Genetic analysis of growth traits in Polled Nellore cattle raised on pasture in tropical region using Bayesian approaches

Genetic parameters, genetic trends and correlated responses of growth traits considering maternal ability in Nelore cattle

The growth of Nelore cattle was analysed considering the following performance parameters; the effect of the calving order of cows on the phenotypic expression of birth weight (BW), average daily gain from birth to weaning (BWG), and weaning weight (WW), the estimated genetic parameters for the traits, including the covariance components between direct and maternal genetic effects. Genetic trends and correlated responses were also obtained for the studied traits. The calving order of cows, as well as other fixed effects used to obtain the adjusted phenotypic means, were statistically significant (p < 0.001) for studied traits. Direct heritability was estimated at 0.24 ± 0.01 (BW), 0.15 ± 0.01 (BWG), and 0.18 ± 0.01 (WW), while maternal heritability was 0.06 ± 0.01 (BW), 0.12 ± 0.01 (BWG), and 0.11 ± 0.01 (WW). The correlations between direct and maternal effects within the same trait were negligible. Moderate to higher direct genetic correlations (ranging from 0.54 ± 0.04 to 0.98 ± 0.01) and maternal genetic correlations (ranging from 0.34 ± 0.09 to 0.99 ± 0.002) were estimated between the studied traits. Unlike direct genetic effects, there was no significant change in maternal genetic effects over time (p > 0.05). These results indicated the need for revising selection indexes for enhancing maternal ability. Correlated responses were generally lower compared to direct responses, except for BWG. The selection for BWG, considering the maternal genetic effect, would be more efficient to improve maternal ability of the cows for pre-weaning growth in relation to selection for WW. Our results found that direct genetic merit improves pre-weaning weight and this trait can be incorporated into the breeding goal as reflected in the WW.

Estimating genetic parameters of reproductive, carcass, and meat quality traits in Polled Nellore cattle

Considering the economic and commercial efficiency of the beef production chain, the yield and quality of the meat produced must also be included in breeding programs. For the Nellore breed, including the polled herd, these aspects have not been much studied. The aim of this study was to estimate genetic parameters for scrotal circumference adjusted to 365 (SC365) and 450 (SC450) days of age, age at first calving (AFC), accumulated productivity (AP), stayability (STAY), longissimus muscle area (LMA), thickness of subcutaneous fat over the 12th-13th ribs (BF), thickness of subcutaneous fat over the rump (RF), and shear force measured by Warner-Bratzler shear force (WBSF) of polled Nellore cattle. Bayesian analyses were performed by adopting a linear animal model, whereas STAY analyses used the linear threshold model. Heritability estimates were 0.31 (SC365), 0.37 (SC450), 0.16 (AFC), 0.25 (AP), 0.16 (STAY), 0.30 (LMA), 0.13 (BF), 0.24 (RF), and 0.15 (WBSF), indicating moderate response to selection. Genetic and residual correlations between SC365 and SC450 were high (0.91 and 0.74, respectively), as well as the genetic correlations of AP with SC365, SC450, AFC, and STAY (0.61, 0.62, - 0.69, and 0.83, respectively). Genetic and residual correlations of WBSF with reproductive and carcass characteristics exhibited high standard deviations, however favorable. Based on the results, it is expected that in the medium term, animals with greater sexual precocity will also have greater accumulated productivity and longer permanence of females in the herd, along with superior carcass traits. However, due to the low heritabilities and small genetic associations with reproductive traits, fat thickness characteristics (BF and RF) will still require direct selection.

Novel insights into genome-wide associations in Bos indicus reveal genetic linkages between fertility and growth

Bos indicus breed Sahiwal, famous for its optimum performance, has so far been genetically improved for performance traits based on phenotypic records and the genomic knowhow regarding genes, regions and biological processes underlying the complex quantitative traits is lacking. In this context, a Genome-wide Association Study was performed for fertility and growth traits in Sahiwal cattle to shed light on its genomic profile. A total of 46 SNPs were found associated with the traits at genome-wide suggestive threshold of P ≤ 10^-4. USP32, LRPPRC, PLA2G10, RRN3 and ASAP1 were identified as putative candidate genes for body weight at different ages. However, several genes mapped for growth traits like GREB1, PLA2G10, RAD51C, BIRC6, TEX14 and PEBP4 had significant physiological underpinnings in determining fertility of the animals. Moreover, Quantitative trait loci (QTL) identification revealed potential overlaps with the already reported QTLs for both fertility and growth for most of the traits. Further, candidate SNP enrichment analysis revealed an enriched biological process for birth weight with a significant reproductive role. Based on the findings, genetic linkages underlying fertility and growth could be discerned in Sahiwal population and may be utilized for improving fertility traits in future.

Genetic parameters and direct and maternal effects for important traits in late-feathering Qingyuan partridge hens in China

Qingyuan partridge chicken is an important indigenous chicken in China. In its breeding schemes, chickens are usually selected at the age of 105-day-old for five traits, including body weight (BW), shank length (SL), shank girth (SG), comb height (CH) and feather maturity (FM). At present, genetic parameters of the aforementioned traits have still not been studied in Qingyuan partridge chickens. The objectives of this study were the following: (1) to investigate whether the optimal statistical models of these traits need to consider maternal genetic and permanent environmental effects in late-feathering Qingyuan partridge hens, and (2) to estimate genetic parameters for these traits based on the optimal models. The numbers of records for BW, SL, SG, CH and FM were 13,721, 13,671, 13,670, 13,669 and 13,672, respectively. Variance components were estimated using average information-restricted maximum likelihood method, and the optimal model was determined based on Bayesian information criterion. More specifically, the optimal model for BW considered maternal genetic and permanent environmental effects in addition to direct additive genetic effect; SL, SG and FM considered direct and maternal genetic effects; and CH considered direct and maternal genetic effects, and the covariance between them. The direct heritabilities of these traits estimated using the optimal models were 0.21 ± 0.04, 0.30 ± 0.05, 0.40 ± 0.05, 0.59 ± 0.09 and 0.09 ± 0.04, respectively; the maternal heritabilities were 0.01 ± 0.04, 0.05 ± 0.05, 0.04 ± 0.05, 0.09 ± 0.09 and 0.03 ± 0.04, respectively. Maternal genetic effect evidently played an important part in FM and maternal heritability accounted for 30 per cent of total heritability. Furthermore, the direct and maternal genetic effects for CH were estimated to be negatively and moderately correlated (-0.51 ± 0.11). For all traits, neglecting existent maternal effects biased the estimation of direct heritability. Therefore, to implement optimum breeding strategies for improvement of these traits in Qingyuan partridge hens, maternal effects should be taken into consideration.

Bodyweight performance, estimated carcass traits and methane emissions of beef-cattle categories grazing Andropogon gayanus, Melinis minutiflora and Stylosanthes capitata mixed swards and Brachiaria humidicola pasture

Cow–calf operations constitute the main land-use system in the 18 million ha of well drained tropical savannas of Colombia located in the Orinoco basin. There, numerous sex and age animal categories are present, ranging from suckling calves to old cull cows and steers, which in variable proportions are stocked at one animal unit (AU)/5–10 ha, depending on the ranch and distance from markets. In parallel, early-on farm observations showed that when sown pastures are introduced, graziers recur to opportunistic partial fattening of cull animals for a rapid economic return. The paper reports animal weight gains of cull cows, old steers, and young heifers and yearlings over seven consecutive years grazing on a low fertiliser-input well managed Andropogon gayanus-based pasture and four contemporary years on Brachiaria humidicola. The first 2 years involved three stocking rates (SR; 1.38, 1.85 and 2.32 animal units/ha), whereas a single SR of 1.33 animal units/ha was used for the remainder. A large database that included chemical, and in vitro and in vivo digestibility, values for all forages involved, was used as an input to a mathematical model to estimate methane (CH4) emissions. Estimations were compared with weight-based predictions derived from chamber measurements recorded recently in tropical Australia. Faecal mineral concentration varied little (not significantly) among SR and animal categories. Weight gains of old steers were 4–24% larger than those of cull cows, which, in turn, were larger than those of young steers and heifers (P &lt; 0.01). Excepting one year, the performance of cull cows and old steers did not differ between pastures, confirming earlier on-ranch observations of reasonable weight gains of adult cattle on both pastures. The predicted carcass composition of cull cows and old steers did not differ between pastures either. Over the length of the experiment, cull cows emitted significantly less CH4 than did old steers (129 vs 141 g/day) on A. gayanus, while emissions on B. humidicola amounted to 128 and 137 g/day respectively. Despite between-year differences in animal performance, they are indicative of well managed pasture sustainability. They also show some of the trade-offs involved in the use of contrasting animal categories and pastures in terms of weight performance and predicted carcass composition and CH4 production. The authors expect that the present results will contribute to a rational, science-based discussion of the role of beef systems vis-à-vis environment in a region with limited production alternatives.

Genetic trends and trade-offs between growth and reproductive traits in a Nellore herd

The knowledge of genetic trends and trade-offs between growth and reproductive traits might be useful to understand the evolution of these traits in livestock and natural populations of animals. We estimated the genetic trends and trade-offs between pre-weaning growth and calving intervals of Nellore animals from a commercial farm. Two-trait animal models were used to estimate covariance components and breeding values (EBV) for direct and maternal genetic effects of pre-weaning growth and direct genetic effects of calving intervals. Regression analyses were performed to examine the relationship between direct and maternal EBV of pre-weaning growth and direct EBV of calving intervals (dependent variables) and the coefficient of generation of each animal (independent variable). We also performed regression analyses to examine the relationship between direct EBV of calving intervals (dependent variables) and direct and maternal EBV of pre-weaning growth (independent variables). The genetic trends for direct and maternal genetic effect for pre-weaning growth were significant and presented genetic evolution in the studied Nellore herd. The genetic trends for the reproductive traits were also significant but indicated genetic changes in an unfavorable way. The genetic correlations between direct effects of pre-weaning growth and calving intervals traits and the genetic correlations between maternal effects of pre-weaning growth traits and direct effects of calving interval traits were not different from zero. The presence of trade-offs between the direct effects of growth and reproductive traits were confirmed through regression from direct EBV of calving intervals over EBV of pre-weaning growth traits. In addition, regression analyses showed that selection to increase pre-weaning growth also increased calving intervals. Our results showed that pre-weaning growth and calving intervals are increasing over generations and that trade-offs occurred between those traits in the studied Nellore herd.

Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle

This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection.

Multi-Trait GWAS and New Candidate Genes Annotation for Growth Curve Parameters in Brahman Cattle

Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates.

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.

Genetic analysis of the temperament of Nellore cattle using linear and threshold models

Temperament is an important trait for the management and welfare of animals and for reducing accidents involving people who work with cattle. The present study aimed to estimate the genetic parameters related to the temperament score (T) and weaning weight (WW) of Nellore cattle, reared in a beef cattle breeding program in Brazil. Data were analyzed using two different two-trait statistical models, both considering WW and T: (1) a linear-linear model in which variance components (VCs) were estimated using restricted maximum likelihood; and (2) a linear-threshold model in which VCs were estimated via Bayesian inference. WW was included in the analyses of T to minimize any possible effects of sequential selection and to allow for estimation of the genetic correlation between these two traits. The heritability estimates for T were 0.21 ± 0.003 (model 1) and 0.26 (model 2, with a 95% credibility interval (95% CI) of 0.21 to 0.32). The estimated genetic correlations between WW and T were of a moderate magnitude (-0.33 ± 0.01 (model 1) and -0.34 (95% CI: -0.40, -0.28, model 2). The genetic correlations between the estimated breeding values (EBVs) obtained for the animals based on the two models were high (>0.92). The use of different models had little influence on the classification of animals based on EBVs or the accuracy of the EBVs.