Estimates of genetic parameters for growth, reproductive, and carcass traits in Nelore cattle using the single step genomic BLUP procedure

Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle

BACKGROUND

The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC.

RESULTS

Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism.

CONCLUSIONS

GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions.

Strategies for genomic predictions of an indicine multi-breed population using single-step GBLUP

Brazilian livestock breeding programmes strive to enhance the genetics of beef cattle, with a strong emphasis on the Nellore breed, which has an extensive database and has achieved significant genetic progress in the last years. There are other indicine breeds that are economically important in Brazil; however, these breeds have more modest sets of phenotypes, pedigree and genotypes, slowing down their genetic progress as their predictions are less accurate. Combining several breeds in a multi-breed evaluation could help enhance predictions for those breeds with less information available. This study aimed to evaluate the feasibility of multi-breed, single-step genomic best linear unbiased predictor genomic evaluations for Nellore, Brahman, Guzerat and Tabapua. Multi-breed evaluations were contrasted to the single-breed ones. Data were sourced from the National Association of Breeders and Researchers of Brazil and included pedigree (4,207,516), phenotypic (328,748), and genomic (63,492) information across all breeds. Phenotypes were available for adjusted weight at 210 and 450 days of age, and scrotal circumference at 365 days of age. Various scenarios were evaluated to ensure pedigree and genomic information compatibility when combining different breeds, including metafounders (MF) or building the genomic relationship matrix with breed-specific allele frequencies. Scenarios were compared using the linear regression method for bias, dispersion and accuracy. The results showed that using multi-breed evaluations significantly improved accuracy, especially for smaller breeds like Guzerat and Tabapua. The validation statistics indicated that the MF approach provided accurate predictions, albeit with some bias. While single-breed evaluations tended to have lower accuracy, merging all breeds in multi-breed evaluations increased accuracy and reduced dispersion. This study demonstrates that multi-breed genomic evaluations are proper for indicine beef cattle breeds. The MF approach may be particularly beneficial for less-represented breeds, addressing limitations related to small reference populations and incompatibilities between G and A22. By leveraging genomic information across breeds, breeders and producers can make more informed selection decisions, ultimately improving genetic gain in these cattle populations.

Estimation of genetic parameters for maintenance energy requirements and residual feed intake in Nellore cattle

We estimated heritabilities and genetic and phenotypic correlation estimates for maintenance energy requirements (NEmR), residual feed intake (RFI), growth, carcass and reproductive indicator traits, using data from 41 feed efficiency trials in Brazil, comprising 4381 males and females. Continuous traits were analysed using a linear animal model and threshold traits were analysed using a threshold animal model. The heritability estimates were low for RFI (0.190) and NEmR (0.193); other heritabilities were mainly moderate (growth and carcass traits) or high (sexual precocity traits). The genetic correlation of RFI with NEmR was high (0.701). The genetic correlations of NEmR were low with carcass and reproductive traits, and moderate with growth traits. Thus, selection to improve weaning weight and female sexual precocity indicator traits would not affect maintenance energy requirement. Genetic selection to reduce maintenance energy requirements is feasible and would also reduce DMI and RFI. Selection to improve RFI can be used to identify animals with lower maintenance energy requirements. Long-term selection to reduce RFI and NEmR would have favourable effects on yearling weight, carcass muscle indicator traits and female sexual precocity. Genetic (co)variance component estimates for NEmR, in conjunction with economic values of selection criteria, may be used to develop novel approaches for genetic selection to improve efficiency of beef production.

B-spline polynomials models for analyzing growth patterns of Guzerat young bulls in field performance tests

OBJECTIVE

The aim of this study was to identify suitable polynomial regression for modeling the average growth trajectory and to estimate the relative development of the rib eye area, scrotal circumference, and morphometric measurements of Guzerat young bulls.

METHODS

A total of 45 recently weaned males, aged 325.8±28.0 days and weighing 219.9±38.05 kg, were evaluated. The animals were kept on Brachiaria brizantha pastures, received multiple supplementations, and were managed under uniform conditions for 294 days, with evaluations conducted every 56 days. The average growth trajectory was adjusted using ordinary polynomials, Legendre polynomials, and quadratic B-splines. The coefficient of determination, mean absolute deviation, mean square error, the value of the restricted likelihood function, Akaike information criteria, and consistent Akaike information criteria were applied to assess the quality of the fits. For the study of allometric growth, the power model was applied.

RESULTS

Ordinary polynomial and Legendre polynomial models of the fifth order provided the best fits. B-splines yielded the best fits in comparing models with the same number of parameters. Based on the restricted likelihood function, Akaike's information criterion, and consistent Akaike's information criterion, the B-splines model with six intervals described the growth trajectory of evaluated animals more smoothly and consistently. In the study of allometric growth, the evaluated traits exhibited negative heterogeneity (b<1) relative to the animals' weight (p<0.01), indicating the precocity of Guzerat cattle for weight gain on pasture.

CONCLUSION

Complementary studies of growth trajectory and allometry can help identify when an animal's weight changes and thus assist in decision-making regarding management practices, nutritional requirements, and genetic selection strategies to optimize growth and animal performance.

Genetic parameters for visual scores, growth and carcass traits in Nellore Cattle

Growth and carcass traits are essential selection criteria for beef cattle breeding programs. However, it is necessary to combine these measurements with body composition traits to meet the demand of the consumer market. This study aimed to estimate the genetic parameters for visual scores, growth (pre and post-weaning weights), and carcass (rib eye area (REA), back and rump fat thickness) traits in Nellore cattle using Bayesian inference. Data from 12,060 animals belonging to the HoRa Hofig Ramos herd were used. Morphological traits were evaluated by the MERCOS methodology. The heritability estimates obtained ranged from low to high magnitude, from 0.15 to 0.28 for visual scores, 0.13 to 0.44 for growth, and from 0.42 to 0.46 for carcass traits. Genetic correlations between visual scores and growth traits were generally of moderate to high magnitudes, however, visual scores showed low correlations with carcass traits, except between sacral bone and structure and REA. Selection for visual score traits can lead to favorable responses in body weight and vice versa, but the same is not true for carcass traits. Morphological categorical traits can be used as complementary tools that add value to selection.

Identification of genetic variants affecting reproduction traits in Vrindavani cattle

Genome-wide association studies (GWAS) are one of the best ways to look into the connection between single-nucleotide polymorphisms (SNPs) and the phenotypic performance. This study aimed to identify the genetic variants that significantly affect the important reproduction traits in Vrindavani cattle using genome-wide SNP chip array data. In this study, 96 randomly chosen Vrindavani cows were genotyped using the Illumina Bovine50K BeadChip platform. A linear regression model of the genome-wide association study was fitted in the PLINK program between genome-wide SNP markers and reproduction traits, including age at first calving (AFC), inter-calving period (ICP), dry days (DD), and service period (SP) across the first three lactations. Information on different QTLs and genes, overlapping or adjacent to genomic coordinates of significant SNPs, was also mined from relevant databases in order to identify the biological pathways associated with reproductive traits in bovine. The Bonferroni correction resulted in total 39 SNP markers present on different chromosomes being identified that significantly affected the variation in AFC (6 SNPs), ICP (7 SNPs), DD (9 SNPs), and SP (17 SNPs). Novel potential candidate genes associated with reproductive traits that were identified using the GWAS methodology included UMPS, ITGB5, ADAM2, UPK1B, TEX55, bta-mir-708, TMPO, TDRD5, MAPRE2, PTER, AP3B1, DPP8, PLAT, TXN2, NDUFAF1, TGFA, DTNA, RSU1, KCNQ1, ADAM32, and CHST8. The significant SNPs and genes associated with the reproductive traits and the enriched genes may be exploited as candidate biomarkers in animal improvement programs, especially for improved reproduction performance in bovines.

Genetic correlation estimates between calving ease in primiparous cows and economically important traits in Nellore cattle

This study aimed to estimate (co)variance components and genetic parameters for calving ease (CE) and their genetic correlations with growth, reproductive, carcass, and feed efficiency traits in Nellore cattle. Phenotypes for CE are scored in two categories: normal calving and assisted calving. The traits considered were probability of precocious calving, age at first calving, stayability, adjusted scrotal circumference at 365 days of age, accumulated cow productivity, age at puberty of males, gestation length, birth weight, adjusted weights at 210 and 450 days of age, adult cow weight, frame score, hip height, rib eye area, subcutaneous backfat thickness, rump fat thickness, intramuscular fat percentage, residual feed intake and dry matter intake. The estimation of genetic parameters was performed using a two-trait threshold-linear animal model, except for CE, stayability, and probability of precocious calving, which were evaluated through a two-trait threshold animal model. The direct (0.27) and maternal (0.19) heritability estimates for CE in heifers primiparous Nellore indicated that selecting for this trait is feasible. The selection to improve the female sexual precocity should consider CE during the selection and mating decisions to reduce calving problems. Genetic correlation estimates between CE and BW suggest that selecting low birth weight to reduce calving problems is not an appropriate strategy to improve calving ease in heifers Nellore. Therefore, adopting a multi-trait selection model with CE and BW in the Nellore breed would reduce calving difficulties, particularly in sexually precocious heifers, without impairing the growth, reproductive, feed efficiency conversion, and carcass indicator traits.

Genetic associations between stayability to consecutive calvings and traits of economic interest in taurine and zebu breeds

Stayability (STAY) is a way to evaluate the productive longevity of females. Measuring the STAY at each cow calving allows earlier indicators of longevity to be obtained. Our objective with this study was to verify the association between STAY and consecutive calvings and traits potentially used as selection criteria in beef cattle, such as age at first calving (AFC), days to calving (DC), weaning weight (WW), and yearling weight (YW). Data from the Nelore, Angus/Brangus, and Hereford/Braford breeds were used. The estimation of variance components and subsequent prediction of breeding values were performed for all traits. The estimated breeding values (EBV) were used to analyse the association between STAY and the other traits. The Pearson's correlation estimated between the EBV for the intercept coefficient for STAY to consecutive calvings and those of AFC, DC, WW (direct and maternal effects), and YW was favourable and of low magnitude (<0.25) depending on the breed studied. The influence of the genetic merit of AFC on the chance of selection for STAY was favourable and relevant regardless of the intensity of selection and breed. DC and WW (maternal effect) traits were favourably influenced by the chance of selection for STAY, irrespective of breed. The WW (direct effect) did not affect the chance of selection for STAY for the Nelore and Hereford/Braford breeds and negatively influenced, but to a small extent, the Angus/Brangus breed. For YW, an increase in genetic merit affected the chances of selection for STAY, depending on the breed and selection intensity evaluated. The influence of the genetic merit for AFC, DC, and WW (maternal effect) on the chance of selection for STAY to consecutive calvings was favourable and relevant regardless of the selection intensity scenario evaluated. The WW (direct effect) did not influence the chance of selection for STAY. For the scenario with high selection intensity, the selection for YW favourably influenced the chance of selection for STAY in Angus/Brangus and Hereford/Braford breeds but not in Nelore.

Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle

The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.

Effect of food supplementation on in vitro embryo production and growth performance in prepubertal Nelore heifers

In vitro embryos production from prepubertal heifers can help contribute to breeding programs; however, strategies are necessary to increase their embryo production. The aim of this study was to investigate the effects of two nutritional plans on oocyte recovery, embryo production and growth performance of prepubertal Nelore heifers. Thirty-four Nelore heifers with age of 6.5 months were divided into two feeding treatments (NP1 and NP2). The NP1 diets served as the control and NP2 diets were formulated to contain an average of 1.22-fold more energy than NP1. After 3 months of supplementation, the animals underwent follicular aspiration (ovum pick-up, OPU) every 21 d for 3 months and embryos were produced in vitro. Wither height, chest depth, body weight and subcutaneous fat of animals were measured. The number of retrieved and viable oocytes per OPU were 1.49-fold and 1.42-fold greater in NP2 heifers (p = 0.018 and p = 0.049, respectively) than those in NP1 heifers. Heifers administered NP2 produced 29.7% blastocysts, a percentage higher than NP1 animals that produced 24.40% embryos (p < 0.05). Consequently, females in the NP2 treatment showed improved body development. These results indicate a positive effect of a higher energy diet on assisted reproduction and body development in prepubertal heifers.

Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle

BACKGROUND

Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models.

RESULTS

Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability's of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation.

CONCLUSIONS

This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.

Genetic association between feed efficiency, growth, scrotal circumference, and carcass traits in Guzerat cattle

The objective of this study was to estimate the genetic parameters for feed efficiency-related traits and their genetic correlations with growth, male fertility, and carcass traits using multi-trait analysis in Guzerat cattle. Further, it aimed to predict the direct and correlated responses for feed efficiency traits when selection was applied for growth, male fertility, and carcass traits. The evaluated traits were adjusted weight at 120 (W120), 210 (W210), 365 (W365), and 450 days of age (W450), adjusted scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), scrotal circumference, ribeye area (REA), backfat thickness (BFT), rump fat thickness (RFT), residual feed intake (RFI), and dry matter intake (DMI). The genetic parameters were obtained by the restricted maximum likelihood method (REML), using an animal model in multi-trait analyses. The heritability estimates for W120, W210, W365, W450, SC365, and SC450 varied from low to high (0.17 to 0.39). The carcass traits, REA, BFT, and RFT, displayed low to moderate heritability estimates, 0.27, 0.10, and 0.31, respectively. The heritability estimates for RFI (0.15) and DMI (0.23) were low and moderate, respectively. The RFI showed low genetic correlations with growth traits, ranging from - 0.07 to 0.22, from 0.03 to 0.05 for scrotal circumference, and from - 0.35 to 0.16 for carcass, except for DMI, which ranged from 0.42 to 0.46. The RFI and DMI presented enough additive genetic variability to be used as selection criteria in Guzerat breed genetic improvement program. Additionally, the response to selection for RFI would be higher when selection is performed directly for this trait. The selection for residual feed intake would not promote unfavorable correlated responses for scrotal circumference, carcass (yield and finish), and growth traits. Therefore, the selection for more efficient animals would not compromise the productive, reproductive, and carcass performance, contributing to reduce the production costs, increasing the profitability and sustainability of beef cattle production in tropical areas.

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.

Genomic prediction ability and genetic parameters for residual feed intake calculated using different approaches and their associations with growth, reproductive, and carcass traits in Nellore cattle

This study aimed to estimate prediction ability and genetic parameters for residual feed intake (RFI) calculated using a regression equation for each test (RFI_test) and for the whole population (RFI_pop) in Nellore beef cattle. It also aimed to evaluate the correlations between RFI_pop and RFI_test with growth, reproductive, and carcass traits. Genotypic and phenotypic records from 8354 animals were used. An analysis of variance (ANOVA) was performed to verify the adequacy of the regression equations applied to estimate the RFI_test and RFI_pop. The (co)variance components were obtained using the single-step genomic best linear unbiased prediction under single and two-trait animal model analyses. The genetic and phenotypic correlations between RFI_test and RFI_pop with dry matter intake, frame, growth, reproduction, and carcass-related traits were evaluated. The prediction ability and bias were estimated to compare the RFI_test and RFI_pop genomic breeding values (GEBV). The RFI_pop ANOVA showed a higher significance level (p < 0.0001) than did the RFI_test for the fixed effects. The RFI_pop displayed higher additive genetic variance estimated than the RFI_test, although the RFI_pop and RFI_test displayed similar heritabilities. Overall, the RFI_test showed higher residual correlations with growth, reproductive, and carcass traits, while the RFI_pop displayed higher genetic correlations with such traits. The GEBV for the RFI_test was slightly biased than GEBV RFI_pop. The approach to calculate the RFI influenced the decomposition and estimation of variance components and genomic prediction for RFI. The application of RFI_pop would be more appropriate for genetic evaluation purpose to adjust or correct for non-genetic effects and to decrease the prediction bias for RFI.

Genomic prediction in Brazilian Guzerá cattle: application of a single-step approach to productive and reproductive traits

This study aimed to investigate the feasibility of genomic prediction for productive and reproductive traits in Guzerá cattle using single-step genomic best linear unbiased prediction (ssGBLUP). Evaluations included the 305-day cumulative yields (first lactation, in kg) of milk, lactose, protein, fat, and total solids; adjusted body weight (kg) at the ages of 450, 365, and 210 days; and age at first calving (in days), from a database containing 197,283 measurements from Guzerá males and females born between 1954 and 2018. The pedigree included 433,823 animals spanning up to 14 overlapping generations. A total of 1618 animals were genotyped. The analyses were performed using ssGBLUP and traditional BLUP methods. Predictive ability and bias were accessed using cross-validation: predictive ability was similar between the methods and ranged from 0.27 to 0.47 for the genomic-based model and from 0.30 to 0.45 for the pedigree-based model; the bias was also similar between the methods, ranging from 0.88 to 1.35 in the genomic-based model and from 0.96 to 1.41 in the pedigree-based model. The individual accuracies of breeding values were evidently increased in the genomic evaluation, with values ranging from 0.41 to 0.56 in the genomic-based model and from 0.26 to 0.54 in the pedigree-based model. Even based on a small number of genotyped animals and a small database for some traits, the results suggest that ssGBLUP is feasible and may be applied to national genetic evaluation of the breed to increase the accuracy of breeding values without greatly impacting predictive ability and bias.

Heritability and genetic correlations between marbling in longissimus dorsi muscle and conventional economic traits in Nellore beef cattle

In Nellore beef cattle, studies addressing genetic correlations between ultrasound marbling content and other economically important traits are still incipient. Therefore, this work aimed to estimate heritability and genetic correlations between ultrasound marbling content in the longissimus dorsi muscle (MARB) and growth, reproductive, feed efficiency, and carcass-related traits in a Nellore beef cattle population from Brazil. Phenotypic records of 614,395 Nellore animals were used and included adjusted weight at 210 (W210) and 450 (W450) days of age, adult cow weight (AW), early heifer pregnancy (EH), stayability (STAY), adjusted scrotal circumference at 365 days of age (SC365), ribeye area (REA), subcutaneous backfat thickness (BF), rump fat thickness (RF), and marbling (MARB). The genetic parameters for all traits but EH and STAY were estimated considering a linear animal model, whereas for those two nonlinear traits, a threshold animal model was used. The direct and correlated response to selection for MARB versus the other traits, and the relative efficiency of selection, were also calculated. The heritability estimate for MARB was 0.31 and for the other conventional evaluated traits was low to moderate, with values ranging from 0.14 to 0.41. The genetic correlations between MARB and growth, reproductive, feed efficiency, and carcass-related trait were very low, with values close to zero, with similar correlated responses. The MARB displayed adequate genetic variability to respond to selection and crossbreeding programs looking forward to higher meat quality and differential market standards for the Nellore beef. The selection for growth, reproductive, feed efficiency, and carcass-related traits would not affect MARB in Nellore beef cattle and vice versa. Therefore, this trait should be included as a selection criterion in the Nellore breeding program.

Prediction ability for growth and maternal traits using SNP arrays based on different marker densities in Nellore cattle using the ssGBLUP

This study aimed to investigate the prediction ability for growth and maternal traits using different low-density customized SNP arrays selected by informativeness and distribution of markers across the genome employing single-step genomic BLUP (ssGBLUP). Phenotypic records for adjusted weight at 210 and 450 days of age were utilized. A total of 945 animals were genotyped with high-density chip, and 267 individuals born after 2008 were selected as validation population. We evaluated 11 scenarios using five customized density arrays (40 k, 20 k, 10 k, 5 k and 2 k) and the HD array was used as desirable scenario. The GEBV predictions and BIF (Beef Improvement Federation) accuracy were obtained with BLUPF90 family programs. Linear regression was used to evaluate the prediction ability, inflation, and bias of GEBV of each customized array. An overestimation of partial GEBVs in contrast with complete GEBVs and increase of BIF accuracy with the density arrays diminished were observed. For all traits, the prediction ability was higher as the array density increased and it was similar with customized arrays higher than 10 k SNPs. Level of inflation was lower as the density array increased of and was higher for MW210 effect. The bias was susceptible to overestimation of GEBVs when the density customized arrays decreased. These results revealed that the BIF accuracy is sensible to overestimation using low-density customized arrays while the prediction ability with least 10,000 informative SNPs obtained from the Illumina BovineHD BeadChip shows accurate and less biased predictions. Low-density customized arrays under ssGBLUP method could be feasible and cost-effective in genomic selection.

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.

Genetic study of quantitative traits supports the use of Guzerá as dual-purpose cattle

Objective

The aim of this study was to estimate genetic parameters for 305-day cumulative milk yield and components, growth, and reproductive traits in Guzerá cattle.

Methods

The evaluated traits were 305-day first-lactation cumulative yields (kg) of milk (MY305), fat (FY305), protein (PY305), lactose (LY305), and total solids (SY305); age at first calving (AFC) in days; adjusted scrotal perimeter (cm) at the ages of 365 (SP365) and 450 (SP450) days; and adjusted body weight (kg) at the ages of 210 (W210), 365 (W365), and 450 (W450) days. The (co)variance components were estimated using the restricted maximum likelihood method for single-trait, bi-trait and tri-trait analyses. Contemporary groups and additive genetic effects were included in the general mixed model. Maternal genetic and permanent environmental effects were also included for W210.

Results

The direct heritability estimates ranged from 0.16 (W210) to 0.32 (MY305). The maternal heritability estimate for W210 was 0.03. Genetic correlation estimates among milk production traits and growth traits ranged from 0.92 to 0.99 and from 0.92 to 0.99, respectively. For milk production and growth traits, the genetic correlations ranged from 0.33 to 0.56. The genetic correlations among AFC and all other traits were negative (−0.43 to −0.27). Scrotal perimeter traits and body weights showed genetic correlations ranging from 0.41 to 0.46, and scrotal perimeter and milk production traits showed genetic correlations ranging from 0.11 to 0.30. The phenotypic correlations were similar in direction (same sign) and lower than the corresponding genetic correlations.

Conclusion

These results suggest the viability and potential of joint selection for dairy and beef traits in Guzerá cattle, taking into account reproductive traits.

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.

Genetic evaluation for reproductive and productive traits in Brahman cattle

Our objectives were to estimate genetic parameters for male and female reproductive traits and their genetic correlations with body weight and carcass traits, evaluate the genetic trends over the years, and verify the effect of inbreeding on the phenotypes of Brahman cattle. The traits evaluated were body weights at 120, 210, 365, and 450 days of age (W120, W210, W365, and W450); scrotal circumference at 365 and 450 days of age (SC365 and SC450), age at first calving (AFC), gestation length (GL), stayability (STAY), ribeye area (REA), backfat thickness (BFT), and rump fat thickness (RFT). Direct heritability estimates ranged from 0.10 ± 0.03 (AFC) to 0.43 ± 0.06 (GL). Maternal heritability estimates for body weights, scrotal circumferences, and GL ranged from 0.07 ± 0.02 to 0.15 ± 0.03. The proportion of the maternal permanent environment for W120 and W210 was equal to 0.11 ± 0.02. Genetic correlations varied between -0.60 ± 0.25 (STAY and BFT) to 0.97 ± 0.01 (W365 and W450). Except for AFC, all genetic trends were significant (p < 0.05) and presented favorable annual genetic gains. Unfavorable effects due to the increase of inbreeding coefficients were observed for body weights and AFC, suggesting greater attention be paid to the applied mating systems to control inbreeding. Reproductive traits, such as AFC and STAY, could be assisted indirectly by scrotal circumference selection. The emphasis applied to body weight selection, especially at W210, may assist REA. The BFT and RFT traits presented genetic variability and have responded to selection, although not included in the Brahman selection index.

Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle

Simple Summary

In this study, we investigated the association between single nucleotide polymorphisms (SNPs) and reproductive traits in order to identify candidate genes and biological pathways associated with these traits in Nelore beef cattle. The genome-wide association analysis revealed genomic regions that could explain part of the genetic variance of the studied traits. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, being important for reproductive efficiency. The identification of candidate genes that were associated with the studied traits as well as genes enriched in the functional terms and pathways may be useful for exploring the genetic architecture underlying reproductive traits and may be used in Nelore breeding programs.

Abstract

The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.

Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo

Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.

Selection criteria for feed efficiency-related traits and their association with growth, reproductive and carcass traits in Nelore cattle

Context Livestock feed costs have a higher impact on the profitability of beef production systems and are directly related to feed efficiency. However, these traits are hard and have high costs to measure, reducing the availability of phenotypic records and reliability of genetic evaluations. Thus, the use of genomic information can increase the robustness of genetic studies that address them. Aims The aim of the present study was to estimate genetic parameters for feed efficiency, growth, reproductive and carcass traits in Nelore cattle and the correlated response among them, using genomic information. Methods Residual feed intake (RFI), dry-matter intake, feed conversion ratio, feed efficiency (FE), residual average daily gain (RG), residual feed intake and average daily gain (RIG), birthweight, weight at 120, 240, 365 and 450 days of age, scrotal circumference at 365 and 450 days of age, rib-eye area, backfat thickness and rump fat thickness were evaluated. The genetic parameters were estimated using the single-step genomic best linear unbiased prediction approach. Key results The FE-related traits showed low to moderate heritability ranging from 0.07 to 0.23. Feed efficiency-related traits showed low genetic correlations with reproductive (–0.24 to 0.27), carcass (–0.17 to 0.27) and growth (–0.19 to 0.24) traits, except for growth with dry-matter intake (0.32–0.56) and weight at 365 days of age with FE (–0.40). Conclusions The selection to improve growth, reproductive and carcass traits would not change RFI, RG and RIG. The choice of the most adequate selection criterion depends on the production system, that is, RFI might be used for low-input beef cattle systems, and RIG would be used for more intensive and without-any-dietary-restrictions beef cattle systems. Implications The estimates of heritability and genetic correlations suggest that genetic selection for feed efficiency using RFI, RG and RIG in Nellore cattle leads to higher genetic gain than does that using FE and feed conversion ratio without affecting other profitability traits.

Genetic parameters and purebred-crossbred genetic correlations for growth, meat quality, and carcass traits in pigs

Growth, meat quality, and carcass traits are of economic importance in swine breeding. Understanding their genetic basis in purebred (PB) and commercial crossbred (CB) pigs is necessary for a successful breeding program because, although the breeding goal is to improve CB performance, phenotype collection and selection are usually carried out in PB populations housed in biosecure nucleus herds. Thus, the selection is indirect, and the accuracy of selection depends on the genetic correlation between PB and CB performance (rpc). The objectives of this study were to 1) estimate genetic parameters for growth, meat quality, and carcass traits in a PB sire line and related commercial CB pigs and 2) estimate the corresponding genetic correlations between purebred and crossbred performance (rpc). Both objectives were investigated by using pedigree information only (PBLUP) and by combining pedigree and genomic information in a single-step genomic BLUP (ssGBLUP) procedure. Growth rate showed moderate estimates of heritability for both PB and CB based on PBLUP, while estimates were higher in CB based on ssGBLUP. Heritability estimates for meat quality traits were diverse and slightly different based on PB and CB data with both methods. Carcass traits had higher heritability estimates based on PB compared with CB data based on PBLUP and slightly higher estimates for CB data based on ssGBLUP. A wide range of estimates of genetic correlations were obtained among traits within the PB and CB data. In the PB population, estimates of heritabilities and genetic correlations were similar based on PBLUP and ssGBLUP for all traits, while based on the CB data, ssGBLUP resulted in different estimates of genetic parameters with lower SEs. With some exceptions, estimates of rpc were moderate to high. The SE on the rpc estimates was generally large when based on PBLUP due to limited sample size, especially for CBs. In contrast, estimates of rpc based on ssGBLUP were not only more precise but also more consistent among pairs of traits, considering their genetic correlations within the PB and CB data. The wide range of estimates of rpc (less than 0.70 for 7 out of 13 traits) indicates that the use of CB phenotypes recorded on commercial farms, along with genomic information, for selection in the PB population has potential to increase the genetic progress of CB performance.

Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems

Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file. Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development. The main genes identified for RFT were GSK3β, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.

Genetic Parameters of Birth Weight and Weaning Weight and Their Relationship with Gestation Length and Age at First Calving in Hanwoo (Bos taurus coreanae)

Simple Summary

Hanwoo cattle is considered one of the most economically important species and sources of nutrition for Koreans. Thus, both the reproductive performance and growth traits play an important role in the continuous development and productivity of Hanwoo farming. Therefore, to improve beef production and the profitability of Hanwoo farming, estimations of genetic parameters for birth weight (BW) and weaning weight (WW) and their relationship with age at first calving (AFC) and gestation length (GL) are necessary to understand and improve their responses to selection. Thus, this study estimated the variance components, heritability estimates of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to age at first calving (AFC), and gestation length (GL). Results revealed a moderate and high heritability estimate for BW and WW, which suggests a sluggish and rapid response of these traits to selection, respectively. The moderate and high genetic correlation between BW and reproductive traits (AFC and GL) revealed that the selection of a heavier BW might result in a longer AFC and GL. Although the genetic correlation for BW and AFC was moderate and positive, the phenotypic correlation of close to zero may indicate that the phenotypic expression for these traits is likely to be influenced by the genotype-environment interaction (GxE). Moreover, the genetic and phenotypic correlation between WW and reproductive traits (AFC and GL) indicates that the selection of a heavier WW may not influence the AFC and GL of Hanwoo cow. These estimated genetic parameters and correlations for the studied traits can be utilized for genetic breeding programs of Hanwoo cattle.

Abstract

Hanwoo is one of the most economically important animal species in Korea due to its significant contribution to nutrition. However, the current selection index only focuses to improve carcass traits of Hanwoo. Thus, this study aimed to estimate the genetic parameters of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to the age at first calving (AFC) and gestation length (GL) of Hanwoo. The genetic parameters for birth weight (BW) and weaning weight (WW) were estimated using the data obtained from 52,173 and 35,800 Hanwoo calves born from February 1998 to March 2017, respectively. Further, these data were used to determine their genetic and phenotypic correlation to age at first calving (AFC) and gestation length (GL). The heritability estimates of BW and WW and correlation coefficients were obtained using the average information restricted maximum likelihood (AIREML) procedure, fit in single and two-trait linear animal models. The estimated direct heritability for BW and WW was moderate (0.22 ± 0.02) and high (0.51 ± 0.03), respectively, while the maternal heritability for both traits was 0.12 ± 0.01 and 0.17 ± 0.01, respectively. The genetic correlation of BW and reproductive traits (AFC and GL) showed a moderate and high positive correlation coefficient of 0.33 ± 0.06 and 0.53 ± 0.02, respectively, while close to zero and low positive phenotypic correlations of 0.06 ± 0.01 and 0.21 ± 0.06 were also observed between the correlated traits, respectively. For the correlation analysis between WW and AFC, both the genetic and phenotypic correlation showed close to zero values of 0.04 ± 0.06 and −0.01 ± 0.01, respectively. Meanwhile, the genetic and phenotypic correlation between WW and GL showed low and negative correlations of −0.09 ± 0.06 and −0.09 ± 0.01, respectively. These obtained estimated variances for BW and WW and their corresponding genetic and phenotypic correlation to AFC and GL can be used as information for genetic improvement and subsequent economic improvement of Hanwoo farming.

Genomic evaluation for novel stayability traits in Nellore cattle

Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability traits: STAY42, STAY53 and STAY64, which are measured at 52, 64 and 76 months of cow's age, considering at least 2, 3 and 4 calving, respectively. ssGBLUP yielded the highest prediction accuracy for all traits. The heritability estimates for STAY42, STAY53, STAY63 and STAY64 were 0.090, 0.151, 0.152 and 0.143, respectively. The genetic correlations between traits ranged from 0.899 (STAY42 and STAY53) to 0.985 (STAY53 and STAY63). The high genetic correlation between STAY42 and STAY53 suggests that besides being related to cow longevity, STAY53 is also associated with the early-stage reproductive efficiency. Thus, STAY53 is recommended as a suitable selection criterion for reproductive efficiency due to its higher heritability, favourable genetic correlation with other traits, and measured earlier in life, compared with the conventional stayability trait, that is STAY63.

Estimation of Genetic Parameters for Reproductive Traits in Hanwoo (Korean Cattle)

Simple Summary

Due to the extensive marbling of its beef, Hanwoo (Korean native cattle) has continuously gained popularity and has become a mainstay in South Korea’s animal industry. In any beef cattle production system, reproductive performance is one of the main economic aspects taken into consideration. Therefore, genetic parameter estimates are necessary to obtain indices in order to maximize the response to selection, which in turn could lead to higher profitability. To date, knowledge on the genetic parameters for reproductive traits in Hanwoo cattle is still limited. Therefore, this study estimated the variance components, heritability, phenotypic, and genetic correlations of age at first calving (AFC), calving interval (CI), days open (DO), and gestation length (GL) of Hanwoo cattle. This was done using single-trait and multi-trait animal models. Results revealed the low heritability estimates for AFC, CI, DO, and GL in both single-trait and multi-trait models, which indicated the probable slow response of these traits due to direct selection. Moreover, phenotypic and genetic correlations varied from low to high among the reproductive traits of interest. Nevertheless, heritability estimates and genetic correlations shown in this study will prove to be vital as initial estimates are considered in the genetic improvement program of Hanwoo cattle.

Abstract

Genetic parameters for the reproductive traits of Hanwoo cattle were estimated using data obtained from 15,355 cows in 92 herds across South Korea, which were inseminated from May 1997 to July 2016. An “average information” restricted maximum likelihood (REML) procedure that fit in single-trait and multi-trait animal models was used to estimate the variance components of age at first calving (AFC), calving interval (CI), days open (DO), and gestation length (GL). Results showed the low estimates of heritability for all reproductive traits from both single-trait and multi-trait models. Estimates of heritability for AFC were 0.08 and 0.10 with single-trait and multi-trait models, respectively, while the estimates of heritability using the same animal models ranged from 0.01 to 0.07, 0.01 to 0.09, and 0.10 to 0.16 for CI, DO, and GL, accordingly. While AFC showed positive genetic correlations of 0.52 and 0.46 with CI and DO, respectively, the estimates of genetic and phenotypic correlations of GL with AFC were close to zero. Moreover, phenotypic correlations of GL with CI and DO were also close to zero; however, the corresponding genetic correlations were 0.13 and –0.38 for CI and DO, respectively. These estimated variance components and genetic correlations for reproductive traits can be utilized for genetic improvement programs of Hanwoo cattle.

Genome-wide association study for age at puberty in young Nelore bulls

Selection for bulls that would reach puberty early reduces the generation interval and increases fertility and herd productivity. Despite its economic importance, there are few QTL associated with age at puberty described in the literature. In this study, a weighted single-step genome-wide association study was performed to detect genomic regions and putative candidate genes related to age at puberty in young Nelore bulls. Several protein-coding genes related to spermatogenesis functions were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for age at puberty in Nelore bulls, such as ADAM11, BRCA1, CSNK2A, CREBBP, MEIOC, NDRG2, NECTIN3, PARP2, PARP9, PRSS21, RAD51C, RNASE4, SLX4, SPA17, TEX14, TIMP2 and TRIP13 gene. Enrichment analysis by DAVID also revealed several GO terms related to spermatogenesis such as DNA replication (GO:0006260), male meiosis I (GO:0007141), double-strand break repair (GO:0006302), base excision repair (GO:0006284), apoptotic process (GO:0006915), cell-cell adhesion (GO: 0098609) and focal adhesion (GO:0005925). The heritability for age at puberty shows that this trait can be improved based on traditional EBV selection. Adding genomic information to the system helps to elucidate genes and molecular mechanisms controlling the sexual precocity and could help to predict sexual precocity in Nelore bulls with greater accuracy at younger age, which would speed up the breeding programme for this breed.

Genomic regions and enrichment analyses associated with carcass composition indicator traits in Nellore cattle

The aim of this study was to estimate genetic parameters and identify genomic regions associated with carcass traits obtained by ultrasound and visual scores in Nellore cattle. Data from ~66,000 animals from the National Association of Breeders and Researchers (ANCP) were used. The variance components for backfat thickness, rump fat thickness and Longissimus muscle area (LMA) were estimated considering a linear model whereas a threshold model for body structure (BS), finishing precocity (FP) and musculature (MS) traits. The SNP solutions were estimated using the ssGBLUP approach by considering windows of 10 consecutive SNPs. Regions that accounted for more than 1.0% of the additive genetic variance were used. Genes identified within the significant windows, such as FOXA3, AP2S1, FKRP, NPASI and ATP6V1G1, were found to be related with MS, while OMA1 and FFGY with BS and FP traits. The PLTP, TNNC2 and GPAT2 genes were found in the regions associated with LMA, as well as TKT, FNDC5 and CHRND can strongly be related with fat deposition. Gene enrichment analysis revealed processes that might be directly influenced the organism growth and development. These results should help to better understand the genetic and physiological mechanisms regulating growth and body composition, muscle tissue development and subcutaneous fat expression, and this information might be useful for future genomic studies in Nellore cattle.