Estimation of genetic parameters for reproductive indices in sheep.

This study aimed to estimate two reproductive efficiency indices in sheep based on the ratio between litter weight (at birth and weaning) and dam weight, as well as their genetic parameters. Phenotypic and pedigree data comprising the period from 1990 to 2018 were obtained from the Santa Inês sheep database of Embrapa Tabuleiros Costeiros. For estimation of the genetic parameters of the indices, a repeatability model was applied in single- and two-trait analyses by a Bayesian approach. The mean reproductive efficiency index was 0.069 ± 0.0163 and 0.43 ± 0.0955 at birth and weaning, respectively. These values indicate that, on average, ewes give birth to 69 g of lamb per kg body weight and wean 430 g of lamb per kg body weight. Described here for the first time, the heritability estimate obtained in single- and two-trait analyses was 0.24 for the index based on birth weights and ranged from 0.13 to 0.15 for the index based on weaning weights. The estimates indicate the possibility of genetic gain by selection and are similar to those reported for reproductive traits in sheep, representing an option for selection criterion. The genetic correlation between indices was positive and moderate (0.26). The repeatability estimates were high (0.49 for the birth weight index and 0.71 for the weaning weight index). These values indicate good prediction of future performance with few observations. The weaning weight index might be a good culling criterion of females.

A comprehensive characterization of longevity and culling reasons in Canadian Holstein cattle based on various systematic factors.

The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in Canadian Holstein cows. After data editing and quality control, records from 3,096,872 cows culled from 9,683 herds spread across Canada were used for the analyses covering the periods from 1996 to 2020. Reproductive issues were the main culling reason accounting for 23.02%, followed by milk production (20.82%), health (20.39%), conformation problems (13.69%), economic factors (13.10%), accidents (5.67%), age-related causes (1.67%), and workability (1.63%). Nearly fifty-eight percent of cows were culled after 47 months of age. The observed frequencies of culling due to economic factors were lower than expected from 1996 to 2014 and higher than expected between 2015 and 2020. Reproduction issues had the highest culling frequencies during fall (24.54%), winter (24.02%), and spring (22.51%), while health issues were the most frequent (22.51%) culling reason in the summer season. Health issues (25.50%) and milk production (27.71%) were the most frequent culling reasons in the provinces of Quebec and Ontario, respectively. Reproductive issues showed the highest frequency across climates based on the Köppen climate classification, except for Csb (Dry-summer subtropical or Mediterranean climate) and Bsk (Middle latitude steppe climate), which correspond to small regions in Canada, where production was the most frequent culling reason (29.42% and 21.56%, respectively). Reproductive and milk performance issues were the two main culling reasons in most ecozones, except in Boreal Shield and Atlantic Marine, where health issues had the highest frequencies (25.12 and 23.75%, respectively). These results will contribute to improving management practices and selective decisions to reduce involuntary culling of Holstein cows.

Selection effect for growth traits on energy requirements in beef Nelore steers.

Growth data of 77,372 Nelore steers were used to estimate the selection effect on energy requirements considering two beef production systems: cow-calf and slaughter cycles. All the animals had measures from 120 days to 7 years old. The parameters necessary to evaluate the selection effect on energy requirements were obtained by random regression analysis using Legendre polynomials. The models included additive direct and maternal effects, and animal and maternal permanent environmental effects as random terms. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of animal age (cubic regression) were considered random covariables. The coefficients from the model M3353_5 were used to calculate the genetic gains necessary to predict the increase in phenotypes. The selection was simulated for body weight (BW) and weight gain (WG) at different ages and energy requirements were calculated using NRC equations. The cost of feed was calculated for a cow-calf and slaughter cycle of production considering a system of Brachiaria decumbens pasture without supplementation. In slaughter system, the selection for weight of 365 days of age is the best option. In cow-calf systems, the selection W120 is the best choice.

Genomic Regions Associated with the Position and Number of Hair Whorls in Horses.

The position and number of hair whorls have been associated with the behavior, temperament, and laterality of horses. The easy observation of whorls assists in the prediction of reactivity, and thus permits the development of better measures of handling, training, mounting, and riding horses. However, little is known about the genetics involved in the formation of hair whorls. Therefore, the aim of this study was to perform a genome-wide association analysis to identify chromosome regions and candidate genes associated with hair whorl traits. Data from 342 Quarter Horses genotyped for approximately 53,000 SNPs were used in an association study using a single-step procedure. The following traits were analyzed: vertical position of hair whorl on the head, number of whorls on the head, and number of whorls on the left and right sides of the neck. The traits had between one and three genomic windows associated. Each of them explained at least 4% of the additive variance. The windows accounted for 20-80% of additive variance for each trait analyzed. Many of the prospected genes are related to hair follicle growth. Some of these genes exert a pleiotropic effect on neurological and behavioral traits. This is the first indication of biological and physiological activity that might explain the association of hair whorls and temperament.

Influence of coat color on genetic parameter estimates in horses.

The aim of this study was to verify the effect of the inclusion of coat color on the genetic parameter estimation for linear measurements in Campolina horses. Two models (1 and 2) were applied. For model 1, coat color effect was not included as variable of the contemporary group formation; in model 2, it was included. Model 2 presented the best fitting with a Deviance Information Criterion (DIC) of -979,459.020 compared with -1,818,458.572 DIC from model 1. The average of heritability estimates ranged from low to high magnitude (0.15 to 0.53) for model 1 and from moderate to high magnitude for model 2 (0.21 to 0.47). The estimated values varied according to the analyses (models 1 and 2). The highest heritability was found for withers height (0.52), croup height (0.53), and back height (0.51). The genetic correlations ranged from values of moderate to high magnitude for models 1 (0.23 to 0.98) and 2 (0.29 to 0.99), respectively. The finding that genetic variance differed among models 1 and 2 may indicate that genotypes react differently to different coat colors, a fact implying the existence of interaction between these traits and the effect under study. The coat color influence might be explained as a pleiotropic effect of the genes that cause this phenotypic variation and also influence morphometric measures. The inclusion of the coat color effect better estimated the additive genetic variance of morphometric traits in horses. As a consequence, the genetic parameters were also more accurately estimated when it is included in the evaluation model.

Water buffaloes (Bubalus bubalis) only have A2A2 genotype for beta-casein.

Beta-casein is a milk protein that has two variants: A1 and A2. Some individuals have difficulties digesting beta-casein A1, which can cause gastrointestinal disorders. A2 milk has emerged as an alternative. This milk only contains beta-casein A2 and is obtained from females carrying the A2A2 genotype of the gene. In cattle, allele and genotype frequencies vary according to breed and marker-assisted selection is performed to obtain A2A2 animals and the consequent production of A2 milk that is easier to digest. This study aimed to evaluate the alleles of beta-casein in buffaloes. A total of 657 buffaloes of four different breeds were genotyped and all animals carried the A2A2 genotype, i.e., allele A1 does not exist in the buffalo species. Thus, all milk products of buffaloes are naturally A2. This result adds value to products derived from buffalo milk.

The effect of mitochondrial DNA polymorphisms on cattle reproduction.

The aim of this study was to identify SNPs located in mitochondrial DNA that are associated with reproductive traits in beef cows. A total of 1999 Nelore females genotyped with the high-density Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) were used to study the association of mitochondrial DNA variants with reproductive traits using a single-step procedure. In a preliminary analysis, the present results indicate a small participation of the mitogenome in the expression of reproductive traits in beef cattle. However, possible difficulties related to the biological characteristics of mitochondrial DNA and its inheritance, genotyping, and annotation of the phenotypes studied may also explain the results.

Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome.

Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome-wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above-mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes.

Sensitivity of breeding values of meat quail as a result of tryptophan: lysine ratios in the diet / Sensibilidade de valores genéticos de codornas de corte em função das relações triptofano: lisina da dieta

We aimed to evaluate the random regression models that promote the best fit of residual variance predicting the breeding values of quail body weights and the sensitivity of its breeding values to the variations of different tryptophan:lysine ratios in the diets via reaction norms. A total of 1112 meat quails from LF1 and LF2 lines with 35 days of age were evaluated. During the period of 1 to 21 days of age, birds were fed with different tryptophan:lysine ratios (0.17, 0.20, 0.23, 0.26 and 0.29%) containing 2900 kcal ME/kg and 26.10% crude protein, followed by basal diet provided up to 35 days. The best model fit for residual variance was evaluated comparing heterogeneity (2, 3 and 4 classes) and homogeneity (1 class), including sex as fixed effect and the additive genetic effect as random. The second order Legendre polynomial was used to analyze the genotype x environment interaction using reaction norms. The model considering two classes of residual variance was the one that promoted the best fit of the data, being adopted to predict the breeding values. Thus, we observed changes in the sensitivity of the breeding values, characterized by the rearrangement of the breeding values, according to the different ratios of amino acids, suggesting the genotype x environment interaction.(AU)

Objetivou-se avaliar o modelo de regressão aleatória que promove o melhor ajuste da variância residual para a predição dos valores genéticos dos pesos corporais de codornas de corte e a sensibilidade dos seus valores genéticos às variações de diferentes relações triptofano:lisina. Foram avaliadas 1112 codornas de corte das linhagens LF1 e LF2, do nascimento aos 35 dias de idade. No período de 1 a 21 dias de idade as aves receberam alimentação com dietas de diferentes relações triptofano:lisina (0,17, 0,20, 0,23, 0,26 e 0,29%), contendo 2900 kcal EM/kg e 26,10% de proteína bruta, seguido pelo fornecimento de ração basal até os 35 dias. Foi avaliado o ajuste da variância residual comparando a homogeneidade (1 classe) e a heterogeneidade (2, 3 e 4 classes) incluindo o sexo como efeito fixo e o efeito genético aditivo como aleatório. O polinômio de Legendre de segunda ordem foi utilizado para a análise da interação genótipo x ambiente utilizando normas de reação. O modelo que considerou duas classes de variância residual foi o que promoveu o melhor ajuste dos dados e foi adotado para predição dos valores genéticos. Desta forma, foi observada alteração na sensibilidade dos valores genéticos, caracterizados pelo reordenamento dos valores genéticos, em função das diferentes relações estudadas, indicando a presença de interação genótipo x ambiente.(AU)

Sensitivity of breeding values of meat quail as a result of tryptophan: lysine ratios in the diet / Sensibilidade de valores genéticos de codornas de corte em função das relações triptofano: lisina da dieta

We aimed to evaluate the random regression models that promote the best fit of residual variance predicting the breeding values of quail body weights and the sensitivity of its breeding values to the variations of different tryptophan:lysine ratios in the diets via reaction norms. A total of 1112 meat quails from LF1 and LF2 lines with 35 days of age were evaluated. During the period of 1 to 21 days of age, birds were fed with different tryptophan:lysine ratios (0.17, 0.20, 0.23, 0.26 and 0.29%) containing 2900 kcal ME/kg and 26.10% crude protein, followed by basal diet provided up to 35 days. The best model fit for residual variance was evaluated comparing heterogeneity (2, 3 and 4 classes) and homogeneity (1 class), including sex as fixed effect and the additive genetic effect as random. The second order Legendre polynomial was used to analyze the genotype x environment interaction using reaction norms. The model considering two classes of residual variance was the one that promoted the best fit of the data, being adopted to predict the breeding values. Thus, we observed changes in the sensitivity of the breeding values, characterized by the rearrangement of the breeding values, according to the different ratios of amino acids, suggesting the genotype x environment interaction.

Objetivou-se avaliar o modelo de regressão aleatória que promove o melhor ajuste da variância residual para a predição dos valores genéticos dos pesos corporais de codornas de corte e a sensibilidade dos seus valores genéticos às variações de diferentes relações triptofano:lisina. Foram avaliadas 1112 codornas de corte das linhagens LF1 e LF2, do nascimento aos 35 dias de idade. No período de 1 a 21 dias de idade as aves receberam alimentação com dietas de diferentes relações triptofano:lisina (0,17, 0,20, 0,23, 0,26 e 0,29%), contendo 2900 kcal EM/kg e 26,10% de proteína bruta, seguido pelo fornecimento de ração basal até os 35 dias. Foi avaliado o ajuste da variância residual comparando a homogeneidade (1 classe) e a heterogeneidade (2, 3 e 4 classes) incluindo o sexo como efeito fixo e o efeito genético aditivo como aleatório. O polinômio de Legendre de segunda ordem foi utilizado para a análise da interação genótipo x ambiente utilizando normas de reação. O modelo que considerou duas classes de variância residual foi o que promoveu o melhor ajuste dos dados e foi adotado para predição dos valores genéticos. Desta forma, foi observada alteração na sensibilidade dos valores genéticos, caracterizados pelo reordenamento dos valores genéticos, em função das diferentes relações estudadas, indicando a presença de interação genótipo x ambiente.

Association of Apolipoprotein B and Adiponectin Receptor 1 Genes with Carcass, Bone Integrity and Performance Traits in a Paternal Broiler Line.

Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers.

Parâmetros genéticos da curva de produção de ovos de uma linha fêmea de frango de corte / Evaluation of posture rating curves of a female line of broilers

Objetivou-se com este trabalho estimar os parâmetros genéticos e fenotípicos dos parâmetros da curva de produção de ovos, pelo o modelo de polinômios segmentados ("x p"- idade das aves ao pico de postura, "P"- nível de produção no pico, "s" - taxa de decréscimo semanal na produção de ovos após o pico e "t" - tempo entre o início da postura e o pico de produção de ovos). Foram utilizados dados da produção de ovos semanal da 25ª até 64ª semanas de idade, provenientes de 2.398 matrizes de uma linhagem de frangos de corte. A estimação dos componentes de covariâncias, herdabilidade e correlações para esses parâmetros da curva de postura foram obtidas por máxima verossimilhança restrita. As tendências genéticas foram estimadas com as médias dos valores genéticos dos parâmetros da curva em função do ano de nascimento das matrizes. As médias das herdabilidades foram de baixa a média magnitudes, 0,25 (x p), 0,18 (P), 0,17 (s) e 0,10 (t). As correlações genéticas entre o parâmetro t e os demais parâmetros da curva foram positivas, variando de 0,21 até 1,00, sendo menor entre t e s e maior entre os parâmetros x p e t. Entre os parâmetros x p e P, a correlação também foi positiva, de magnitude média (0,39). As correlações foram negativas entre os parâmetros s e x p e s e P, apresentando-se menor entre s e x p (-0,17) e maior entre s e P (-0,91). As tendências genéticas encontradas para os parâmetros indicaram uma redução no tempo entre o início e pico de produção e idade ao pico de postura. O nível de produção apresentou uma queda no valor genético ao longo do período avaliado. Pode-se observar possível ganho genético para os parâmetros da curva de produção de ovos, contudo, deve-se atentar para as correlações genéticas positivas entre os parâmetro x p e P, o que pode levar a um aumento do nível de produção e a um aumento na idade ao pico de produção. O mesmo caso acontece com os parâmetros x p e s, indicando que as aves mais precoces ao pico poderão apresentar menor persistência.

The objective of this study was to estimate genetic parameters and phenotypic parameters of egg production curve, using the segmented polynomial model( " x p " - the peak age of the birds in attitude, "P" - at peak production level, "s" - rate of decline in weekly egg production after peak, and "t" - time between the onset of lay and peak egg production). We used data from the weekly egg production from 25 to 64 weeks of age from 2,398 arrays of a lineage of broilers chickens. Estimation of covariance components, heritability and correlations for these parameters curve posture were obtained by restricted maximum likelihood. Genetic trends were estimated with the average breeding values the of parameters of the curve as a function of birth year of the arrays. The mean heritabilities were low to medium magnitude, 0.25 (x p), 0.18 (P), 0.17 (s) e 0.10 (t). Genetic correlations among the parameter "t" and the other parameters of the curve were positive ranging from 0.21 to 1.00, being lower between "t" and "s", and higher between the parameters x p and t. Between the parameters x p and P the correlation was also positive, of an average magnitude (0.39). Correlations were negative between parameters "s" and "x p", and "s" and "P", presenting itself lower between "s" and "x p" (-0.17) and higher between "s" and "P" (-0.91). The genetic trends found for the parameters of the model indicated a reduction in time between the production's onset and peak, and age at production's peak. The level of production showed a decline in breeding value over the period evaluated. It can be observed a potential genetic gain for the egg's production parameters' curve; however, it must be paid special attention to the positive genetic correlations between the parameter x p and P. What can lead to an increase in the level of production and may lead to an increase in age at peak production. The same applies to the parameters x p indicating that birds with earlier peaks may present lower persistence.