The aims of this study were to determine anti-müllerian hormone (AMH) cutoff values for selecting Gir (Bos taurus indicus) oocyte donors and estimate the impact of using AMH concentrations as a selection criterion. In Exp. 1, Gir heifers (n=120) were sampled for AMH analysis and submitted to ovum pick-up and in vitro embryo production (OPU-IVEP). AMH cutoff values were calculated using ROC analysis or, alternatively, by the successive exclusion of heifers with the lowest AMH values. The correlations between AMH and OPU-IVEP outcomes were significant (P<0.001), though low or moderate (r= 0.34-0.52). We estimated an improvement (P<0.05) after the use of AMH cutoff values to select donors of +15.3% for total oocyes, +19.4% for viable COC, and +23.4% for blastocysts. This selection pressure, however, led to the exclusion of 32.8%, 37.9%, and 50.0% of the initial potential donors, respectively. In Exp. 2, we analyzed data from OPU-IVEP sessions of 658 Gir donors with known genomic values for predicted transmitting ability for milk (GPTAm) and age at first calving (GPTAafc). The selection based on the number of oocytes recovered had no effect (P>0.05) on the average GPTAm nor GPTAafc values of the remaining donors. In summary, plasma AMH ≥700 pg/mL is a cutoff value that can be used to select Gir heifers with a greater potential as oocyte donors. Nevertheless, this selection leads to the exclusion of up to 50% of potential donors. Finally, exclusion of poor responders had no effect on mean genomic estimates for milk production or age at first calving in the selected subset of donors.

Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.

The domestication of animals has rendered horns less necessary for survival. Moreover, the use of polled and disbudded animals is interesting in order to avoid injuries of animals and handlers, among other advantages. We therefore conducted a comparative economic analysis of different traditional disbudding techniques versus selective breeding for polledness in Nelore cattle, the main beef breed of tropical systems in Brazil. The cost to obtain animals without horns was estimated in three different scenarios: disbudding with hot iron, disbudding with caustic paste, and phenotypic selection for polled animals. Price quotations of the materials were obtained in different states of the country and averaged. An initial frequency of horned animals of 92.16% was obtained based on the records of the Brazilian Association of Zebu Breeders. Selective breeding was found to be the best cost-effective scenario. This result differs from intensive production systems of dairy cattle in which traditional disbudding continues to be the best cost-effective scenario. The main explanation is the lack of difference in the price of Nelore semen from polled and horned bulls. Phenotypic selection for polled animals is the best cost-effective method, and it is in accordance with welfare practices. Care should be taken regarding the intensive use of few polled breeding animals in order to avoid inbreeding depression in other traits.

Beef cattle affected by feet and legs malformations (FLM) cannot perform their productive and reproductive functions satisfactorily, resulting in significant economic losses. Accelerated weight gain in young animals due to increased fat deposition can lead to ligaments, tendon and joint strain and promote gene expression patterns that lead to changes in the normal architecture of the feet and legs. The possible correlated response in the FLM due to yearling weight (YW) selection suggest that this second trait could be used as an indirect selection criterion. Therefore, FLM breeding values and the genetic correlation between FLM and yearling weight (YW) were estimated for 295,031 Nellore animals by fitting a linear-threshold model in a Bayesian approach. A genome-wide association study was performed to identify genomic windows and positional candidate genes associated with FLM. The effects of single nucleotide polymorphisms (SNPs) on FLM phenotypes (affected or unaffected) were estimated using the weighted single-step genomic BLUP method, based on genotypes of 12,537 animals for 461,057 SNPs. Twelve non-overlapping windows of 20 adjacent SNPs explaining more than 1% of the additive genetic variance were selected for candidate gene annotation. Functional and gene prioritization analysis of candidate genes identified six genes (ATG7, EXT1, ITGA1, PPARD, SCUBE3, and SHOX) that may play a role in FLM expression due to their known role in skeletal muscle development, aberrant bone growth, lipid metabolism, intramuscular fat deposition and skeletogenesis. Identifying genes linked to foot and leg malformations enables selective breeding for healthier herds by reducing the occurrence of these conditions. Genetic markers can be used to develop tests that identify carriers of these mutations, assisting breeders in making informed breeding decisions to minimize the incidence of malformations in future generations, resulting in greater productivity and animal welfare.

The goal of this study was to determine the distribution of preantral follicles in bovine ovaries. Follicular distribution in the ovaries (n = 12) was evaluated in the region of the greater curvature of the ovary (GCO) and the region close to the ovarian pedicle (OP) of Bos taurus indicus heifers of the Nelore breed. Two fragments were obtained from each region of the ovary (GCO and OP). The mean weight of the ovaries was 4.04 ± 0.32 g. The mean antral follicle count (AFC) was 54.58 ± 3.55 follicles (minimum and maximum variation of 30 and 71 follicles, respectively). In total, 1123 follicles were visualized in the region of the GCO; 949 (84.5%) of them were primordial follicles and 174 (15.5%) were developing follicles. The region close to the OP contained 1454 follicles, of which 1266 (87%) were primordial follicles and 44 (12.9%) were developing follicles. The OP region showed a higher proportion of intact follicles in the primordial (P < 0.0001) and primary (P = 0.042) stages compared with the GCO region. The proportion of secondary follicles was similar in the OP and GCO regions. The ovaries of two bovine females (16%; 2/12) contained multi-oocytes follicles, which were characterized as primary follicles. Therefore, the distribution of preantral follicles in the bovine ovary was heterogeneous, with the region close to the OP containing a greater number of preantral follicles compared with the GCO region (P < 0.05).

This study aimed to estimate prediction ability and genetic parameters for residual feed intake (RFI) calculated using a regression equation for each test (RFItest) and for the whole population (RFIpop) in Nellore beef cattle. It also aimed to evaluate the correlations between RFIpop and RFItest 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 RFItest and RFIpop. 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 RFItest and RFIpop with dry matter intake, frame, growth, reproduction, and carcass-related traits were evaluated. The prediction ability and bias were estimated to compare the RFItest and RFIpop genomic breeding values (GEBV). The RFIpop ANOVA showed a higher significance level (p < 0.0001) than did the RFItest for the fixed effects. The RFIpop displayed higher additive genetic variance estimated than the RFItest, although the RFIpop and RFItest displayed similar heritabilities. Overall, the RFItest showed higher residual correlations with growth, reproductive, and carcass traits, while the RFIpop displayed higher genetic correlations with such traits. The GEBV for the RFItest was slightly biased than GEBV RFIpop. The approach to calculate the RFI influenced the decomposition and estimation of variance components and genomic prediction for RFI. The application of RFIpop would be more appropriate for genetic evaluation purpose to adjust or correct for non-genetic effects and to decrease the prediction bias for RFI.

Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% Fst approach, we detected a candidate region (22.6-23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions.

The aim of the present study was to use different models that include body composition phenotypes for the evaluation of residual feed intake (RFI) in Nellore bulls of different ages. Phenotypic and genotypic data of bulls that had participated in feed efficiency tests of a commercial (COM) and an experimental (EXP) herd between 2007 and 2019 were used. The mean entry age in the two herds was 645 and 279 days, respectively. The phenotypes were evaluated: rib eye area (REA), backfat thickness (BFT), residual feed intake (RFIKOCH), RFI adjusted for REA (RFIREA), RFI adjusted for BFT (RFIBFT), and RFI adjusted for REA and BFT (RFIREA BFT). The (co)variance components and prediction of genomic estimated breeding values (GEBV) were obtained by REML using ssGBLUP in single and two-trait analyses. Spearman\'s correlations were calculated based on the GEBV for RFIKOCH. The RFI phenotypes exhibited moderate heritability estimates in both herds (0.17 ± 0.03 to 0.27 ± 0.04). The genetic correlation between phenotypes was positive and high (0.99) in the two herds, a fact that permitted the creation of a single database (SDB). The heritability estimates of the SDB were also of moderate magnitude for the different definitions of RFI (0.19 ± 0.04 to 0.21 ± 0.04). The genetic correlations were positive and high between RFI traits 0.97 ± 0.01 to 0.99 ± 0.01), and positive and low/moderate between REA and BFT (0.01 ± 0.10 to 0.31 ± 0.12). The selection of animals based on the GEBV for RFIKOCH did not alter the ranking of individuals selected for RFIREA, RFIBFT, and RFIREA BFT. The results of the present study suggest that records of Nellore bulls of different ages and with different body compositions can be combined in a SDB for RFI calculation. Therefore, young animals can be evaluated in feed efficiency tests in order to reduce costs and the generation interval and possibly to obtain a higher response to selection.

BACKGROUND: Genotype by environment interactions (G × E) can play an important role in cattle populations and should be included in breeding programs in order to select the best animals for different environments.
OBJECTIVE: The aim of this study was to investigate the G × E for milk production of Gyr cattle in Brazil and Colombia by applying a reaction norm model used genomics information, and to identify genomic regions associated with milk production in the two countries.
METHODS: The Brazilian and Colombian database included 464 animals (273 cows and 33 sires from Brazil and 158 cows from Colombia) and 27,505 SNPs. A two-trait animal model was used for milk yield adjusted to 305 days in Brazil and Colombia as a function of country of origin, which included genomic information obtained with a single-step genomic reaction norm model. The GIBBS3F90 and POSTGSf90 programs were used.
RESULTS: The results obtained indicate G × E based on the reranking of bulls between Brazil and Colombia, demonstrating environmental differences between the two countries. The findings highlight the importance of considering the environment when choosing breeding animals in order to ensure the adequate performance of their progeny. Within this context, the reranking of bulls and the different SNPs associated with milk production in the two countries suggest that G × E is an important effect that should be included in the genetic evaluation of Dairy Gyr cattle in Brazil and Colombia.
CONCLUSIONS: The Gyr breeding program can be optimized by choosing a selection environment that will allow maximum genetic progress in milk production in different environments within and between countries.

Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot.