Genetic parameters for cloacal gland, sexual maturity, reproductive organs weight, and body weight in meat-type quail

Selection to increase body weight in poultry can hamper reproduction traits and compromise production efficiency. Thus, attention to reproduction traits is essential to improving the sustainability of breeding programs. Data from a domestic quail breeding program for meat production were used to estimate genetic parameters. We analyzed five traits: 4-week body weight, age at sexual maturity for males and females, cloacal gland area, female, and male reproductive organs weights. A multi-trait mixed model analysis with fixed effects of generation/hatch was performed, assuming environmental covariance equals zero for sex-limited traits. Heritability estimates range from low to moderate for male sexual maturity and cloacal gland area, and high for other traits. Intersexual genetic correlation for age at sexual maturity is positive, which can lead to correlated responses in the other sex. Reproductive organs weights are genetically correlated with body weight, but not significantly between sexes and nor with sexual maturity. Genetic correlations for the cloacal gland area were positive with body weight and negative with age at sexual maturity of males and females, demonstrating a potential use of this trait for selection with favorable outcomes in reproduction. The use of the cloacal gland area can be used in the same way as the scrotal circumference in mammals, improving female reproduction traits by selecting a trait recorded in males.

A systematic review with meta-analysis of heritability estimates for temperament-related traits in beef and dairy cattle populations

Temperament (docility) is a key breeding goal in the cattle industry due to its direct relationship with animal welfare, cattle handler's safety and animal productivity. Over the past six decades, numerous studies have reported heritability estimates for temperament-related traits in cattle populations ranging from low to high values. Therefore, the primary objective of this study was to perform a comprehensive systematic review with meta-analysis to obtain weighted estimates of heritability for temperament-related traits in worldwide cattle populations. After data editing and quality control, 106 studies were included in the systematic review, of which 29.2% and 70.8% reported estimates of heritability for temperament-related traits in dairy and beef cattle populations, respectively. Meta-analyses were performed for 95 heritability estimates using a random model approach. The weighted heritability estimates were as follow: (a) flight score at weaning = 0.23 (95% CI: 0.15-0.32); (b) flight speed at weaning = 0.30 (95% CI: 0.26-0.33); (c) joint analysis of flight speed and flight score at weaning = 0.27 (95% CI: 0.22-0.31); (d) flight speed at yearling = 0.26 (95% CI: 0.21-0.30); (e) joint analysis of flight speed at weaning and yearling = 0.27 (95% CI: 0.24-0.30); (f) movement score = 0.12 (95% CI: 0.08-0.15); (g) crush score at weaning = 0.21 (95% CI: 0.17-0.25); (h) pen score at weaning = 0.27 (95% CI: 0.19-0.34); (i) pen score at yearling = 0.20 (95% CI: 0.17-0.23); (j) joint analysis of pen score at weaning and yearling = 0.22 (95% CI: 0.18-0.26); (k) cow's aggressiveness at calving = 0.10 (95% CI: 0.01-0.19); (l) general temperament = 0.13 (95% CI: 0.06-0.19); (m) milking temperament = 0.16 (95% CI: 0.11-0.21); and (n) joint analysis of general and milking temperament = 0.14 (95% CI: 0.11-0.18). The heterogeneity index ranged from 0% to 77%, and the Q-test was significant (p < 0.05) for four single-trait meta-analyses. In conclusion, temperament is moderately heritable in beef cattle populations, and flight speed at weaning had the highest weighted heritability estimate. Moreover, between-study heterogeneity was low or moderate in beef cattle traits, suggesting reasonable standardization across studies. On the other hand, low-weighted heritability and high between-study heterogeneity were estimated for temperament-related traits in dairy cattle, suggesting that more studies are needed to better understand the genetic inheritance of temperament in dairy cattle populations.

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.

Weighted genomic prediction for growth and carcass-related traits in Nelore cattle

This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass-related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24 480 for marbling (MAR) and 82 981 for subcutaneous backfat thickness (BFT) and rump fat thickness (RFT). The pedigree harbored information from 244 254 animals born between 1977 and 2016, including 6283 sires and 50 742 dams. Animals (n = 7769) were genotyped with the low-density panel (Clarifide® Nelore 3.0), and the genotypes were imputed to a panel containing 735 044 markers. A linear animal model was applied to estimate the genetic parameters and to perform the weighted single-step genome-wide association study (WssGWAS). A total of seven models for genomic prediction were evaluated combining the SNP weights obtained in the iterations of the WssGWAS and the candidate QTL. The heritability estimated for W450 (0.35) was moderate, and for carcass-related traits, the estimates were moderate for REA (0.27), MAR (0.28) and RFT (0.28), and low for BFT (0.18). The prediction accuracy for W450 incorporating reported QTL previously described in the literature along with different SNPs weights was like those described for the default ssGBLUP model. The use of the ssGWAS to weight the SNP effects displayed limited advantages for the REA prediction accuracy. Comparing the ssGBLUP with the BLUP model, a meaningful improvement in the prediction accuracy from 0.09 to 0.63 (700%) was observed for MAR. The highest prediction accuracy was obtained for BFT and RFT in all evaluated models. The application of information obtained from the WssGWAS is an alternative to reduce the genomic prediction dispersion for growth and carcass-related traits, except for MAR. Furthermore, the results obtained herein pointed out that is possible to improve the prediction accuracy and reduce the genomic prediction dispersion for growth and carcass-related traits in young animals.

Meta-analysis of genetic parameters for growth traits in meat, wool and dual-purpose sheep breeds in the world using a random-effects model

BACKGROUND

There is large variation in genetic parameters in literature for growth traits in sheep. Reliable estimation of genetic parameters is required for developing breeding programmes.

OBJECTIVES

The aim of this study was to aggregate results of different studies by meta-analysis to improve reliability of estimated parameters.

METHODS

In the current study, 221 papers that have been published between 1995 and 2021 were reviewed. Using a random-effects model in the Comprehensive Meta-Analysis software, direct and maternal heritabilities, as well as, genetic and phenotypic correlations between growth traits were estimated in meat (M), wool (W) and dual-purpose (D) sheep breeds. The growth traits in this study were birth weight, 3-month weight, 6-month weight, 9-month weight and yearling weight.

RESULTS

The combined direct heritability was the lowest for birth weight (0.190 ± 0.004, 0.198 ± 0.003 and 0.196 ± 0.004 for M, W and D breeds, respectively) and the highest for yearling weight (0.264 ± 0.010, 0.304 ± 0.005 and 0.285 ± 0.020 for M, W and D breeds, respectively). The maternal heritability was the lowest for yearling weight (0.085 ± 0.003, 0.055 ± 0.002 and 0.052 ± 0.005 for M, W and D breeds, respectively) and the highest for 6-month weight (0.240 ± 0.088, 0.164 ± 0.001 and 0.162 ± 0.006 for M, W and D breeds, respectively). The phenotypic and genetic correlations were lower between the weights measured at more distant intervals. The lowest genetic correlation was observed between birth weight and yearling weight (0.290 ± 0.051 for W breeds).

CONCLUSIONS

The small standard errors could indicate that the aggregation of results from different studies improved the reliability of estimated parameters and reduced range of 95% confidence intervals. Hence, the results could be used with greater level of confidence in sheep breeding programmes.

A meta-analysis of genetic parameter estimates for milk and serum minerals in dairy cows

This study aimed to conduct a meta-analysis based on a random-effects model to combine different published heritability estimates and genetic correlations for milk and serum minerals in dairy cows. In total, 59 heritability and 25 genetic correlation estimates from 12 articles published between 2009 and 2021 were used. The heritability estimates for milk macro-minerals were moderate to high and ranged from 0.311 (for Na) to 0.420 (for Ca). On the other hand, milk micro-minerals had lower heritabilities with a range from 0.013 (for Fe) to 0.373 (for Zn). The heritability estimates for serum macro-minerals were generally low and varied from 0.126 (for K) to 0.206 (for Mg). The estimates of genetic correlation between milk macro-minerals varied from -0.024 (between Na and K) to 0.625 (between Mg and P). The genetic correlations of milk Ca and P with milk yield were -0.171 and -0.211, respectively. The estimates of genetic parameters reported in this meta-analysis study are appropriate to utilize in breeding plans when valid estimates are not available for milk minerals in dairy cow populations.

Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers

Simple Summary

Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs.

Abstract

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

Estimation of genetic parameter for feed efficiency and resilience traits in three pig breeds

Recently, automatic feeders have become popular for collecting daily feed intake data in the pig industry, making it possible to evaluate genetic effects on feed efficiency and resilience traits, expressed as day-to-day fluctuations in feeding records. This study aimed to understand the influence of genetic factors on feed efficiency traits, including residual intake and BW gain (RIG), and resilience traits, as well as to compare the differences in genetic parameter estimates among three purebred pig breeds. A total of 6 103 pigs from three breeds (Large White: 1 193 pigs, Landrace: 3 010 pigs, and Duroc: 1 900 pigs) were raised in a specific pathogen-free environment. The growth and feed intake records during the testing period were obtained using automatic feeders, and the average daily gain (ADG) and average feed intake (AFI) were calculated. Feed conversion ratio (FCR), residual feed intake (RFI), residual gain, and RIG were calculated as feed efficiency traits, and the log-transformed variance of deviation for the daily feed intake (LnVar_FI), daily occupation time (LnVar_OC), and the daily number of visits to the feeder (LnVar_VT) was calculated as resilience traits. After estimating the genetic parameters for each breed, a meta-analysis was performed to obtain the weighted mean of heritability estimates (h_m²) and genetic correlation estimates (GC_m) for the three breeds. The h_m² were moderate and ranged from 0.31 to 0.39 for feed efficiency traits and 0.31 to 0.40 for resilience traits, and there were no significant differences in heritability estimates among the three breeds except for AFI, RFI, and RIG. For feed efficiency traits, the FCR and RIG showed favourably moderate GC_m with AFI (0.29 and -0.33, respectively) and ADG (-0.39 and 0.31, respectively). For resilience traits, the LnVar_FI and LnVar_VT showed favourably low to moderate GC_m with FCR (0.33 and 0.28, respectively) and RIG (-0.37 and 0.28, respectively), and there were no genetic relationships of LnVar_OC with FCR and RIG (the absolute value of GC_m was 0.01). There was no significant difference in the genetic correlation estimates among the three breeds for feed efficiency and resilience traits. Our results suggest that feed efficiency and resilience traits were heritable, and resilience traits showed favourable or no genetic correlation with feed efficiency traits. In addition, the influence of genetic factors on feed efficiency and resilience traits could be the same among breeds.

Genetic analysis of growth, visual scores, height, and carcass traits in Nelore cattle

Covariance components were estimated for growth traits (BW, birth weight; WW, weaning weight; YW, yearling weight), visual scores (BQ, breed quality; CS, conformation; MS, muscling; NS, navel; PS, finishing precocity), hip height (HH), and carcass traits (BF, backfat thickness; LMA, longissimus muscle area) measured at yearling. Genetic gains were obtained and validation models on direct and maternal effects for BW and WW were fitted. Genetic correlations of growth traits with CS, PS, MS, and HH ranged from 0.20 ± 0.01 to 0.94 ± 0.01 and were positive and low with NS (0.11 ± 0.01 to 0.20 ± 0.01) and favorable with BQ (0.14 ± 0.02 to 0.37 ± 0.02). Null to moderate genetic correlations were obtained between growth and carcass traits. Genetic gains were positive and significant, except for BW. An increase of 0.76 and 0.72 kg is expected for BW and WW, respectively, per unit increase in estimated breeding value (EBV) for direct effect and an additional 0.74 and 1.43, respectively, kg per unit increase in EBV for the maternal effect. Monitoring genetic gains for HH and NS is relevant to maintain an adequate body size and a navel morphological correction, if necessary. Simultaneous selection for growth, morphological, and carcass traits in line with improve maternal performance is a feasible strategy to increase herd productivity.

Identification of novel candidate genes for age at first calving in Nellore cows using a SNP chip specifically developed for Bos taurus indicus cattle

The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.

Random-effect meta-analysis of genetic parameter estimates for carcass and meat quality traits in beef cattle

Considerable variability of genetic parameter estimates is observed among different studies for the same trait, which is associated with the distinct effects included in the statistical model, population breed, and sample sizes. The random-effect meta-analysis summarizes genetic parameters considering the heterogeneity among studies. Therefore, the aim of this study was to perform a random-effect meta-analysis of heritability and genetic correlation estimates for carcass and meat quality traits in beef cattle. A total of 152 estimates of heritability and 83 genetic correlations for longissimus muscle area (LMA), back fat thickness (BFT), and marbling score (MRB) were used. High heterogeneity among published studies was observed for all traits, indicating the need of a random-effects model to perform the analysis. Estimates of heritability through the meta-analysis using the random-effects model were high (0.30 to 0.34), indicating that fast genetic progress can be obtained for these traits. However, genetic correlations had low magnitude (lower than 0.25), which suggested that all three traits should be included in the selection scheme.

Estimated genetic associations among reproductive traits in Nellore cattle using Bayesian analysis

Scrotal circumference of bulls is correlated with pubertal age of female offspring. Hormonal control of reproductive function is similar in males and females, which may result in genetic correlation among different reproductive traits measured in the two sexes. The estimation of heritability and genetic correlations allows for the computation of direct and correlated genetic gains which are important for predicting of outcomes as a result of genetic-based selection. The aim of this study was to estimate genetic parameters and relative efficiency of indirect selection for age at first calving (AFC), stayability (STAY) and scrotal circumference at 365 days of age (SC365) in Nellore cattle. The STAY variable can be defined as the probability of a cow remain in the herd enough time to raise a certain number of calves that pay for her development and maintenance costs. A bivariate Bayesian analysis was used to estimate variance components using a linear-animal model for SC365 and AFC and threshold-linear model for SC365 and STAY and for AFC and STAY. For STAY, the value of 1 was assigned to cows that calved at least three times by 76 months of age; otherwise, the value 0 was assigned. The posteriori means of heritability estimates were 0.29, 0.08 and 0.09 for SC365, AFC and STAY, respectively. Genetic correlations were favorable from a cow productivity perspective between SC365 and AFC, and SC365 and STAY (-0.45 and 0.12, respectively). Indirect selection approaches were more efficient than direct selection for AFC (ERS = 1.87) when animals were selected for SC365.