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

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

Growth of young cattle grazing high-moisture winter forages in a temperate environment was not affected by access to drinking water

Context Early sown, annual ryegrass pastures and winter crops provide a high-quality feed for livestock and also have a high water content during autumn and early winter compared with typical temperate pastures. Aim We hypothesised that beef cattle grazing annual ryegrass or forage oats would not need additional access to drinking water to maintain their intake and growth. Methods In Experiment 1, 48 weaned, castrated male Hereford calves with liveweight 154 kg (±6.7 kg; s.d.) grazed Italian ryegrass at a daily allowance of 4.5 kg dry matter (DM)/100 kg liveweight in two treatments including with or without access to drinking water. In Experiment 2, 60 Hereford steers with liveweight 382 kg (±20.6 kg; s.d.) were offered a daily allowance of 5 kg DM/100 kg liveweight of forage oats in a 2 × 2 factorial design either with or without access to drinking water and with or without sorghum grain silage supplemented at 1% of liveweight. The experiments were analysed as a completely randomised design, with individual pasture plots as the experimental unit. Key results Daily growth rates of calves in the two treatments were similar (P > 0.05); however, calves with access to drinking water consumed 60% more water than did the calves without drinking water (P < 0.001). Access to drinking water had no effect (P > 0.05) on the daily growth rate of steers (P > 0.05); however, the daily growth rate of supplemented steers was 9% higher than that of the unsupplemented steers (P < 0.05). Total water intake was affected by access to drinking water (P < 0.005) but not access to supplementation (P > 0.05). Conclusions Both calves and steers derived no production benefits by having access to drinking water when grazing actively growing annual ryegrass pasture or forage oats. Nevertheless, livestock should be monitored closely so that appropriate interventions can be made if there are changes in the pasture availability or weather. Implications Grazing early sown winter forages by livestock can help circumvent the autumn–winter feed gap and these forages can be utilised more cost-effectively by not having to provide drinking water when the DM content is low.

Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.

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.

Genomic prediction ability for feed efficiency traits using different models and pseudo-phenotypes under several validation strategies in Nelore cattle

There is a growing interest to improve feed efficiency (FE) traits in cattle. The genomic selection was proposed to improve these traits since they are difficult and expensive to measure. Up to date, there are scarce studies about the implementation of genomic selection for FE traits in indicine cattle under different scenarios of pseudo-phenotypes, models, and validation strategies on a commercial large scale. Thus, the aim was to evaluate the feasibility of genomic selection implementation for FE traits in Nelore cattle applying different models and pseudo-phenotypes under validation strategies. Phenotypic and genotypic information from 4 329 and 3 467 animals were used, respectively, which were tested for residual feed intake, DM intake, feed efficiency, feed conversion ratio, residual BW gain, and residual intake and BW gain. Six prediction methods were used: single-step genomic best linear unbiased prediction, Bayes A, Bayes B, Bayes Cπ, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayes R. Phenotypes adjusted for fixed effects (Y*), estimated breeding value (EBV), and EBV deregressed (DEBV) were used as pseudo-phenotypes. The validation approaches used were: (1) random: the data was randomly divided into ten subsets and the validation was done in each subset at a time; (2) age: the partition into training and testing sets was based on year of birth and testing animals were born after 2016; and (3) EBV accuracy: the data was split into two groups, being animals with accuracy above 0.45 the training set; and below 0.45 the validation set. In the analyses that used the Y* as pseudo-phenotype, prediction ability (PA) was obtained by dividing the correlation between pseudo-phenotype and genomic EBV (GEBV) by the square root of the heritability of the trait. When EBV and DEBV were used as the pseudo-phenotype, the simple correlation of this quantity with the GEBV was considered as PA. The prediction methods show similar results for PA and bias. The random cross-validation presented higher PA (0.17) than EBV accuracy (0.14) and age (0.13). The PA was higher for Y* than for EBV and DEBV (30.0 and 34.3%, respectively). Random validation presented the highest PA, being indicated for use in populations composed mainly of young animals and traits with few generations of data recording. For high heritability traits, the validation can be done by age, enabling the prediction of the next-generation genetic merit. These results would support breeders to identify genomic approaches that are more viable for genomic prediction for FE-related traits.

Ovulation and ovulation rate in ewes under grazing conditions: factors affecting the response to short-term supplementation

The relationships between ovulation rate and nutrition remain confused, probably because of uncontrolled variation in experimental conditions. To help resolve the problem, we analyzed data from 20 experiments conducted between 2002 and 2016, in Uruguay with grazing ewes. All experiments were carried out by a single laboratory under comparable conditions of experimental design and measured variables. The studies used a total of 3 720 ewes, of purebred Corriedale, Polwarth, or East Friesian x Polwarth genotypes. In all experiments, a control group grazed native pastures and extra nutrition was provided to the treatment groups using either improved pastures or supplements. Ovulation rate was measured by counting corpora lutea using laparoscopy or rectal ultrasound or by counting foetuses at ultrasound on day 45 of gestation. For statistical analysis, data were grouped according to nutritional treatment (control or supplemented) and, within these groups, type of supplement to provide energy or protein (protected or not from rumen degradation). Across all experiments, 92-99% of the ewes ovulated and the effects of diet, length of supplementation, and initial live weight and genotype are reported. Within diets, ovulation was most affected by overall energy intake during supplementation (P < 0.01). Ewes that grazed native pastures supplemented with protein supplements had higher ovulation rates (P < 0.05) than control ewes grazing only native pastures. The addition of tannins to the protein supplement, to protect it from degradation in the rumen, did not further increase the ovulation rate. In unsupplemented ewes that had access to legume pastures, ovulation rates did not increase when the legume pasture was rich in tannins although only ewes that grazed tanniniferous legumes had marginally higher ovulation rates than the control ewes (P < 0.05). When ewes grazing native pastures were supplemented with energy, their ovulation rate did not increase above those of nonsupplemented ewes. Live weight at the start of supplementation also affected ovulation rate. We conclude that ovulation was most affected by overall energy intake, whereas the factors that affected ovulation rate during short-tern nutritional supplementation were intake of protein from highly digested supplements or dietary protein protected from ruminal degradation.

Genome-enabled prediction of meat and carcass traits using Bayesian regression, single-step genomic best linear unbiased prediction and blending methods in Nelore cattle

Several methods have been used for genome-enabled prediction (or genomic selection) of complex traits, for example, multiple regression models describing a target trait with a linear function of a set of genetic markers. Genomic selection studies have been focused mostly on single-trait analyses. However, most profitability traits are genetically correlated, and an increase in prediction accuracy of genomic breeding values for genetically correlated traits is expected when using multiple-trait models. Thus, this study was carried out to assess the accuracy of genomic prediction for carcass and meat quality traits in Nelore cattle, using single- and multiple-trait approaches. The study considered 15 780, 15 784, 15 742 and 526 records of rib eye area (REA, cm²), back fat thickness (BF, mm), rump fat (RF, mm) and Warner-Bratzler shear force (WBSF, kg), respectively, in Nelore cattle, from the Nelore Brazil Breeding Program. Animals were genotyped with a low-density single nucleotide polymorphism (SNP) panel and subsequently imputed to arrays with 54 and 777 k SNPs. Four Bayesian specifications of genomic regression models, namely, Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression; blending methods, BLUP; and single-step genomic best linear unbiased prediction (ssGBLUP) methods were compared in terms of prediction accuracy using a fivefold cross-validation. Estimates of heritability ranged from 0.20 to 0.35 and from 0.21 to 0.46 for RF and WBSF on single- and multiple-trait analyses, respectively. Prediction accuracies for REA, BF, RF and WBSF were all similar using the different specifications of regression models. In addition, this study has shown the impact of genomic information upon genetic evaluations in beef cattle using the multiple-trait model, which was also advantageous compared to the single-trait model because it accounted for the selection process using multiple traits at the same time. The advantage of multi-trait analyses is attributed to the consideration of correlations and genetic influences between the traits, in addition to the non-random association of alleles.

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (G×E) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of G×E interactions for heifer's early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal's sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM_A) or pedigree and genomic information (RNM_H), were used to infer G×E interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme-dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment-specific scheme-low EC (-3.0 and -1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28-0.56 for SC and 0.26-0.49 for HP, using RNM_H, and 0.26-0.52 for SC and 0.22-0.45 for HP, using RNM_A. The lowest correlation observed between unfavorable (-3.0) and favorable (3.0) EC levels were 0.30 for HP and -0.12 for SC, indicating the presence of G×E interaction. The G×E interaction effect implied differences in animals' genetic merit and re-ranking of animals on different environmental conditions. SNP marker-environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM_H captured G×E interaction effects better than RNM_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment-specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the G×E interaction leads to more accurate variance components and genetic parameter estimates.

Genetic-quantitative analysis for reproductive traits in Nellor cattle selected for sexual precocity

Context The selection of animals for sexual precocity and reproductive efficiency is a trend to reduce the production cycle, promote higher economic viability to the system, increase selection intensity and higher genetic gain, as well to promote the profitability of production systems. To include these traits as selection criterion in cattle breeding programs, estimating genetic parameters and studying the possibility of obtaining genetic gains is required. The hypothesis tested was that the indicators of sexual precocity traits present genetic variance and moderate heritability that allows these to be used as a criterion of selection to obtain improvement for sexual precocity, without negative implications for the reproductive efficiency in Nellore cattle. Aims This study was carried out to estimate the genetic parameters for reproductive traits (scrotal circumference at 365 and 450 days of age, gestation length, days open, calving interval, real fertility, cumulative productivity, calf weight:cow weight ratio) and age at first conception and first calving in a Nellore cattle herd under selection for sexual precocity. Methods Data of reproductive traits and indicators of sexual precocity traits from 4081 Nellore cattle born between 2009 and 2015 were used. The covariance components, heritabilities and correlations were estimated using the restricted maximum likelihood method, available in the BLUPF90 package, in single- and multiple-trait animal mixed models. Key results Estimates of heritability and standard errors for scrotal circumference at 365 and 450 days of age, gestation length, days open, calving interval, real fertility, cumulative productivity, calf weight:cow weight ratio, age at first conception (AFCo) and age at first calving (AFCa) were 0.33 ± 0.03, 0.33 ± 0.01, 0.23 ± 0.03, 0.34 ± 0.11, 0.23 ± 0.12, 0.21 ± 0.16, 0.23 ± 0.08, 0.25 ± 0.10, 0.21 ± 0.08 and 0.24 ± 0.08 respectively. The genetic correlations estimated between AFCo and the other reproductive traits ranged from –0.61 to 0.14 (standard error 0.1–0.21), and between AFCa and the other reproductive traits ranged from –0.60 to 0.16 (standard error 0.1–0.19), all of them in a favourable direction. Conclusions Selection for sexual precocity based on AFCo and AFCa may promote improvement in reproductive efficiency and fertility, except for the calf weight:cow weight ratio, whose correlation was close to zero. Implications The estimates of heritabilities and genetic correlations suggest that selection programs for reproductive traits and indicators of sexual precocity traits for the Nellore breed may provide genetic gain. In addition, considering the genetic correlation obtained between AFCo and AFCa (0.96), when the selection objective is to increase the sexual precocity of heifers, we could use the age of the first conception as criterion, as the measurement of this trait occurs at a lower age at first calving, which implies reducing the time required for animal evaluation and decision-making.

Reaction norm for yearling weight in beef cattle using single-step genomic evaluation

When the environment on which the animals are raised is very diverse, selecting the best sires for different environments may require the use of models that account for genotype by environment interaction (G × E). The main objective of this study was to evaluate the existence of G × E for yearling weight (YW) in Nellore cattle using reaction norm models with only pedigree and pedigree combined with genomic relationships. Additionally, genomic regions associated with each environment gradient were identified. A total of 67,996 YW records were used in reaction norm models to calculate EBV and genomic EBV. The method of choice for genomic evaluations was single-step genomic BLUP (ssGBLUP). Traditional and genomic models were tested on the ability to predict future animal performance. Genetic parameters for YW were obtained with the average information restricted maximum likelihood method, with and without adding genomic information for 5,091 animals. Additive genetic variances explained by windows of 200 adjacent SNP were used to identify genomic regions associated with the environmental gradient. Estimated variance components for the intercept and the slope in traditional and genomic models were similar. In both models, the observed changes in heritabilities and genetic correlations for YW across environments indicate the occurrence of genotype by environment interactions. Both traditional and genomic models were capable of identifying the genotype by environment interaction; however, the inclusion of genomic information in reaction norm models improved the ability to predict animals' future performance by 7.9% on average. The proportion of genetic variance explained by the top SNP window was 0.77% for the regression intercept (BTA5) and 0.82% for the slope (BTA14). Single-step GBLUP seems to be a suitable model to predict genetic values for YW in different production environments.

Shearing ewes in the first third of gestation improves offspring performance

The effect of shearing ewes at 50 days of gestation on birth and weaning weight, vigour of the lambs in the first hour of life and the survival of single and twin lambs was investigated. Ultrasound pregnancy diagnosis was used to allocate 140 Polwarth ewes on Day 50 of gestation to one of four treatments, including two factors: shearing time (prepartum (PS) and postpartum (U)) and litter size (single (S) and twin (T)) resulting in the following treatments: single-bearing ewes shorn at 50 days of gestation (SPS, n = 39), single-bearing ewes unshorn (SU, n = 40), twin-bearing ewes shorn at 50 days of gestation (TPS, n = 28) and twin-bearing ewes unshorn (TU, n = 33). All ewes grazed together on improved pastures. Body condition score of the ewes was recorded once every 2 weeks from shearing until weaning, and plasma concentration of NEFA in ewes was measured once every 2 weeks from Day 30 postpartum until weaning (Day 104 ± 7). Gestation length, lamb behaviour during the first hour of life, lamb weight at birth and daily weight gain from birth to weaning and lamb survival were measured. Ewe body condition and plasma non-esterified fatty acids concentration was not affected by shearing time or litter size. Birthweight of the lambs was affected by shearing time (P = 0.0002), litter size (P < 0.0001) and sex of the lamb (P = 0.03). Lambs born to PS ewes had higher daily growth rate (P < 0.0001) than lambs born to U ewes (0.149 ± 0.07 vs 0.141 ± 0.07 kg, respectively). Birthweight affected the number of assisted lambs at birth (P = 0.01). Length of gestation was affected by shearing time (P < 0.0001). Sucking ability was improved by shearing time and litter size. Lambs born to PS ewes tried to suck (P = 0.01) and successfully sucked (P = 0.009) before lambs born to U ewes (23.3 ± 2 vs 28.7 ± 2 and 37.6 ± 1 vs 38.4 ± 1 min, respectively). Attempt and success to suck was affected by litter size (P = 0.004 and P = 0.05). TPS-born lambs tried to suck before (P = 0.004) and successfully sucked earlier (P = 0.0004) than TU lambs (26.1 ± 2.5 vs 33.7 ± 2 and 38 ± 1 vs 42.1 ± 2 min, respectively). Shearing time affected lamb survival at 20 days of age (P = 0.04). The improved survival in these lambs, expressed by a higher birthweight and vigour at birth, may be explained by better nutrition in utero in response to shearing during early pregnancy. In contrast to previous research on prepartum shearing, the present experiment shearing was done at 50 days of gestation. Early shearing in gestation might coincide with a period of high cell proliferation, intense vascular development and increased uterine and umbilical blood flows in the placenta which is in rapid development, and may result in improved outcomes when compared with shearing done on Day 70 or later of gestation.

SNP detection using RNA-sequences of candidate genes associated with puberty in cattle

Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.

Runs of homozygosity: current knowledge and applications in livestock

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F_ROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F_PED ). The better results of F_ROH suggest that F_ROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.

Inclusion of cytoplasmic lineage effect and direct-maternal genetic covariance for genetic evaluation of growth traits in Nellore cattle

We evaluated the impact of cytoplasmic lineage effects (Lc) for growth traits on genetic evaluation, including the genetic covariance between direct and maternal effects (σ_am). Pedigree data from 496,190 Nellore animals and observations on birth weight (BW, N = 243,391), weaning weight (WW, N = 431,681), and post-weaning weight gain adjusted to 345 days (PWG, N = 172,131) were analyzed. Four univariate models were used to obtain estimates of (co)variance components using the restricted maximum likelihood method in the BLUPF90 program. Model 1 included Lc and σ_am. Model 2 included Lc and σ_am was set to zero. Model 3 did not include Lc. Model 4 did not include Lc and σ_am was set to zero. These models considered the effects of the Lc as random. Phenotypic variance obtained through cytoplasmic lineage effects was determined for all traits, ranging from 0.07 to 0.15, 0.15 to 0.03, and 0.05 to 0.03% for BW, WW, and PWG, respectively, for models 1 and 2. Correlations between direct and maternal genetic components were positive for WW and negative for BW and PWG. No differences were observed for genetic parameter estimates or animal ranking with the inclusion of σ_am. For BW, the likelihood ratio suggested that model 1 best fits the data, while model 4 was the most appropriate for WW and PWG. Thus, these models are recommended for genetic evaluations. Despite the low magnitude of cytoplasmic lineages, this effect could predict breeding value and improve the selection of animals for BW in this Nellore population.

Cyclin T2A Gene Maps on Human Chromosome 2q21

Cyclin T2a was recently identified as one of the regulatory subunits of the cdk–cyclin complex P-TEFb, the most studied positive factor in the regulation of transcription elongation. By fluorescent in situ hybridization (FISH), the gene codifying for cyclin T2a has been mapped on human chromosome 2q21. This locus also has been linked to different forms of myopathy. By use of a new specific antiserum raised against cyclin T2a, the immunohistochemical pattern of expression of cyclin T2a in human tissues has been examined and compared to that of cyclin T1, described in the previous report. The observation that immunohistochemical expression of cyclin T2a was high in skeletal muscle cells, whereas it was undetectable in two cases of centronuclear myopathy, together with its chromosomal location, suggests an involvement of the cdk9–cyclin T2a complex in this disease.

Valores econômicos para sistemas de recria e engorda de bovinos Nelore e cruzado

Foi desenvolvido o modelo bioeconômico nominado de Beef Management System para a obtenção de valores econômicos em quatro sistemas de recria e engorda de bovinos. Dos modelos analisados, dois utilizaram machos inteiros da raça Nelore e os outros dois machos inteiros cruzados (½ sangue taurino; ½ sangue zebu). Para cada grupamento genético estipulou-se dois modelos de produção, um 100 % a pasto e o outro com recria em pastagem e posterior confinamento. O estudo foi conduzido por meio de simulações em planilhas eletrônicas interligadas do programa Microsoft Office Excel. Os valores econômicos foram estimados para as características de ganho médio diário (GMD), rendimento de carcaça (RC), consumo alimentar (CA) e energia de mantença (EM), para cada um dos modelos propostos. Para obtenção dos valores econômicos, estipulou-se um aumento de 1 % no GMD e RC, e diminuiu-se 1 % da EM e CA. Com o aumento de 1 % no RC e no GMD, o custo de produção diminuiu 14,69 kg de carne (1 unidade de arroba) em todos os modelos estudados. A redução de 1 % na EM dos animais resultou em uma diminuição de 0,45 % no custo de produção de 14,69 kg de carne em ambos os modelos a pasto com confinamento e 0,55 % em ambos os modelos 100 % a pasto. Com a redução de 1 % na CA, o custo de produção de 14,69 kg de carne diminuiu 0,83 e 0,84 % nos modelos a pasto com confinamento de animais Nelores e cruzados e 0,85 e 0,83 % nos modelos 100 % a pasto de animais Nelores e cruzados. Essas características possuem um grande impacto econômico nos sistemas de recria e engorda, com grande vantagem para a característica de RC, uma vez que esta proporcionou os maiores valores econômicos para todos os sistemas estudados. Por meio das variáveis que compuseram os modelos estudados tornou-se possível mensurar a real importância do impacto genético das características e seus respectivos valores econômicos.

Genetic correlations between visual slaughter conformation scores and growth and reproductive traits in Canchim cattle

We obtained heritability and (co)variance component estimates for slaughter conformation scores at 420 days of age (SCS420), age at calving (first, AFC; second, ASC), calving occurrence until 38 months of age (CP38), weight at 420 days of age (W420), and scrotal circumference at 420 days (SC420) in Canchim (5/8 Charolais + 3/8 Zebu) cattle. A total of 23,168 records of Canchim animals, including 12,493 females and 10,675 males, were analyzed. SCS420 indicated carcass structure, muscle development, and subcutaneous fat deposition. The slaughter conformation score of each animal was relative to the whole contemporary group; 1 corresponded to the lowest expression of the trait and 6 to the highest. Heritabilities, and genetic and residual correlation estimates between SCS420 and reproductive and weight traits, were estimated by multitrait analyses using an animal model with Bayesian inference, employing a linear model for AFC, ASC, SC420, and W420 and a threshold model for CP38 and SCS420. Heritability estimates for SCS420, AFC, ASC, CP38, W420, and SC420 were 0.11, 0.15, 0.15, 0.15, 0.30, and 0.30, respectively. Genetic correlation estimates between SCS420 and the other traits were 0.08 (AFC), 0.58 (ASC), 0.08 (CP38), 0.43 (W420), and 0.17 (SC420). Visual slaughter conformation scores respond to individual selection and can be used as selection criteria in Canchim cattle. Selection to improve sexual precocity would not be effective in improving carcass conformation and composition, and selection for animals with high breeding values for yearling weight may improve slaughter conformation at the yearling stage.

Genotype × environment interaction for age at first calving, scrotal circumference, and yearling weight in Nellore cattle using reaction norms in multitrait random regression models

The aim of this study was to evaluate the effect of genotype × environment interaction (G×E) on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) and to estimate genetic correlations between these traits in Nellore cattle using reaction norms in multitrait random regression models. In this study, 28,871, 41,386, and 89,152 records of Nellore cattle for AFC, SC, and YW, respectively, were used. The data were obtained from farms located in the north, northeast, midwest, and southeast regions of Brazil that participate in the DeltaGen Breeding Program. Environmental levels were defined as a function of contemporary groups, that is, animals born in the same herd and year, from the same management group (from birth to yearling), and of the same sex. Postweaning weight gain was used as a criterion to evaluate the environmental conditions for all traits. For reaction norm analyses, residual variances were modeled with homogeneous and heterogeneous classes. The model for SC and YW included the fixed effects of contemporary group and age of the animal as a covariate as well as random direct additive genetic and residual effects. The same model, excluding the covariate age of the animal, was used for AFC. The heritability estimates were low to high for AFC (0.09 to 0.50), high for SC (0.51 to 0.67), and moderate to high for YW (0.33 to 0.71). The genetic correlations (within each trait) along the environmental levels varied from -0.27 to 1.0 for AFC, from 0.73 to 1.0 for SC, and from 0.26 to 1.0 for YW. The genetic correlations between different traits in different environments varied from -0.14 to -0.60 between AFC and SC, from -0.05 to -0.32 between AFC and YW, and from -0.05 to 0.72 between YW and SC. The genetic correlations have had different magnitudes for AFC, SC, and YW, which could indicate the presence of G×E. The present results should support researchers and farmers in defining selection criteria to improve growth traits and sexual precocity. Our results suggest that animals for breeding have to be selected in the same environment and management conditions as their progeny will be reared.

Genetic association of growth traits with carcass and meat traits in Nellore cattle

The aim of this study was to estimate genetic and phenotypic associations of growth traits with carcass and meat traits in Nellore cattle. Data from male and female animals were used for weaning weight (WW; N = 241,416), yearling weight (YW, N = 126,596), weight gain from weaning to yearling (GWY, N = 78,687), and yearling hip height (YHH, N = 90,720), respectively; 877 male animals were used for hot carcass weight (HCW) and 884 for longissimus muscle area (LMA), backfat thickness (BT), marbling score (MS), and shear force (SF). The variance components were estimated by the restricted maximum likelihood method using three-trait animal models that included WW. The model for WW included direct and maternal additive genetic, maternal permanent environmental, and residual effects as random effects; contemporary group as fixed effects; and age of dam at calving and age of animal as covariates (linear and quadratic effects). For the other traits, maternal effects and the effect of age of dam at calving were excluded from the model. Heritability ranged from 0.10 ± 0.12 (LMA) to 0.44 ± 0.007 (YW). Genetic correlations ranged from -0.40 ± 0.38 (WW x LMA) to 0.55 ± 0.10 (HCW x YW). Growth, carcass, and meat traits have sufficient genetic variability to be included as selection criteria in animal breeding programs.

Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers

This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P<0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24±0.06 to 0.45±0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02±0.18 for LIVY and BMY to 0.97±0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.

Associations between single nucleotide polymorphisms and carcass traits in Nellore cattle using high-density panels

The objective of this study was to evaluate associations between single nucleotide polymorphism (SNP) markers and carcass traits measured postmortem in Nellore cattle. Records of loin eye area (LEA) and backfat thickness (BF) from 740 males and records of hot carcass weight (HCW) from 726 males were analyzed. All of the animals were genotyped using the BovineHD BeadChip. Association analyses were performed by the restricted maximum likelihood method that considered one SNP at a time. Significant SNPs were identified on chromosomes 2 and 6 for LEA and on chromosomes 7, 1, and 2 for BF. For HCW, associations with SNPs were found on chromosomes 13, 14, and 28, in addition to genome regions that were directly related to this trait, such as the EFCAB8 and VSTM2L genes, and to bone development (RHOU). Some SNPs were located in very close proximity to genes involved in basal metabolism (BLCAP, NNAT, CTNNBL1, TGM2, and LOC100296770) and the immune system (BPI).

Reaction norms for the study of genotype-environment interaction for growth and indicator traits of sexual precocity in Nellore cattle

The objective of this study was to quantify the magnitude of genotype-environment interaction (GxE) effects on age at first calving (AFC), scrotal circumference (SC), and yearling weight (YW) in Nellore cattle using reaction norms. For the study, 89,152 weight records of female and male Nellore animals obtained at yearling age were used. Genetic parameters were estimated with a single-trait random-regression model using Legendre polynomials as base functions. The heritability estimates were of low to medium magnitude for AFC (0.05 to 0.47) and of medium to high magnitude for SC (0.32 to 0.51) and YW (0.13 to 0.72), and increased as the environmental gradient became more favorable. The genetic correlation estimates ranged from 0.25 to 1.0 for AFC, from 0.71 to 1.0 for SC, and from 0.42 to 1.0 for YW. High Spearman correlation coefficients were obtained for the three traits, ranging from 0.97 to 0.99. The reaction norms along the environmental gradient of 10 sires each with the highest or lowest breeding value for YW predicted by single-trait analysis demonstrated more plastic phenotypes for YW and more robust phenotypes for SC. The effect of GxE was most important for YW and AFC with respect to SC. When animals are selected for higher SC or YW or lower AFC, considering or not the GxE effect, it is expected that the same animals will be selected. The reaction norms obtained based on sire breeding values along the environmental gradient showed that animals with extreme breeding values respond differently as environmental conditions improve.

Sequenciamento parcial dos genes TOX e NCOA2 em bubalinos

Os bubalinos são animais com uma importância grande para a produção de alimentos, além da ação sócio-econômica na região tropical. A caracterização de genes possibilita o estudo de características próprias da espécie e o desenvolvimento de tecnologia para sua produção. Esse trabalho estudou parcialmente os genes thymus high mobility group box protein (TOX) e o Nuclear Receptor Coactivator 2 (NCOA2) em femêas bubalinas da raça Murrah pela técnica de PCR-sequenciamento. Seis SNPs foram identificados em cada gene. Dois SNPs adjacentes no gene TOX criaram/destruíram um sitio de produção de um miRNA e são bons candidatos para serem estudos no futuro. A homologia das regiões desses genes com as correspondentes em bovinos é muito alta (99 %).

Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle

The objective of this study was to identify associations between known polymorphisms in genes related to adipose tissue and sexual precocity in Nellore cattle. A total of 1689 precocious and non-precocious heifers belonging to farms participating in Conexão Delta G breeding program were studied. SNPs from the Illumina High-Density Bovine SNP BeadChip were used. This chip contains 777,000 SNPs located within the region of the candidate genes at a distance of up to 5 kb, considering that linkage disequilibrium (LD) exists at this distance. Linear models were used for statistical analysis. The fastPHASE and GenomeStudio programs were used for haplotype reconstruction and LD analysis based on r2 statistics. Fifty-seven candidate genes and 443 SNPs were analyzed: among the latter, 370 SNPs formed 83 haplotypes, while the remaining SNPs were studied separately. Statistical analysis showed that only three haplotypes, one haplotype consisting of two SNPs located in the FABP4 gene and two haplotypes consisting of four and two SNPs located in the PPP3CA gene, had a significant effect on sexual precocity at P < 0.05. It can be concluded that the FABP4 and PPP3CA genes influence sexual precocity and may therefore be used in selection programs designed to improve sexual precocity in Nellore cattle.

Growth performance, and carcass and meat quality traits in progeny of Poll Nellore, Angus and Brahman sires under tropical conditions

This study aimed to characterise progeny of sires representing major families in the Poll Nellore breed. Fourteen Poll Nellore sires, two Angus sires and one Brahman sire were mated by AI to ~400 multiparous Poll Nellore dams. Calves were raised and stocked on pasture in central Brazil until reaching ~18 months of age, then fed a sugarcane bagasse-based diet on an ad libitum basis until reaching market weight and finish (average 23 months). There were 236 Poll Nellore (N), 38 Angus × Poll Nellore (AN) and 31 Brahman × Poll Nellore (BN) calves born in total. The weaning and 423-day weight weights, and growth rates and pre- and post-weaning were greater (P < 0.05) in males than in female calves, and were influenced by breed and by sire within the N animals. The weaning weights were higher (P < 0.05) in AN and BN than in N calves. The 423-day weight weights were greater (P < 0.05) in AN calves, followed by BN, with straightbred N being lightest. Feedlot average daily gain was unaffected (P > 0.05) by sex or by sire within N, but was lowest (P < 0.05) in N cattle, and highest in AN and BN animals, which did not differ (P > 0.05). Heifers reached the end of the study with lower bodyweight (BW) and dressing percentage than steers, resulting in lower carcass weights, smaller longissimus muscle areas (LMA), but greater 12th to 13th rib backfat (BF) and similar marbling score and mean shear force. However, the proportion of carcasses grading Choice or Prime was numerically greater in heifers than in steers (23.6% vs 9.8%). AN cattle reached greater harvest weights than BN, and those were heavier than N cattle (P < 0.001). However, dressing percentages were lowest in AN animals, so that there was no significant difference in carcass weight between AN and BN cattle. AN carcasses also had greater LMA, BF and marbling scores than the N carcasses. The proportion of carcasses grading Choice or Prime was numerically greater in AN cattle than in the BN and N groups (25.9%, 11.8% and 15.9%, respectively). Steaks from AN calves were more tender than N steaks, with the BN steaks being intermediate. There was significant variation among N sires for final BW, dressing percentage, carcass weight, LMA and marbling score, but not for BF or mean shear force. The percentages of carcasses of N cattle grading Choice or Prime ranged from 0% to 61.5%. Three N sires produced progeny with greater than 40% of carcasses grading Choice or above (Berílio OB, Furador OB, and Litoral OB). Likewise, three N sires (Blitz OB, Furador OB and Sossego OB) had progeny with 67%, 62% and 75%, respectively, of steaks classified as tender. This study confirmed that Zebu cattle have inferior carcass and meat quality relative to AN crossbreds under tropical conditions, however there is substantial variation within the N breed for these traits, and several sires have a proportion of their progeny comparable in terms of meat tenderness to those of Angus sires.

Plane of nutrition of Corriedale ewe lambs from foetal life to the onset of breeding affects weight at service and reproductive outcome

The objective of this study was to identify periods in the life (foetal and postnatal) of Corriedale ewe lambs where different nutrition levels can affect bodyweight at breeding and pregnancy rate in their first year of life. The effect of three different phases of nutrition on the growth and pregnancy rate (n = 133) of Corriedale ewe lambs of 7 months of age were evaluated. Phase 1 included the last phase of gestation of their mothers (30 last days of gestation, Day –30; partum = Day 0) until marking (Day 24). Phase 2 was between marking and weaning (Day 114) and phase 3 between weaning to the onset of breeding (Day 207). For phase 1, 350 adult ewes had access to improved pastures (phase 1, H) or native pastures (phase 1, L). After lambing, all ewes and their lambs were offered native pastures. After marking only ewes bearing females lambs were kept. In phase 2, 67 lambs born to H and 66 lambs born to L ewes were sorted in two new treatments: access to native pastures supplemented with ~1% of their bodyweight with soybean meal (phase 2, H) or access to native pastures alone (phase 2, L). In phase 3, each of the lambs of the four treatments applied during phase 2 were sorted in two new treatments: access to improved pastures (phase 3, H) or native pastures supplemented with 0.7% of liveweight with soybean meal (phase 3, L). Breeding period lasted 41 days and pregnancy diagnosis was performed 86 days after the onset of breeding. The pregnancy rate varied from 0% to 47%. Phase 3 of nutrition was the only phase that affected pregnancy rate (28% vs. 10% for female lambs offered H and L plane of nutrition respectively; P = 0.005). A discriminative analysis demonstrated that the liveweight at breeding was the only variable that affected the success of pregnancy in ewe lambs (P = 0.0025). Moreover, the ewe lambs that were heavier at the onset of breeding (more than 35 kg or in average 38 kg) were the most successful to get pregnant (35% of pregnancy for lambs over 35 kg and 13% for lambs under 35 kg, P = 0.0044). In conclusion, under the conditions of this experiment, the most important parameters to explain successful pregnancy of ewe lambs were the growth rate after weaning, and the liveweight at the onset of breeding.

Association between single-nucleotide polymorphisms and milk production traits in buffalo

The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferroni's correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.

Genetic associations between temperament and performance traits in Nellore beef cattle

The aim of this study was to estimate genetic associations between temperament and performance traits. Temperament was evaluated in yearling male and female Nellore cattle, using four traits: temperament score (TS), for assessing animals' reactions in a corral pen (n = 25,691); movement score (MOV), for animals' movements recorded inside the crush; crush score (CS), for animal's general reactivity inside the crush; and flight speed (FS), for the speed (in m/s) at which the animals exited the crush (n = 11,697, for the last three methods); for all the temperament traits, lower scores indicate animals with calmer temperament. Performance traits were visual scores for conformation (C), finishing precocity (P) and muscling (M) evaluated at yearlings, and average daily gain (ADG) was estimated from weaning to yearling. Bayesian inference using Gibbs sampling was applied to estimate (co)variance components and genetic and phenotypic parameters. Heritability estimates for the temperament traits ranged from 0.07 (CS) to 0.28 (FS). Genetic correlations of the temperament traits with ADG and C, P and M were negative and ranged from -0.02 to -0.31. Phenotypic correlations were negative and consistently lower than the genetic, ranging from -0.08 to -0.02. It was concluded that the temperament traits assessed had favourable genetic correlation estimates with the performance traits studied. However, indirect responses in temperament when selecting for higher ADG and visual scoring system of C, P and M, will be low.