Genetic and environmental heterogeneity of residual variance of weight traits in Nellore beef cattle

Background

Many studies have provided evidence of the existence of genetic heterogeneity of environmental variance, suggesting that it could be exploited to improve robustness and uniformity of livestock by selection. However, little is known about the perspectives of such a selection strategy in beef cattle.

Methods

A two-step approach was applied to study the genetic heterogeneity of residual variance of weight gain from birth to weaning and long-yearling weight in a Nellore beef cattle population. First, an animal model was fitted to the data and second, the influence of additive and environmental effects on the residual variance of these traits was investigated with different models, in which the log squared estimated residuals for each phenotypic record were analyzed using the restricted maximum likelihood method. Monte Carlo simulation was performed to assess the reliability of variance component estimates from the second step and the accuracy of estimated breeding values for residual variation.

Results

The results suggest that both genetic and environmental factors have an effect on the residual variance of weight gain from birth to weaning and long-yearling in Nellore beef cattle and that uniformity of these traits could be improved by selecting for lower residual variance, when considering a large amount of information to predict genetic merit for this criterion. Simulations suggested that using the two-step approach would lead to biased estimates of variance components, such that more adequate methods are needed to study the genetic heterogeneity of residual variance in beef cattle.     

A definition of unknown parent groups based on bull usage patterns across herds

In genetic evaluations, the definition of unknown parent groups (UPG) is usually based on time periods, selection path and flows of foreign founders. The definition of UPG may be more complex for populations presenting genetic heterogeneity due to both, large national expansion and coexistence of artificial insemination (AI) and natural service (NS). A UPG definition method accounting for beef bull flows was proposed and applied to the French Charolais cattle population. It assumed that, at a given time period, unknown parents belonged to the same UPG when their progeny were bred in herds that used bulls with similar origins (birth region and reproduction way). Thus, the birth period, region and AI rate of a herd were pointed out to be the three criteria reflecting genetic disparities at the national level in a beef cattle population. To deal with regional genetic disparities, 14 regions were identified using a factorial approach combining principal component analysis and Ward clustering. The selection nucleus of the French cattle population was dispersed over three main breeding areas. Flows of NS bulls were mainly carried out within each breeding area. On the contrary, the use and the selection of AI bulls were based on a national pool of candidates. Within a time period, herds of different regions were clustered together when they used bulls coming from the same origin and with an estimated difference of genetic level lower than 20% of genetic standard deviation (σg) for calf muscle and skeleton scores (SS) at weaning. This led to the definition of 16 UPG of sires, which were validated as robust and relevant in a sire model, meaning numerically stable and corresponding to distinct genetic subpopulations. The UPG genetic levels were estimated for muscle and SS under sire and animal models. Whatever the trait, differences between bull UPG estimates within a time period could reach 0.5 σg across regions. For a given time period, bull UPG estimates for muscle and SS were generally larger by 0.30 to 0.75 σg than those of cows. Including genetic groups in the evaluation model increased the estimated genetic trends by 20% to 30%. It also provoked re-ranking in favor of bulls and cows without pedigree.     

A rare case of heteropaternal twin calves after natural mating in Brazil

Twin birth is a complex condition observed in most livestock animals, when the female gives birth to two or more offspring, generally out of the same mating. In cattle, it is a rare condition (3 to 5%) and depends on the genetic background and environmental factors. Twin birth is a result of multiple ovulations, being more common in dairy rather than in beef cattle. Calves could be monozygous or dizygous, with the same or of different sexes. When twins are born with different sexes, a sexual condition called Freemartinism occurs in between 90 to 97% of pregnancies, causing infertility in the female calf. Knowing that the twin rate is rare in commercial beef cattle, here we present an even rarer case of twin birth from two different sires after natural mating, also called heteropaternal superfecundation.     

Effects of birth-rearing type on weaning weights in meat sheep are systematically associated with differences in mean performance among flocks

Background

Adjustment of body weights for systematic environmental effects such as dam age and litter size is essential for accurate prediction of breeding values in meat sheep and often accomplished by pre-adjusting records using simple multiplicative adjustment factors, which are derived as ratios of least-squares means of weights of lambs in target and reference classes. However, increasing use of multibreed genetic evaluations that incorporate data from both purebred and commercial flocks has generated concerns regarding the ability of simple additive or multiplicative adjustment factors to properly correct for environmental effects in flocks that differ widely in mean performance. Thus, consistency of adjustment factors across flocks and systematic effects of the level of flock performance on these factors were evaluated using data from the US National Sheep Improvement Program.

Methods

We used birth and weaning weights of lambs from 29 flocks that had at least 500 records per flock and represented several terminal-sire sheep breeds. Effects of lamb sex, dam age class and litter size on birth weights, and of dam age class and combined effects of type of birth and rearing on weaning weights were evaluated. Interactions between these effects and flock were assessed. Bias associated with different adjustment protocols was evaluated for high- and low-performance flocks.

Results

Effects of litter size and differences between yearling and adult dams varied (P < 0.001) among flocks. For weaning weights, additive adjustment factors were not associated with the level of flock performance, but multiplicative adjustment factors were strongly and inversely related to flock means for weaning weights (W). Flock-specific adjustment factors (F = αW^β) reduced bias in adjusted weaning weights associated with differences in flock performance. By contrast, simple multiplicative adjustment factors were appropriate to adjust birth weights.

Conclusions

Differences in weaning weights among single, twin, and triplet lambs were inversely related to the level of flock performance. Use of simple multiplicative adjustment factors led to adjustment bias when applied across flocks with large differences in mean performance. This bias was reduced by using additive adjustment factors or multiplicative factors that were derived as simple exponential functions of flock means for weaning weight.     

Genotype by production environment interaction for birth and weaning weights in a population of composite beef cattle

The objectives of the present study were: (1) to evaluate the importance of genotype×production environment interaction for the genetic evaluation of birth weight (BW) and weaning weight (WW) in a population of composite beef cattle in Brazil, and (2) to investigate the importance of sire×contemporary group interaction (S×CG) to model G×E and improve the accuracy of prediction in routine genetic evaluations of this population. Analyses were performed with one, two (favorable and unfavorable) or three (favorable, intermediate, unfavorable) different definitions of production environments. Thus, BW and WW records of animals in a favorable environment were assigned to either trait 1, in an intermediate environment to trait 2 or in an unfavorable environment to trait 3. The (co)variance components were estimated using Gibbs sampling in single-, bi- or three-trait animal models according to the definition of number of production environments. In general, the estimates of genetic parameters for BW and WW were similar between environments. The additive genetic correlations between production environments were close to unity for BW; however, when examining the highest posterior density intervals, the correlation between favorable and unfavorable environments reached a value of only 0.70, a fact that may lead to changes in the ranking of sires across environments. The posterior mean genetic correlation between direct effects was 0.63 in favorable and unfavorable environments for WW. When S×CG was included in two- or three-trait analyses, all direct genetic correlations were close to unity, suggesting that there was no evidence of a genotype×production environment interaction. Furthermore, the model including S×CG contributed to prevent overestimation of the accuracy of breeding values of sires, provided a lower error of prediction for both direct and maternal breeding values, lower squared bias, residual variance and deviance information criterion than the model omitting S×CG. Thus, the model that included S×CG can therefore be considered the best model on the basis of these criteria. The genotype×production environment interaction should not be neglected in the genetic evaluation of BW and WW in the present population of beef cattle. The inclusion of S×CG in the model is a feasible and plausible alternative to model the effects of G×E in the genetic evaluations.     

Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than −5°C (TCL5), −15°C (TCL15) and −25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class; however, this heritability remained consistent across the cold load of TCL25 class. In contrast, the maternal heritability of BW was constant with cold load increase in all TCL classes, although a slight increase of maternal heritability was observed for TCL5 and TCL15. The direct and maternal genetic correlation for BW and maternal genetic correlation for WW across different cold loads between all TCL classes were high (r > 0.99), whereas the lowest direct genetic correlations observed for WW were 0.88 for TCL5 and 0.85 for TCL15. The Spearman rank correlation between the estimated breeding value of top bulls (n = 79) using univariate and reaction norm models across TCL classes showed some re-ranking in direct and maternal effects for both BW and WW particularly for TCL5 and TCL15. In general, cold stress did not have a big impact on direct and maternal genetic effects of BW and WW.     

Estimation of genetic parameters and variance components for growth traits in Romosinuano cattle in the Colombian humid tropics

(Co)variance components and genetic parameters were estimated for body weights of a Romosinuano herd located in Sinú Valley, Cordoba, Colombia. Restricted maximum likelihood methods were used with a univariate animal model for birth weight, weaning weight (270 days), 16-month weight (480 days), weaning daily gain, and post-weaning daily gain. Models included random animal direct and maternal genetic effects, maternal permanent environmental effect (c2), and sex-year-month of birth and age of dam, as fixed effects. Estimates of direct effect for birth weight, weaning weight, 480-day weight, weaning daily gain, and post-weaning daily gain were: 0.25 +/- 0.0001, 0.34 +/- 0.063, 0.33 +/- 0.066, 0.32 +/- 0.062, and 0.17 +/- 0.052, respectively. Estimates of direct maternal genetic effects were low and ranged from 0.06 +/- 0.003 for birth weight to 0.20 +/- 0.054 for weaning daily gain. The genetic correlations between direct and maternal genetic effects were negative and low for 480-day weight (-0.05 +/- 0.219) and showed values of -0.37 +/- 0.007, -0.34 +/- 0.133, -0.33 +/- 0.135, and -0.38 +/- 0.232 for birth, weaning weight, weaning, and post-weaning daily gain, respectively. Permanent environmental maternal effects were not significant; the highest values were found for weaning weight, and weaning daily gain (0.086 +/- 0.031 and 0.078 +/- 0.031, respectively). We conclude that direct and maternal effects should be included in a selection program for all of these traits, and also that selection of weaning weights would be the most productive way to improve performance in Romosinuano cattle.     

Prenatal and pre-weaning growth and nutrition of cattle: long-term consequences for beef production

Severe, chronic growth retardation of cattle early in life reduces growth potential, resulting in smaller animals at any given age. Capacity for long-term compensatory growth diminishes as the age of onset of nutritional restriction resulting in prolonged growth retardation declines. Hence, more extreme intrauterine growth retardation can result in slower growth throughout postnatal life. However, within the limits of beef production systems, neither severely restricted growth in utero nor from birth to weaning influences efficiency of nutrient utilisation later in life. Retail yield from cattle severely restricted in growth during pregnancy or from birth to weaning is reduced compared with cattle well grown early in life, when compared at the same age later in life. However, retail yield and carcass composition of low- and high-birth-weight calves are similar at the same carcass weight. At equivalent carcass weights, cattle grown slowly from birth to weaning have carcasses of similar or leaner composition than those grown rapidly. However, if high energy, concentrate feed is provided following severe growth restriction from birth to weaning, then at equivalent weights post-weaning the slowly-grown, small weaners may be fatter than their well-grown counterparts. Restricted prenatal and pre-weaning nutrition and growth do not adversely affect measures of beef quality. Similarly, bovine myofibre characteristics are little affected in the long term by growth in utero or from birth to weaning. Interactions were not evident between prenatal and pre-weaning growth for subsequent growth, efficiency, carcass, yield and beef-quality characteristics, within our pasture-based production systems. Furthermore, interactions between genotype and nutrition early in life, studied using offspring of Piedmontese and Wagyu sired cattle, were not evident for any growth, efficiency, carcass, yield and beef-quality parameters. We propose that within pasture-based production systems for beef cattle, the plasticity of the carcass tissues, particularly of muscle, allows animals that are growth-retarded early in life to attain normal composition at equivalent weights in the long term, albeit at older ages. However, the quality of nutrition during recovery from early life growth retardation may be important in determining the subsequent composition of young, light-weight cattle relative to their heavier counterparts. Finally, it should be emphasised that long-term consequences of more specific and/or acute environmental influences during specific stages of embryonic, foetal and neonatal calf development remain to be determined. This need for further research extends to consequences of nutrition and growth early in life for reproductive capacity.     

Genetic correlations between mature cow weight and productive and reproductive traits in Nellore cattle

We investigated genetic associations between mature cow weight (MW) and weaning weight (WW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to yearling (GWY), weaning hip height (WHH), yearling hip height (YHH), scrotal circumference (SC), and age at first calving (AFC). Data from 127,104 Nellore animals born between 1993 and 2006, belonging to Agropecuária Jacarezinho Ltda., were analyzed. (Co)variance components were obtained by the restricted maximum likelihood method, applying an animal model in a multi-traits analysis. The model included direct genetic and residual effects as random effects, the fixed effects of contemporary group, and the linear and quadratic effects of animal age at recording (except for AFC, GBW, and GWY) and age of cow at calving as covariates (except for MW). The numbers of days from birth to weaning and from weaning to yearling were included as covariates for GBW and GWY, respectively. Estimated direct heritabilities were 0.43 ± 0.02 (MW), 0.33 ± 0.01 (WW), 0.36 ± 0.01 (YW), 0.28 ± 0.02 (GBW), 0.31 ± 0.01 (GWY), 0.44 ± 0.02 (WHH), 0.48 ± 0.02 (YHH), 0.44 ± 0.01 (SC), and 0.16 ± 0.03 (AFC). Genetic correlations between MW and productive traits were positive and of medium to high magnitude (ranging from 0.47 ± 0.03 to 0.71 ± 0.01). A positive and low genetic correlation was observed between MW and SC (0.24 ± 0.04). A negative genetic correlation (-0.19 ± 0.03) was estimated between MW and AFC. Selection to increase weight or weight gains at any age, as well as hip height, will change MW in the same direction. Selection for higher SC may lead to a long-term increase in MW. The AFC can be included in selection indices to improve the reproductive performance of beef cattle without significant changes in MW.     

Heritability estimates and adjustment factors for the effects of bull age and age of dam on yearling testicular size in breeds of bulls

Scrotal circumference, testicular length and body weight were measured in 3,090 yearling bulls of 12 breed groups finishing growth performance tests during a 5 yr period. Breeds were Limousin, Hereford, Charolais, Angus, Red Poll, Simmental, Pinzgauer, Brown Swiss, Gelbvieh and three crossbred breed groups. All bulls were born during a 60-d calving season starting in late March of each year and were subjected to similar management and environmental influences during the study. The bulls were the progeny of 307 sires averaging approximately 26 sires per breed group and 10 sons per sire. Breed group, sire within breed group, year and age-of-dam effects were important (P<0.01) for all testicular traits at both a constant age (354 d) and constant body weight (418 kg). Paternal half-sib estimates of heritability were 0.41 +/- 0.06 for ageconstant scrotal circumference, 0.34 +/- 0.06 for testicular length and 0.37 +/- 0.06 for calculated paired testicular volume, respectively. Age-constant genetic correlations between yearling body weight and testicular traits were small, indicating that testicular growth and body growth rates are largely independent, regardless of breed. Testicular size of bulls from 2-yr-old dams was smaller than that of bulls from older dams. Most of these age-of-dam effects on testicular size were removed when testicular size was adjusted for the effects of body weight, suggesting that age-of-dam effects on testicular size are primarily the result of age-of-dam effects on body weight. Age adjustment factors for yearling scrotal circumference did not differ (P>0.20) among breed groups and averaged 0.032 cm per day of age. Adjustment factors for age of dam were +1.3, +0.8, +0.4, and +0.0 cm for sons of 2-, 3-, 4- and 5-yr-old dams, respectively.     

Genetic relationship between weaning weight and milk yield in Nguni cattle

A study was conducted to estimate the genetic relationship between weaning weight and milk yield in Nguni cattle. Milk yield data (n=125) were collected from 116 Nguni cows from Mara Research Station located in Limpopo Province and Loskop South Farm located in Mpumalanga Province using the weigh-suckle-weigh technique. Weaning weight data (n=19 065) were obtained from stud Nguni cattle from 146 herds distributed throughout South Africa. Estimates of (co)variance components for milk yield and weaning weight were calculated using PEST and VCE softwares. The average weaning weight, age of the calf at weaning and 24-h milk yield was 158.94 kg, 210 days and 5.25 kg/day, respectively. Heritability estimates for milk yield, direct and maternal weaning weight were 0.22±0.238, 0.47±0.039 and 0.25±0.029, respectively. Estimates of genetic correlations for milk yield and maternal weaning weight, milk yield and direct weaning weight, direct and maternal weaning weight were 0.97±0.063, −0.71±0.416 and −0.56±0.247, respectively. The results indicate that maternal weaning weight is genetically highly predictive of milk yield in Nguni cattle. Maternal breeding values for weaning weight could therefore be used as a selection criterion to improve milk yield in Nguni cattle.     

Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.     

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

We quantified the potential increase in accuracy of expected breeding value for weights of Nelore cattle, from birth to mature age, using multi-trait and random regression models on Legendre polynomials and B-spline functions. A total of 87,712 weight records from 8144 females were used, recorded every three months from birth to mature age from the Nelore Brazil Program. For random regression analyses, all female weight records from birth to eight years of age (data set I) were considered. From this general data set, a subset was created (data set II), which included only nine weight records: at birth, weaning, 365 and 550 days of age, and 2, 3, 4, 5, and 6 years of age. Data set II was analyzed using random regression and multi-trait models. The model of analysis included the contemporary group as fixed effects and age of dam as a linear and quadratic covariable. In the random regression analyses, average growth trends were modeled using a cubic regression on orthogonal polynomials of age. Residual variances were modeled by a step function with five classes. Legendre polynomials of fourth and sixth order were utilized to model the direct genetic and animal permanent environmental effects, respectively, while third-order Legendre polynomials were considered for maternal genetic and maternal permanent environmental effects. Quadratic polynomials were applied to model all random effects in random regression models on B-spline functions. Direct genetic and animal permanent environmental effects were modeled using three segments or five coefficients, and genetic maternal and maternal permanent environmental effects were modeled with one segment or three coefficients in the random regression models on B-spline functions. For both data sets (I and II), animals ranked differently according to expected breeding value obtained by random regression or multi-trait models. With random regression models, the highest gains in accuracy were obtained at ages with a low number of weight records. The results indicate that random regression models provide more accurate expected breeding values than the traditionally finite multi-trait models. Thus, higher genetic responses are expected for beef cattle growth traits by replacing a multi-trait model with random regression models for genetic evaluation. B-spline functions could be applied as an alternative to Legendre polynomials to model covariance functions for weights from birth to mature age.     

Body condition score of Nellore beef cows: a heritable measure to improve the selection of reproductive and maternal traits

Despite the economic importance of beef cattle production in Brazil, female reproductive performance, which is strongly associated with production efficiency, is not included in the selection index of most breeding programmes due to low heritability and difficulty in measure. The body condition score (BCS) could be used as an indicator of these traits. However, so far little is known about the feasibility of using BCS as a selection tool for reproductive performance in beef cattle. In this study, we investigated the sources of variation in the BCS of Nellore beef cows, quantified its association with reproductive and maternal traits and estimated its heritability. BCS was analysed using a logistic model that included the following effects: contemporary group at weaning, cow weight and hip height, calving order, reconception together with the weight and scores of conformation and early finishing assigned to calves at weaning. In the genetic analysis, variance components of BCS were estimated through Bayesian inference by fitting an animal model that also included the aforementioned effects. The results showed that BCS was significantly associated with all of the reproductive and maternal variables analysed. The estimated posterior mean of heritability of BCS was 0.24 (highest posterior density interval at 95%: 0.093 to 0.385), indicating an involvement of additive gene action in its determination. The present findings show that BCS can be used as a selection criterion for Nellore females.     

Sources of sire-specific genetic variance for birth and weaning weight in Bruna dels Pirineus beef calves

This research investigated two sources of sire-specific genetic effects on the birth weight (BWT) and weaning weight (WWT) of Bruna dels Pirineus beef calves. More specifically, we focused on the influence of genes located in the non-autosomal region of the Y chromosome and the contribution of paternal imprinting. Our analyses were performed on 8130 BWT and 1245 WWT records from 12 and 2 purebred herds, respectively, they being collected between years 1986 and 2010. All animals included in the study were registered in the Yield Recording Scheme of the Bruna dels Pirineus breed. Both BWT and WWT were analyzed using a univariate linear animal model, and the relevance of paternal imprinting and Y chromosome-linked effects were checked by the deviance information criterion (DIC). In addition to sire-specific and direct genetic effects, our model accounted for random permanent effects (dam and herd-year-season) and three systematic sources of variation, that is, sex of the calf (male or female), age of the dam at calving (six levels) and birth type (single or twin). Both weight traits evidenced remarkable effects from the Y chromosome, whereas paternal imprinting was only revealed in WWT. Note that differences in DIC between the preferred model and the remaining ones exceed 39 000 and 2 800 000 DIC units for BWT and WWT, respectively. It is important to highlight that Y chromosome accounted for ∼2% and ∼6% of the total phenotypic variance for BWT and WWT, respectively, and paternal imprinting accounted for ∼13% of the phenotypic variance for WWT. These results revealed two relevant sources of sire-specific genetic variability with potential contributions to the current breeding scheme of the Bruna dels Pirineus beef cattle breed; moreover, these sire-specific effects could be included in other beef cattle breeding programs or, at least, they must be considered and appropriately analyzed.     

Non-linear recursive models for growth traits in the Pirenaica beef cattle breed

One of the main goals of selection schemes in beef cattle populations is to increase carcass weight at slaughter. Live weights at different growth stages are frequently used as selection criteria under the hypothesis that they usually have a high and positive genetic correlation with weight at slaughter. However, the presence of compensatory growth may bias the prediction ability of early weights for selection purposes. Recursive models may represent an interesting alternative for understanding the genetic and phenotypic relationship between weight traits during growth. For the purposes of this study, the analysis was performed for three different set of data from the Pirenaica beef cattle breed: weight at 120 days (W120) and at 210 days (W210); W120 and carcass weight at slaughter at 365 days (CW365); W210 and CW365. The number of records for each analysis was 8592, 4648 and 3234, respectively. A pedigree composed of 56323 individuals was also included. The statistical model comprised sex, year-season of birth, herd and slaughterhouse, plus a non-linear recursive dependency between traits. The dependency was modeled as a polynomial up to the 4th degree and models were compared using a Logarithm of Conditional Predictive Ordinates. The results of model comparison suggest that the best models were the 3rd degree polynomial for W120-W210 and W120-CW365 and the 2nd degree polynomial for W210-CW365. The posterior mean estimates for heritabilities ranged between 0.29 and 0.44 and the posterior mean estimates of the genetic correlations were null or very low, indicating that the relationship between traits is fully captured by the recursive dependency. The results imply that the predictive ability of the performance of future growth is low if it is only based on records of early weights. The usefulness of slaughterhouse records in beef cattle breeding evaluation is confirmed.     

Colonization of Beef Cattle by Shiga Toxin-Producing Escherichia coli during the First Year of Life: A Cohort Study

Each year Shiga toxin-producing Escherichia coli (STEC) are responsible for 2.8 million acute illnesses around the world and > 250,000 cases in the US. Lowering the prevalence of this pathogen in animal reservoirs has the potential to reduce STEC outbreaks in humans by controlling its entrance into the food chain. However, factors that modulate the colonization and persistence of STEC in beef cattle remain largely unidentified. This study evaluated if animal physiological factors such as age, breed, sex, and weight gain influenced the shedding of STEC in beef cattle. A cohort of beef calves (n = 260) from a multi-breed beef calf population was sampled every three months after birth to measure prevalence and concentration of STEC during the first year of life. Metagenomic analysis was also used to understand the association between the STEC colonization and the composition of gut microflora. This study identified that beef calves were more likely to shed STEC during the first 6 months and that STEC shedding decreased as the animal matured. Animal breed group, sex of the calf, and average weight gain were not significantly associated with STEC colonization. The metagenomic analysis revealed for the first time that STEC colonization was correlated with a lower diversity of gut microflora, which increases as the cattle matured. Given these findings, intervention strategies that segregate younger animals, more likely to be colonized by STEC from older animals that are ready to be harvested, could be investigated as a method to reduce zoonotic transmission of STEC from cattle to humans.     

Importance of adaptation and genotype × environment interactions in tropical beef breeding systems

This paper examines the relative importance of productive and adaptive traits in beef breeding systems based on Bos taurus and tropically adapted breeds across temperate and (sub)tropical environments. In the (sub)tropics, differences that exist between breeds in temperate environments are masked by the effects of environmental stressors. Hence in tropical environments, breeds are best categorised into breed types to compare their performance across environments. Because of the presence of environmental stressors, there are more sources of genetic variation in tropical breeding programmes. It is therefore necessary to examine the genetic basis of productive and adaptive traits for breeding programmes in those environments. This paper reviews the heritabilities and genetic relationships between economically important productive and adaptive traits relevant to (sub)tropical breeding programmes. It is concluded that it is possible to simultaneously genetically improve productive and adaptive traits in tropically adapted breeds of beef cattle grazed in tropical environments without serious detrimental consequences for either adaptation or production. However, breed-specific parameters are required for genetic evaluations. The paper also reviews the magnitude of genotype × environment (G × E) interactions impacting on production and adaptation of cattle, where 'genotype' is defined as breed (within a crossbreeding system), sire within breed (in a within-breed selection programme) or associations between economically important traits and single nucleotide polymorphisms (SNPs - within a marker-assisted selection programme). It is concluded that re-ranking of breeds across environments is best managed by the use of the breed type(s) best suited to the particular production environment. Re-ranking of sires across environments is apparent in poorly adapted breed types across extreme tropical and temperate environments or where breeding animals are selected in a temperate environment for use in the (sub)tropics. However, G × E interactions are unlikely to be of major importance in tropically adapted beef cattle grazed in either temperate or (sub)tropical environments, although sex × environment interactions may provide new opportunities for differentially selecting to simultaneously improve steer performance in benign environments and female performance in harsher environments. Early evidence suggests that re-ranking of SNPs occurs across temperate and tropical environments, although their magnitude is still to be confirmed in well-designed experiments. The major limitation to genetic improvement of beef cattle over the next decade is likely to be a deficiency of large numbers of accurately recorded phenotypes for most productive and adaptive traits and, in particular, for difficult-to-measure adaptive traits such as resistance to disease and environmental stressors.     

Genetics of efficient feed utilization and national cattle evaluation: a review

Selection for the wide range of traits for which most beef breed associations calculate expected progeny differences focus on increasing the outputs of the production system, thereby increasing the genetic potential of cattle for reproductive rates, weights, growth rates, and end-product yield. Feed costs, however, represent a large proportion of the variable cost of beef production and genetic improvement programs for reducing input costs should include traits related to feed utilization. Feed conversion ratio, defined as feed inputs per unit output, is a traditional measure of efficiency that has significant phenotypic and genetic correlations with feed intake, growth rate, and mature size. One limitation is that favorable decreases in feed to gain either directly or due to correlated response to increasing growth rate do not necessarily relate to improvement in efficiency of feed utilization. Residual feed intake is defined as the difference between actual feed intake and that predicted on the basis of requirements for maintenance of body weight and production. Phenotypic independence of residual feed intake with growth rate, body weight, and other energy depots can be forced. However, genetic associations may remain when a phenotypic prediction approach is used. Heritability estimates for phenotypic residual feed intake have been moderate, ranging from 0.26 to 0.43. Genetic correlations of phenotypic residual feed intake with feed intake have been large and positive, suggesting that improvement would produce a correlated response of decreased feed intake. Residual feed intake estimated by genetic regression results in a zero genetic correlation with its predictors, which reduces concerns over long-term antagonistic responses such as increased mature size and maintenance requirements. The genetic regression approach requires knowledge of genetic covariances of feed intake with weight and production traits. Cost of individual feed intake measurements on potential replacements must be considered in implementation of national cattle evaluations for efficiency of feed utilization. These costs need to be compared to expected, and, if possible, realized rates of genetic change and the associated reduction in feed input requirements.