while permanency probability in the herd for older cows decreased, this made the herd more dynamic.

Mapping of quantitative trait loci and confirmation of the FAT1 region on chromosome 4 in an F2 population of pigs

The objective was to map QTL on porcine chromosome 4 and to associate them with carcass and internal organ traits in an F2 population. The F1 population was produced by outbreed crossing, using two native Brazilian breed Piau boars and 18 commercial sows. A total of 617 F2 animals issued from 11 F1 boars and 54 F1 sows were typed for a total of five microsatellite markers. The data were analyzed by multiple regressions developed for the analysis of crosses between outbred lines, using the QTL Express software. Significant evidence for QTL was found for pig chromosome 4 regarding carcass and internal organ traits. All QTL were detected in the same region of the chromosome, designated FAT1.

Genetic evaluation for persistency of lactation in Holstein cows using a random regression model

A model for analyzing test day records including both fixed and random coefficients was applied to the genetic evaluation of first lactation data for Holstein cows. Data comprising 87045 test-day milk yield records from calving between 1997 and 2001 from Holstein herds in 10 regions of the Brazilian state of Minas Gerais. Six persistency of lactation measures were evaluated using breeding values obtained by random regression analyses. The Wilmink function was used to model the additive genetic and permanent environmental effects. Residual variance was constant throughout lactation. Ranking for animals did not change among criteria for persistency measurements, but ranking changes were observed when the estimated breeding value (EBV) for persistency of lactation was contrasted with those estimated for 305-day milk yield (305MY). The rank correlation estimates for persistency of lactation and 305MY were practically the same for sire and cows, and ranged from -0.45 to 0.69. The EBVs for milk yield during lactation for sires producing daughters with superior 305MY indicate genetic differences between sires regarding their ability to transmit desirable persistency of lactation traits. This suggests that selection for total lactation milk yield does not identify sires or cows that are genetically superior in regard to persistency of lactation. Genetic evaluation for persistency of lactation is important for improving the efficiency of the milk production capacity of Holstein cows.

Association between G316A growth hormone polymorphism and economic traits in pigs

The association between G316A growth hormone polymorphism and quantitative traits was investigated in an F2 population of pigs. Association analyses were performed using a statistical model that included genotype, sex, batch and sex by genotype interaction as fixed effects and sire as random effect. The polymorphism was associated with the number of right teats (p = 0.03), heart weight (p = 0.04), lung weight (p = 0.05), carcass length determined by the Brazilian carcass classification method (p = 0.04), picnic shoulder weight (p = 0.07), jowl weight (p = 0.01), pH 24 h after slaughtering (p = 0.03) and drip loss (p = 0.01). Interaction between genotype and sex was observed for six performance traits. The additive effect was significant (p < 0.10) for heart weight, jowl weight and pH 24 h after slaughtering. The effect of dominance was significant (p < 0.05) for number of right teats, heart weight, carcass length, picnic shoulder weight and pH 24 h after slaughtering. This study shows that the growth hormone gene is a potential candidate for investigating the phenotypic variation of quantitative traits in pigs, and suggests its possible application in breeding programs.

Genetic diversity between herds of Alpine and Saanen dairy goats and the naturalized Brazilian Moxotó breed

Brazilian naturalized goat breeds are adapted to the semiarid conditions prevalent in the Northeast region of the country (which has the largest Brazilian goat heard) and represent an as yet uninvestigated source of genetic diversity. Currently, imported goat breeds are crossed with Brazilian naturalized goat breeds, endangering the genetic potential of the naturalized breeds. We used 11 microsatellite markers to determine the genetic diversity among imported (non-naturalized) dairy Alpine and Saanen goats and naturalized Brazilian Moxotó goats. We genotyped 292 goats from three herds (one private, one from the University of Minas Gerais and the Moxotó conservation herd from Embrapa Caprinos) and found that the general heterozygosity was 0.6952 for Alpine, 0.7043 for Saanen and 0.4984 for Moxotó goats. The number of alleles ranged from 5 (INRA005) to 11 (BM3205), with an average of 7 alleles per locus in the imported breeds and 3.5 alleles per locus in the Moxotó breed. Mean differentiation between populations was higher for herds (F ST S = 0.0768) than for breeds (F ST P = 0.0263), indicating similarity between the imported breeds and the existence of crosses between them. Nei's genetic distance was highest between the Moxotó breed and the imported breeds. These indicate that further studies using these molecular markers would be fruitful.

Association of MYF5 gene allelic variants with production traits in pigs

We studied the phenotypic effects of polymorphisms at the MYF5 gene in a divergent F2 swine population and found that one polymorphism was due to an insertion and another to a deletion. The genotypes of 359 F2 animals were obtained and the Normal/Normal (NN) and Normal/Insertion (NI) genotypes analyzed to determine associations with phenotypic data for performance, carcass and meat quality traits. Significant differences were observed (p < 0.05) between NN and NI animals for drip (NN = 3.14 ± 1.56; NI = 3.69 ± 2.78 percent), cooking (NN = 32.26 ± 2.41; NI = 33.21 ± 2.31 percent) and total loss (NN = 34.16 ± 2.63 and NI = 34.97 ± 2.08 percent). The Deletion marker was not statistically tested. The results indicate that the allelic variant Insertion is associated with a deleterious effect on meat quality traits and should be monitored in marker assisted selection programs.

Estimation of genetic parameters for test-day milk yield in Holstein cows using a random regression model

Test-day milk yield records of 11,023 first-parity Holstein cows were used to estimate genetic parameters for milk yield during different lactation periods. (Co)variance components were estimated using two random regression models, RRM1 and RRM2, and the restricted maximum likelihood method, compared by the likelihood ratio test. Additive genetic variances determined by RRM1 and additive genetic and permanent environmental variances estimated by RRM2 were described, using the Wilmink function. Residual variance was constant throughout lactation for the two models. The heritability estimates obtained by RRM1 (0.34 to 0.56) were higher than those obtained by RRM2 (0.15 to 0.31). Due to the high heritability estimates for milk yield throughout lactation and the negative genetic correlation between test-day yields during different lactation periods, the RRM1 model did not fit the data. Overall, genetic correlations between individual test days tended to decrease at the extremes of the lactation trajectory, showing values close to unity for adjacent test days. The inclusion of random regression coefficients to describe permanent environmental effects led to a more precise estimation of genetic and non-genetic effects that influence milk yield.

Relationship between the Porcine Stress Syndrome gene and pork quality traits of F2 pigs resulting from divergent crosses

The PSS genotypes of 596 F2 pigs produced by initial mating of Brazilian commercial sows and native boars were characterized by PCR-RFLP and the pork quality traits were evaluated. Among the 596 pigs studied, 493 (82.7 percent) were NN and 103 (17.3 percent) were Nn. There were no differences between NN and Nn pigs in the following pork qualities: pHu (5.71 ± 0.16 vs 5.70 ± 0.11), intramuscular fat (1.55 ± 0.64 percent vs 1.65 ± 0.67 percent), shear force (5552 ± 878 g/1.2 cm vs 5507 ± 826 g/1.2 cm), lightness (44.96 ± 2.05 vs 45.01 ± 1.92), redness (0.64 ± 0.60 vs 0.79 ± 0.55), yellowness (6.62 ± 0.56 vs 6.65 ± 0.48), hue (84.28 ± 5.53 vs 83.41 ± 4.85), or chroma (6.68 ± 0.52 vs 6.73 ± 0.52). However, pork from Nn pigs had a significantly (p < 0.05) lower pH45 (6.41 ± 0.27 vs 6.51 ± 0.26) and greater drip (3.92 ± 1.90 percent vs 3.06 ± 1.60 percent), cooking (33.29 ± 2.26 percent vs 32.50 ± 2.54 percent) and total (35.67 ± 2.48 percent vs 34.01 ± 2.58 percent) loss compared to that of NN pigs. These results indicate that, even in divergent crosses, PSS gene carriers produce pork of poorer quality.

Relationship between the Porcine Stress Syndrome gene and carcass and performance traits in F2 pigs resulting from divergent crosses

The PSS genotypes of 596 F2 pigs produced by initial mating of Brazilian native boars commercial sows and were characterized by PCR-RFLP and their carcass and performance traits were evaluated. Among the 596 animals analyzed, 493 (82.72 percent) were characterized as NN and 103 (17.28 percent) as Nn. With respect to carcass traits, Nn animals presented higher (p < 0.05) right half carcass weight, left half carcass weight, loin depth and loin eye area, and lower shoulder backfat thickness, backfat thickness between last and next to last but one lumbar vertebrae and backfat thickness after last rib at 6.5 cm from the midline compared to NN animals. Nn animals also showed (p < 0.05) higher values for most of the cut yields, indicating higher cutting yields for animals carrying the n allele and lower values for bacon depth, confirming lower fat deposition in carcass. In addition, Nn animals presented (p < 0.05) lower values for the performance trait weight at 105 days of age. These results indicate that animals carrying the PSS gene generate leaner carcasses, higher cut yields, and that the effects of the gene can be observed even in divergent crosses.

Genetic trends in the performance and reproductive traits of pigs

The selection and evaluation of breeds and purebred lines to be used as the parental stock is an important step for the success of any animal breeding program. In this study, the feed:gain ratio, backfat thickness corrected for 100 kg, age to 100 kg, average daily gain, and age of sow at first farrowing were used to evaluate the genetic trends for direct and maternal additive genetic values in Large White pigs. The total number of piglets born or born alive and the litter weight at birth were used as indicators of the genetic trends for the direct additive values. The genetic trends were calculated by regression of the average predicted genetic values per year for each trait versus the offspring's year of birth (for performance traits) or versus the dam year of birth (for reproduction traits). The genetic trend estimates for direct effects showed that selection decisions made during the breeding program effectively improved the performance traits. However, for reproductive traits, the regression estimates showed no definite trend. The genetic trends for the maternal effects were generally positive but of low magnitude.

Maternal effects on the genetic evaluation of Tabapuã beef cattle

The aim of this investigation was to study the influence of maternal effects on the genetic evaluation of sire production in Tabapuã beef cattle. Single and multiple trait analyses were done with adjusted animal weights at 120, 240 and 420 days of age. Antagonism was observed between additive direct and maternal genetic effects, with the maternal effect being higher until weaning. The inclusion of maternal effects in the models removed part of the additive variance only in single trait analyses and resulted in smaller means and standard deviations for the sire breeding values. The use of maternal effect associated with single or multiple traits may affect sire ranking. The contradictory results of the single and multiple trait analyses for additive direct and maternal effects indicate that caution is needed when considering recommendations about the importance of maternal effects in Tabapuã beef cattle.