ABSTRACT: This study aimed to evaluate the logistic and quadratic response plateau models to describe the growth of Mangalarga Marchador horses to identify the model that best describes growth for the variables height at withers and body length. Data were used from 230 horses aged 6 to 176 months, divided by sex and 16 age classes. All computational work was performed using R statistical software. The logistic model was the best suited to express growth in height at withers and body length of male and female Mangalarga Marchadors aged 6 to 176 months. This allowed creating a table of reference values for these measurements over time based on the confidence interval of the model parameters. Estimates of height at withers obtained by the logistic model ranged from 144 to 154 cm in adult males and from 143 to 151 cm in adult females. For body length, values ranged from 146 to 156 cm in adult males and 143 to 156 cm in adult females. Females achieved stability in both height at withers and body length at earlier ages than did males.
RESUMO: O objetivo deste estudo foi avaliar os modelos logístico e platô de resposta quadrática na descrição do crescimento de equinos da raça Mangalarga Marchador identificando o que melhor descreve o crescimento das variáveis altura de cernelha e comprimento corporal. Foram utilizados dados de 230 equinos de 6 a 176 meses de idade que foram divididos por sexo e em 16 classes de idade. Toda a parte computacional envolvida foi realizada utilizando-se o software estatístico R. O modelo logístico foi o mais indicado para expressar o crescimento em altura na cernelha e comprimento corporal de machos e fêmeas da raça Mangalarga Marchador. Foi criada uma tabela de valores referência para estas medidas ao longo da idade com base no intervalo de confiança dos parâmetros deste modelo. Estimativas das alturas de cernelha adultas obtidas pelo modelo logístico variaram de 144 a 154 cm nos machos e de 143 a 151 cm para fêmeas. Já em comprimento corporal os valores adultos variaram de 146 a 156 cm nos machos e 143 a 156 cm para fêmeas. As fêmeas apresentam maior precocidade do que os machos para atingir a estabilidade em ambas variáveis estudadas.
[This corrects the article DOI: 10.1371/journal.pone.0217283.].
Analysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (pâ«n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg, the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the pâ«n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotypes in validation groups of a cross-validation scheme; and when we selected a larger number of markers (more than 100), the correlations exceeded 0.90, showing the efficiency in identifying relevant SNPs (or segregations) for both GWAS and GWS. In the simulation study, we obtained similar results.
Databases, Nucleic Acid , Genome-Wide Association Study , Genome , Models, Genetic , Polymorphism, Single Nucleotide , Animals , Cattle , Genetic Markers
Knowledge of thermoregulatory responses in taurine cattle contribute to identification of animals most adapted to heat and productive when raised under Brazilian climate. The objectives were to verify the morphological and physiological responses related to adaptation to heat of taurine breeds raised under in Brazilian meteorological conditions in different seasons of the year and day periods, and to detect differences within and between breeds to know breed is most adapted. Measurements were made of 74 young bulls (nâ¯=â¯31 Angus; nâ¯=â¯43 Simmental) for the morphological traits: hair length (HL), number of hairs (NH), and coat thickness (CT); and for the physiological traits: respiratory rate (RR) and hair coat surface temperature (ST). The temperature-humidity index (THI) was calculated. The data were subjected to analyses of variance, cluster analysis, and principal component analysis (PCA). The THI (<74) indicates thermal comfort. In the winter, the HL and CT higher than in the spring season (Pâ¯<â¯0.0001) in both breeds. Angus exhibited higher HL and CT (Pâ¯<â¯0.0001). Within each breed, the animals differed from one another for HL (Pâ¯<â¯0.0005). In the spring, CT was similar between the breeds, differing only in the winter season. Angus had higher values (Pâ¯<â¯0.0005) of RR and lower values (Pâ¯<â¯0.0001) of ST. Both breeds had higher (Pâ¯<â¯0.0001) RR and ST in the afternoon. PCA showed that NH and HL better explained variation in adaptation. In general, the breeds have similar morphological responses in the hottest months, but have different physiological responses; Simmental proves to be more physiologically resistant. The afternoon was more stressful than the morning, even though the animals were in a thermal comfort zone. Measuring traits related to hair coat is sufficient for effective evaluation of adaptation, and the season affects the morphological and physiological traits of taurine cattle raised.
Body Temperature Regulation , Cattle/physiology , Thermotolerance , Animal Fur , Animals , Brazil , Cattle/genetics , Hot Temperature , Male , Respiratory Rate , Tropical Climate
BACKGROUND: Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. RESULTS: Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. CONCLUSIONS: Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.
ABSTRACT: The analysis of the growth and development of various species has been done using the growth curves of the specific animal based on non-linear models. The objective of the current study was to evaluate the fit of the Brody, Gompertz, Logistic and von Bertalanffy models to the cross-sectional data of the live weight of the MangalargaMarchador horses to identify the best model and make accurate predictions regarding the growth and maturity in the males and females of this breed. The study involved recording the weight of 214 horses, of which 94 were males and 120 were non-pregnant females, between 6 and 153 months of age. The parameters of the model were estimated by employing the method of least squares, using the iteratively regularized Gauss-Newton method and the R software package. Comparison of the models was done based on the following criteria: coefficient of determination (R²); Residual Standard Deviation (RSD); corrected Akaike Information Criterion (AICc). The estimated weight of the adult horses by the models ranged between 431kg and 439kg for males and between 416kg and 420kg for females. The growth curves were studied using the cross-sectional data collection method. For males the von Bertalanffymodel was found to be the most effective in expressing growth, while in females the Brody model was more suitable. The MangalargaMarchador females achieve adult body weight earlier than the males.
RESUMO: O estudo sobre curvas de crescimento animal com base em modelos não lineares tem sido utilizado para análise do crescimento e desenvolvimento de diversas espécies. Neste trabalho objetivou-se avaliar o ajuste dos modelos Brody, Gompertz, Logístico e vonBertalanffy a dados transversais de peso vivo de equinos Mangalarga Marchador, a fim de selecionar o melhor modelo e predizer sobre o crescimento e a maturidade de machos e fêmeas desta raça. Foram pesados 214 equinos, sendo 94 machos e 120 fêmeas não gestantes, com idade variando entre seis e 153 meses. A estimação dos parâmetros dos modelos foi realizada pelo método de mínimos quadrados, utilizando o processo iterativo de Gauss-Newton, seguindo rotinas do Software R. Os modelos foram comparados pelos critérios: coeficiente de determinação (R²); desvio padrão residual (DPR); critério de informação de Akaike corrigido (AICc). O peso adulto, estimado pelos modelos, variou entre 431kg e 439kg para os machos e entre 416kg e 420kg para fêmeas. O método transversal de obtenção de dados pode ser aplicado no estudo de curvas de crescimento. O modelo de vonBertalanffy foi o mais eficiente para expressar o crescimento nos machos, enquanto que para as fêmeas, o modelo Brody se mostrou mais apropriado. As fêmeas Mangalarga Marchador são mais precoces que os machos para atingir o peso vivo adulto.
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.
Adipose Tissue , Cattle/genetics , Genome-Wide Association Study , Animals , Polymorphism, Single Nucleotide , Quality Control
