EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

Genetic evaluation for latent variables derived from factor analysis in broilers

1. The aim of this study was to investigate the associations between several carcass, performance and meat quality traits in broilers through factor analysis and use the latent variables (i.e. factors) as pseudo-phenotypes in genetic evaluations.2. Factors were extracted using the principal components method and varimax rotation algorithm. Genetic parameters were estimated via Bayesian inference under a multiple-trait animal model.3. All factors taken together explained 71% of the original variance of the data. The first factor, denominated as 'weight', was associated with carcass and body weight traits; and the second factor, defined as 'tenderness', represented traits related to water-holding capacity and shear force. The third factor, 'colour', was associated with traits related to meat colour, whereas the fourth, referenced as 'viscera', was related to heart, liver and abdominal fat.4. The four biological factors presented moderate to high heritability (ranging from 0.35 to 0.75), which may confer genetic gains in this population.5. In conclusion, it seems possible to reduce the number of traits in the genetic evaluation of broilers using latent variables derived from factor analysis.

Genotype by environment interaction for yearling weight in Nellore cattle applying reaction norms models

In the present study, a possible existence of genotype × environment interaction was verified for yearling weight in Nellore cattle, utilising a reaction norms model. Therefore, possible changes in the breeding value were evaluated for 46 032 animals, from three distinct herds, according to the environmental gradient variation of the different contemporary groups. Under a Bayesian approach, analyses were carried out utilising INTERGEN software resulting in solutions of contemporary groups dispersed in the environmental gradient from –90 to +100 kg. The estimates of heritability coefficients ranged from 0.19 to 0.63 through the environmental gradient and the genetic correlation between intercept and slope of the reaction norms was 0.76. The genetic correlation considering all animals of the herds in the environmental gradient ranged from 0.83 to 1.0, and the correlation between breeding values of bulls in different environments ranged from 0.79 to 1.0. The results showed no effect of genotype × environment interaction on yearling weight in the herds of this study. However, it is important to verify a possible influence of the genotype × environment in the genetic evaluation of beef cattle, as different environments might cause interference in gene expression and consequently difference in phenotypic response.

Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

Zebu animals () are known to take longer to reach puberty compared with taurine animals (), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being -0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant ( < 0.05) terms associated with HP-"Munc18 Proteins," "Fucose," and "Hemoglobins"-and with NF-"Cathepsin B," "Receptors, Neuropeptide," and "Palmitic Acid." This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

Implications of SNP weighting on single-step genomic predictions for different reference population sizes

We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage for WssGBLUP was reduced or eliminated when more animals were genotyped. WssGBLUP had greater resolution for genome-wide association (GWA) as did increasing the number of genotyped animals. For few QTL, accuracy was greater for WssGBLUP than ssGBLUP; however, for many QTL, accuracy was the same for both methods. The largest genotyped set was used to assess the dimensionality of genomic information (number of effective SNP). The number of effective SNP was considerably less in weighted G than in unweighted G. Once the number of independent SNP is well represented in the genotyped population, the impact of SNP weighting becomes less important.

Parameters of a dynamic mechanistic model of cattle growth retain enough biological interpretation for genotype-to-phenotype mapping

This study aimed to investigate the predictability of a phenotype when using a dynamic model of cattle growth. Genotypic and phenotypic information on Nellore (Bos indicus) cattle were used in a genome-wide association analysis designed to contrast the biological interpretation of core parameters [conversion efficiency of metabolizable energy to net energy for gain (k_g) and adjusted final shrunk body weight (AFSBW)] to their associated genomic regions and nearby quantitative trait loci (QTLs). Single nucleotide polymorphisms (SNPs) were used to develop prediction equations for k_g and AFSBW, which enter the model for simulative prediction purposes. QTLs and genes, one related to mature body weight and another to growth efficiency, are consistent with the model equations. Significantly associated SNPs were used to compute parameters, which yielded reasonable model outcomes when compared with regular parameter computations. Our results provide evidence of the biological validity of using such parameters as component traits of higher phenotypes and the possibility of using genomic data for genotype-to-parameter mapping.

Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle

Feed intake, feed efficiency, and weight gain are important economic traits of beef cattle in feedlots. In the present study, we investigated the physiological processes underlying such traits from the point of view of systems genetics. Firstly, using data from 1334 Nellore (Bos indicus) cattle and 943,577 single nucleotide polymorphisms (SNPs), a genome-wide association analysis was performed for dry matter intake, average daily weight gain, feed conversion ratio, and residual feed intake with a Bayesian Lasso procedure. Genes within 50-kb SNPs, most relevant for explaining the genomic variance, were annotated and the biological processes underlying the traits were inferred from Database for Annotation, Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our results indicated several putative genomic regions associated with the target phenotypes and showed that almost all genomic variances were in the SNPs located in the intergenic and intronic regions. We further identified five main metabolic pathways related to ion transport, body composition, and feed intake control, which influenced the four phenotypes simultaneously. The systems genetics approach used in this study revealed novel pathways related to feed efficiency traits in beef cattle.

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.

Genetic grouping strategies in selection efficiency of composite beef cattle ( × )

The inclusion of genetic groups in sire evaluation has been widely used to represent genetic differences among animals not accounted for by the absence of parentage data. However, the definition of these groups is still arbitrary, and studies assessing the effects of genetic grouping strategies on the selection efficiency are rare. Therefore, the aim in this study was to compare genetic grouping strategies for animals with unknown parentage in prediction of breeding values (EBV). The total of 179,302 records of weaning weight (WW), 29,825 records of scrotal circumference (SC), and 70,302 records of muscling score (MUSC) from Montana Tropical animals, a Brazilian composite beef cattle population, were used. Genetic grouping strategies involving year of birth, sex of the unknown parent, birth farm, breed composition, and their combinations were evaluated. Estimated breeding values were predicted for each approach simulating a loss of genealogy data. Thereafter, these EBV were compared to those obtained in an analysis involving a real relationship matrix to estimate selection efficiency and correlations between EBV and animal rankings. The analysis model included the fixed effects of contemporary groups and class of the dam age at calving, the covariates of additive and nonadditive genetic effects, and age, and the additive genetic effect of animal as random effects. A second model also included the fixed effects of genetic group. The use of genetic groups resulted in means of selection efficiency and correlation of 70.4 to 97.1% and 0.51 to 0.94 for WW, 85.8 to 98.8% and 0.82 to 0.98 for SC, and 85.1 to 98.6% and 0.74 to 0.97 for MUSC, respectively. High selection efficiencies were observed for year of birth and breed composition strategies. The maximum absolute difference in annual genetic gain estimated through the use of complete genealogy and genetic groups were 0.38 kg for WW, 0.02 cm for SC, and 0.01 for MUSC, with lower differences obtained when year of birth was adopted as a genetic group criterion. Grouping strategy must consider selection decisions and the number of genetic groups formed, in the way that genetic groups represent the genetic differences in population and allow an adequate prediction of EBV.

A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.

Genome-wide association with residual body weight gain in Bos indicus cattle

Weight gain is a key performance trait for beef cat-tle; however, attention should be given to the production costs for better profitability. Therefore, a feed efficiency trait based on per-formance can be an interesting approach to improve performance without increasing food costs. To identify candidate genes and ge-nomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association test. We identified 30 significant single nucleotide polymorphisms (SNPs), especially on chromosomes 2, 8, 12, and 17. Several genes and quantitative train loci (QTLs) present in the regions identified were appointed; we highlight DMRT2 (doublesex and mab-3 related tran-scription factor 2), IFFO2 (intermediate filament family orphan 2), LNX2 (ligand of numb-protein X 2), MTIF3 (mitochondrial transla-tional initiation factor 3), and TRNAG-CCC (transfer RNA glycine anticodon CCC). The metabolic pathways that can explain part of the phenotypic variation in RWG are related to oxidative stress and muscle control.

Two-trait random regression model to estimate the genetic association of scrotal circumference with female reproductive performance in Nelore cattle

In an attempt to determine when scrotal circumference (SC) could be a reasonable indicator of female reproductive performance, a series of two-trait random regression model (regression for SC on age at measurement) using Gibbs sampling was applied to field data of Nelore cattle raised in a tropical environment. The female traits evaluated were age at first calving (AFC), first calving interval (FCI), heifer pregnancy (HP), and stayability (STAY). The posterior means of heritability of female traits ranged from 0.15 for AFC to 0.46 for HP and were about 0.50 for SC. The posterior means of genetic correlations between SC and AFC, FCI, HP, STAY were up to -0.70, -0.25, 0.48, and 0.29, respectively. Genetically, SC could be a reasonable indicator of female puberty (e.g., HP) as long as it is measured at a young age (400-440 days). However, for female reproductive traits measured at an older age (e.g., STAY), SC is merely a modest or even poor indicator. The use of sire expected progeny differences for female reproductive traits will be more effective than the use of expected progeny differences for SC to improve the reproductive performance of female cattle.

Genetic relationships among traits related to reproduction and growth of Nelore females

The objective of the study presented here was to analyze the genetic relationships among heifer pregnancy (HP), age at first calving (AFC), stayability (STAY), average annual productivity of the cow, in kilograms of weaned calf per cow per year (PRODAM), postweaning weight gain (PWG), and hip height (HH) of Nelore females from 12 Brazilian herds. (Co)variance components were obtained by six-trait animal model using Gibbs sampling. The posterior mean of the heritability estimates were 0.37, 0.18, 0.19, 0.16, 0.21, and 0.37 for HP, AFC, STAY, PRODAM, PWG, and HH, respectively. In general, the genetic correlations were strong between traits related to reproduction, for example, -0.85 between HP and AFC, and 0.94 between STAY and PRODAM. Weak genetic correlations were obtained between reproductive and growth traits (absolute values ranging from 0.02 to 0.30). Although weak, the genetic correlations between PWG and reproductive traits were favorable, whereas the genetic correlations between HH and reproductive traits were close to zero and slightly unfavorable for HP, AFC, and STAY. An increase of HH is therefore expected to have little or no negative effect on the reproductive performance of females. The posterior mean of genetic correlation between PWG and HH was moderate (0.50). On the basis of the heritability, genetic correlation estimates, and time to obtain data, HP and PRODAM seems to show the best potential as selection criteria to improve the productive and reproductive performance of Nelore females. In principle, it is possible to select for increased PWG without compromising the reproduction of Nelore females. However, selection for PWG may result in an increase of female HH as a correlated response, a fact that could increase management costs in advanced generations of selection. In the light of the results, all traits studied here can be used as selection criteria and there is no strong evidence of genetic antagonism among traits related to reproduction and growth of Nelore females.

Quantitative genetic study of age at subsequent rebreeding in Nellore cattle by using survival analysis

The continuous trait age at subsequent rebreeding (ASR) was evaluated using survival analysis in Nellore breed cows that conceived for the first time at approximately 14 months of age. This methodology was chosen because the restricted breeding season produces censored data. The dataset contained 2885 records of ASR (in days). Records of females that did not produce calves in the following year after being exposed to a sire were considered censored (48.3% of the total). The statistical model used was a Weibull mixed survival model, which included fixed effects of contemporary groups (CG) and period and a random effect of individual animal. The effect of contemporary groups on ASR was significant (P < 0.01). Heritabilities obtained for ASR were 0.03 and 0.04 in logarithmic and original scales, respectively. These results indicate that the genetic selection response for subsequent reproduction of 2-year-old Nellore breed females is not expected to be effective based on survival analysis. Furthermore, these results suggest that environmental improvement is fundamental to this important trait. It should be highlighted that an increase in the average date of birth can produce an adverse effect in the future, since this cannot be compensated by genetic improvement.

Genotype by environment interaction for post-weaning weight gain, scrotal circumference, and muscling score of composite beef cattle in different regions of Brazil

The objectives of this study were to characterize and define homogenous production environments of composite beef cattle in Brazil in terms of climatic and geographic variables by using multivariate exploratory techniques; to evaluate the presence of genotype by environment interaction (GxE) for post-weaning weight gain (PWG), yearling scrotal circumference (SC), and yearling muscling (MUS). Hierarchical and nonhierarchical cluster analysis was used to group farms located in regions with similar environmental variables into clusters. Six clusters of farms were formed. The effect of sire-cluster interaction was tested by single-trait analysis. Genetic parameters were estimated by multi-trait analysis considering the same trait to be different in each cluster. The effect of sire-cluster interaction was significant (P <0.01) for PWG and MUS. Estimates of genetic correlations among clusters ranged from 0.31 to 0.93 for PWG, 0.64 to 0.89 for SC, and 0.18 to 0.80 for MUS. These results indicate the need for a genetic analysis on a regional basis or inclusion of the GxE effect in the statistical model to permit appropriate evaluation of the animals.

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

The genome-wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354,147 single-nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777,962 SNPs) and Illumina BovineSNP50 (54,609) by imputation were used. After quality control and imputation, 290,620 SNPs remained in the association analysis, using R package Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma. A genomic region with six significant SNPs, at Bonferroni-corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10(-8)) explained 5.62% of the phenotypic variance and had the allele substitution effect of -0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.

Genotype by environment interaction and model comparison for growth traits of Santa Ines sheep

The objectives of the present study were to compare alternative models for the genetic evaluation and assess the importance of genotype by environment interaction (G×E) in the estimation of genetic parameters and genetic evaluation of birth weight (BW), weight at 60 days of age (W60) and weight at 180 days of age (W180) of Santa Ines sheep. Data comprise 7622 BW, 4673 W60 and 2830 W180 records from animals born in 44 Brazilian herds. Four models were used for the analyses: animal model (AM) with homogeneous residual variance (1), or heterogeneous residual variance (2), hierarchical reaction norms model (HRNM) with homogeneous (1) or heterogeneous residual variance (2). The models that best fit the BW, W60 and W180 data were AM2, HRNM1 and HRNM2 respectively. Thus, models for genetic evaluation that consider heterogeneity of variances are recommended to evaluate growth traits of sheep. The correlation between intercept and slope of the HRNM was higher than 0.70 for all traits studied, indicating that animals with higher average breeding values responded better to improvement in environmental conditions, a fact characterizing the scale effect of G×E. Therefore, G×E is an important factor to be considered in the estimation of genetic parameters and genetic evaluation of growth traits of sheep.

Protein synthesis and degradation gene SNPs related to feed intake, feed efficiency, growth, and ultrasound carcass traits in Nellore cattle

We looked for possible associations of SNPs in genes related to protein turnover, with growth, feed efficiency and carcass traits in feedlot Nellore cattle. Purebred Nellore bulls and steers (N = 290; 378 ± 42 kg body weight, 23 months ± 42 days old) were evaluated for daily feed intake, body weight gain (BWG), gross feed efficiency, feed conversion ratio, partial efficiency of growth, residual feed intake (RFI), ultrasound backfat, rump fat, and ribeye area. Genotypes were obtained for SNPs in the growth hormone receptor (GHR-1 and GHR-2); calpain (CAPN4751); calpastatin (UoGCAST); ubiquitin-conjugating enzyme 2I (UBE2I-1 and UBE2I-2); R3H domain containing 1 (R3HDM1-1, -2, -3, and -4), ring finger protein 19 (RNF19); proteasome 26S subunit, non-ATPase, 13 (PSMD13); ribosomal protein, large, P2 (RPLP2); and isoleucine-tRNA synthetase 2, mitochondrial (IARS2) genes. Allelic substitution, additive and dominant effects were tested and molecular breeding values were computed. CAPN4751, GHR-1 and -2, IARS2, R3HDM1-4, and UoGCAST were found to be normally segregating polymorphisms. Additive and dominance effects were observed on BWG, feed efficiency and carcass traits, although dominant effects predominated. Significant allelic substitution effects were observed for CAPN4751, GHR-1 and -2, and UoGCAST on BWG, gross feed efficiency, RFI, and carcass traits, under single- or multiple-marker analyses. Correlations between molecular breeding values and phenotypes were low, excepted for RFI, based on allelic substitution estimates obtained by stepwise linear regression. We conclude that SNPs in genes related to protein turnover are related to economically important traits in Nellore cattle.

Identification and association of polymorphisms in CAPN1 and CAPN3 candidate genes related to performance and meat quality traits in chickens

Meat quality is an important feature for the poultry industry and is associated with consumer satisfaction. The calpain 1 (CAPN1) gene is related to the tenderness process of meat post- mortem, and the calpain 3 (CAPN3) gene plays an important role in myofibrillar organization and growth. The objective of the present study was to identify polymorphisms in these genes and to determine the association between these polymorphisms and traits of economic interest in poultry. Eleven animals (F₁) from an experimental poultry population at Embrapa Swine and Poultry were used to identify the polymorphisms. Four single nucleotide polymorphisms (SNPs) were found in the CAPN1 gene, and one SNP was found in the CAPN3 gene. A polymorphism from each gene was selected for genotyping in 152 chickens from the Embrapa F₂ experimental population and 311 chickens from a commercial population. Polymorphism g.2554T>C (CAPN1) was associated with body weight at 35 to 42 days, thigh weight, breast weight, carcass weight, and meat lightness content. SNP g.15486C>T (CAPN3) was associated with thigh yield, thawing-cooking loss, and shear force. Results suggest the possibility of using molecular markers in CAPN1 and CAPN3 genes as a tool for performance and meat quality traits in poultry breeding programs.

Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens

In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellular differentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P < 0.05), and SNP g.651G>A in FGFBP2 was associated with thawing loss and meat redness content (P < 0.05). Four haplotypes were constructed based on 2 SNPs and were associated with breast weight, thawing loss, and meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits.

Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle

Given the important role of leptin in metabolism, we looked for a possible association of leptin and leptin receptor polymorphisms with carcass and growth traits in Nellore cattle. We examined associations of leptin and leptin receptor SNPs with ultrasound carcass (longissimus dorsi muscle area (ribeye area), backfat thickness and rump fat thickness and growth traits (weaning weight adjusted to 210 days of age, yearling weight adjusted to 550 days of age, weight gain of weaning to yearling and scrotal circumference adjusted to 550 days of age) of 2162 Bos primigenius indicus (Nellore) animals. Allele and genotypic frequencies were calculated for each marker. Allele substitution, additive and dominance effects of the polymorphisms were also evaluated. Some alleles of the molecular markers had low frequencies, lower than 1%, in the sample analyzed, although the same polymorphisms described for B. p. taurus cattle were found. Due to very low allelic frequencies, the E2JW, A59V and UASMS2 markers were not included in the analysis, because they were almost fixed. E2FB was found to be significantly associated with weight gain, ribeye area and backfat thickness. The promoter region markers, C963T and UASMS1, were also found to be significantly associated with ribeye area. T945M was significantly associated with weight gain. We conclude that the leptin and receptor gene markers would be useful for marker-assisted selection.

Single nucleotide polymorphisms in CAPN and leptin genes associated with meat color and tenderness in Nellore cattle

We analyzed single nucleotide polymorphisms in calpain, leptin, leptin receptor, and growth hormone receptor genes and their association with color, drip and cooking losses of longissimus muscle at 7, 14 and 21 days postmortem in 638 purebred Nellore bulls slaughtered between 22 and 26 months of age. Meat samples were vacuum-packed and aged at 4°C. The single nucleotide polymorphisms T945M, GHR2, E2FB, and CAPN4751 were evaluated. All genotypic classes were observed; however, the T/T genotype of T945M and E2FB was found at a low frequency. A significant association of E2FB with drip loss (a measure of water-holding capacity) was detected at seven days of meat aging. CAPN4751 had an additive effect on red and yellow color intensities. The T allele of CAPN4751 was found to be positively associated with improved meat color, but not with meat tenderness, differing from a previous report indicating that it is associated with meat tenderness. We conclude that the potential for use of CAPN4751 as a marker for these meat quality traits requires further research.

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.

Assessment of inbreeding depression in a Guzerat dairy herd: effects of individual increase in inbreeding coefficients on production and reproduction

Influences of inbreeding on daily milk yield (DMY), age at first calving (AFC), and calving intervals (CI) were determined on a highly inbred zebu dairy subpopulation of the Guzerat breed. Variance components were estimated using animal models in single-trait analyses. Two approaches were employed to estimate inbreeding depression: using individual increase in inbreeding coefficients or using inbreeding coefficients as possible covariates included in the statistical models. The pedigree file included 9,915 animals, of which 9,055 were inbred, with an average inbreeding coefficient of 15.2%. The maximum inbreeding coefficient observed was 49.45%, and the average inbreeding for the females still in the herd during the analysis was 26.42%. Heritability estimates were 0.27 for DMY and 0.38 for AFC. The genetic variance ratio estimated with the random regression model for CI ranged around 0.10. Increased inbreeding caused poorer performance in DMY, AFC, and CI. However, some of the cows with the highest milk yield were among the highly inbred animals in this subpopulation. Individual increase in inbreeding used as a covariate in the statistical models accounted for inbreeding depression while avoiding overestimation that may result when fitting inbreeding coefficients.

Additive genetic relationships between scrotal circumference, heifer pregnancy, and stayability in Nellore cattle

Scrotal circumference data from 47,605 Nellore young bulls, measured at around 18 mo of age (SC18), were analyzed simultaneously with 27,924 heifer pregnancy (HP) and 80,831 stayability (STAY) records to estimate their additive genetic relationships. Additionally, the possibility that economically relevant traits measured directly in females could replace SC18 as a selection criterion was verified. Heifer pregnancy was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 d. Females were exposed to sires for the first time at about 14 mo of age (between 11 and 16 mo). Stayability was defined as whether or not a cow calved every year up to 5 yr of age, when the opportunity to breed was provided. A Bayesian linear-threshold-threshold analysis via Gibbs sampler was used to estimate the variance and covariance components of the multitrait model. Heritability estimates were 0.42 ± 0.01, 0.53 ± 0.03, and 0.10 ± 0.01, for SC18, HP, and STAY, respectively. The genetic correlation estimates were 0.29 ± 0.05, 0.19 ± 0.05, and 0.64 ± 0.07 between SC18 and HP, SC18 and STAY, and HP and STAY, respectively. The residual correlation estimate between HP and STAY was -0.08 ± 0.03. The heritability values indicate the existence of considerable genetic variance for SC18 and HP traits. However, genetic correlations between SC18 and the female reproductive traits analyzed in the present study can only be considered moderate. The small residual correlation between HP and STAY suggests that environmental effects common to both traits are not major. The large heritability estimate for HP and the high genetic correlation between HP and STAY obtained in the present study confirm that EPD for HP can be used to select bulls for the production of precocious, fertile, and long-lived daughters. Moreover, SC18 could be incorporated in multitrait analysis to improve the prediction accuracy for HP genetic merit of young bulls.

Association of single nucleotide polymorphisms with carcass traits in Nellore cattle

The association between two single nucleotide polymorphisms (SNPs), T945M and UCP1SNP1, with hot carcass weight (HCW, kg, N = 618), longissimus dorsi muscle area (REA, cm(2), N = 633), and backfat thickness (BF, mm, N = 625), measured in Nellore cattle in Brazil, was evaluated. Likelihood ratio tests were used to evaluate reduced (fixed effects of general mean, contemporary group, yearling weight, age at slaughter, and random effect of infinitesimal genetic value) and full model (reduced model effects plus quantitative trait locus effects). Additive and dominance effects were tested for each SNP. Genotypic and gene frequencies were also obtained for the SNPs and a descriptive phenotype analysis was made. Mean values for HCW, REA and BF were equal to 288.13 +/- 0.55 kg, 73.14 +/- 0.27 cm(2), and 4.28 +/- 0.07 mm, respectively; the coefficients of variation were 4.74, 9.24, and 42.43%, respectively. Gene frequencies for T945M and UCP1SNP1 were f(C) = 0.89, f(T) = 0.11, f(C) = 0.81, and f(G) = 0.19. The SNP T945M had a genotypic frequency of only three animals for TT genotype. Additive effects were observed for T945M on REA and BF, while UCP1SNP1 affected HCW and BF. Based on the significant additive effects of the SNPs and the gene frequencies that we found, we can expect genetic gains with marker assisted selection.

Genetic parameters for productive life traits and reproductive efficiency traits at 6 years in Nellore cattle

The objective of the present study was to estimate (co)variance components for length of productive life (LPL) and some alternative reproductive traits of 6-year-old Nellore cattle. The data set contained 57,410 records for age at first calving from Nellore females and was edited to remove animal records with uncertain paternity and cows with just one piece of calving information. Only animals with age at first calving ranging from 23 to 48 months and calving intervals between 11 and 24 months were kept for analysis. LPL and life production (LP) were used to describe productive life. LPL was defined as the number of months a cow was kept in the herd until she was 6 years old, given that she was alive at first calving and LP was defined as total number of calves in that time. Four traits were used to describe reproductive traits: two breeding efficiencies on original scale were estimated using Wilcox and Tomar functions (BEW and BET, respectively), and two breeding efficiencies transformed (ASBEW and ASBET, respectively), using the function [arcsine (square root (BEi/100))]. Estimates of heritability for measures of LPL and LP were low and ranged from 0.04 to 0.05. Estimates of heritability for breeding efficiencies on original and transformed scales oscillated from 0.18 to 0.32. Estimates of genetic correlations ranged from -0.57 to 0.79 for LPL and other traits and from 0.28 to 0.63 for LP and other traits.

Desenvolvimento de índice de seleção em gado corte sob o enfoque de um modelo bioeconômico

O presente trabalho teve por objetivo desenvolver um modelo bioeconômico para deter-minação de ponderadores econômicos utilizados em índices de seleção em programas de melhoramento genético de bovinos de corte. Foi desenvolvido um cenário padrão, onde, em termos absolutos, as características de maior relevância econômica foram o rendimento de carcaça, as características ligadas à fertilidade do rebanho, seguidas pelas características de peso e ganho de peso e por último as referentes à mortalidade. Os valores genético-econômicos obtidos foram, para habilidade de permanência (HP) 0,879; para probabilidade de prenhes ao 14 meses de idade (PP14) 0,201; para ganho de peso pós-desmama (GPD245) 0,190; para peso a desmama (PD) 0,061; e 0,080 para peso ao sobreano (PS). Portanto, verificou-se que as características reprodutivas, HP e PP14, foram de 4,28 a 13,46 vezes mais importantes economicamente do que as características de crescimento GPD245, PD e PS.

Estimates of genetic trend for carcass traits in a commercial broiler line

Data from the slaughter of 24,001 chickens that were part of a selection program for the production of commercial broilers were used to estimate genetic trend for absolute carcass (CW), breast meat (BRW), and leg (LW) weights, and relative carcass (CY), breast meat (BRY), and leg (LY) weights. The components of (co)variance and breeding values of individuals were obtained by the restricted maximum likelihood method applied to animal models. The relationship matrix was composed of 132,442 birds. The models included as random effects, maternal additive genetic and permanent environmental for CW, BRW, LW, CY, and BRY, and only maternal permanent environmental for LY, besides the direct additive genetic and residual effects, and as fixed effects, hatch week, parents' mating group and sex. The estimates of genetic trend were obtained by average regression of breeding value on generation, and the average genetic trend was estimated by regression coefficients. The genetic trends for CW (+6.0336 g/generation), BRW (+3.6723 g/generation), LW (+1.5846 g/generation), CY (+0.1195%/generation), and BRY (+0.1388%/generation) were positive, and they were in accordance with the objectives of the selection program for these traits. The genetic trend for LY (-0.0019%/generation) was negative, possibly due to the strong emphasis on selection for BRY and the negative correlations between these two traits.

Genetic parameters for growth traits of a Brazilian Bos taurus x Bos indicus beef composite

The genetic analysis of composite data is very complicated, mainly because it is necessary to adjust data to the effects of heterosis and breed complementarity, and because there is usually considerable confounding of these data with several other effects, such as contemporary group effects, breed composition of the animal and maternal breed composition, among others. Data on birth weight (n = 151,083), weaning weight adjusted to 205 days (n = 137,257), yearling weight adjusted to 390 days (n = 61,410), weight gain from weaning to yearling (n = 56,653), and scrotum circumference (n = 23,323) and muscle score (n = 54,770), both adjusted to 390 days, from Bos taurus x Bos indicus composite beef calves born from 1994 to 2003 were analyzed to estimate (co)variance components and genetic parameters of growth traits. The animals belonged to the Montana Tropical program. Estimation was made by three models that approach adjustment to heterozygosis in order to suggest the best model. The RM model included contemporary groups, class of age of dam, outcrossing percentages for direct and maternal effects, and direct and maternal additive genetic breed effects as covariates; the R model was the same as RM, but without additive maternal breed effects, and H was the same as RM, but not considering any additive breed effect. Both R2 values and consistency of genetic parameters indicate that the more complex model (RM), which considers maternal and individual additive genetic breed effect, produces the best estimates when compared to other models. The R model seems to overestimate (co)variance components. The magnitudes of direct and maternal heritability estimates, obtained in this study, would permit genetic improvement for weight and growth traits, as much by selection of direct genetic effects for weight and growth as for the improvement of maternal performance, but in different lineages. Therefore, the correlations between these effects were unfavorable.

Genetic trends of absolute and relative heart weight in a male broiler line

Data of chickens from a broiler-breeding program have been collected and used for determination of genetic trends of absolute and relative heart weight. The genetic trends have been estimated by regression of the genetic values of the traits over hatch-year. Genetic values of 42,912 individuals, obtained by restricted maximum likelihood, were used for regression analysis. The estimates of the genetic trends for absolute and relative heart weight were found to be -0.08 g and -0.004% per hatch-year, respectively. These trends show that heart weight in the line analyzed, in absolute and relative terms, has tended to decrease, which can make the metabolic disorders due to the reduction in heart weight in broilers even worse.

Study of stayability in Nellore cows using a threshold model1

The objectives of the current study were to assess the feasibility of using stayability traits to improve fertility of Nellore cows and to examine the genetic relationship among the stayabilities at different ages. Stayability was defined as whether a cow calved every year up to the age of 5 (Stay5), 6 (Stay6), or 7 (Stay7) yr of age or more, given that she was provided the opportunity to breed. Data were analyzed based on a maximum a posteriori probit threshold model to predict breeding values on the liability scale, whereas the Gibbs sampler was used to estimate variance components. The EBV were obtained using all animals included in the pedigree or bulls with at least 10 daughters with stayability observations, and average genetic trends were obtained in the liability and transformed to the probability scale. Additional analyses were performed to study the genetic relationship among stayability traits, which were compared by contrasting results in terms of EBV and the average genetic superiority as a function of the selected proportion of sires. Heritability estimates and SD were 0.25 +/- 0.02, 0.22 +/- 0.03, and 0.28 +/- 0.03 for Stay5, Stay6, and Stay7, respectively. Average genetic trends, by year, were 0.51, 0.34, and 0.38% for Stay5, Stay6, and Stay7, respectively. Estimates of EBV SD, in the probability scale, for all animals included in the pedigree and for bulls with at least 10 daughters with stayability observations were 7.98 and 12.95, 6.93 and 11.38, and 8.24 and 14.30% for Stay5, Stay6, and Stay7, respectively. A reduction in the average genetic superiorities in Stay7 would be expected if the selection were based on Stay5 or Stay6. Nonetheless, the reduction in EPD, depending on selection intensity, is on average 0.74 and 1.55%, respectively. Regressions of the sires' EBV for Stay5 and Stay6 on the sires' EBV for Stay7 confirmed these results. The heritability and genetic trend estimates for all stayability traits indicate that it is possible to improve fertility with selection based on a threshold analysis of stayability. The SD of EBV for stayability traits show that there is adequate genetic variability among animals to justify inclusion of stayability as a selection criterion. The potential linear relationship among stayability traits indicates that selection for improved female traits would be more effective by having predictions on the Stay5 trait.

Phenotypic and genetic correlations for body structure scores (frame) with productive traits and index for CEIP classification in Nellore beef cattle

The present study was carried out to estimate both (co)variance components and genetic parameters for frame scores obtained using two methods (FRAME_GMA and FRAME_BIF) as well as phenotypic and genetic correlations with traits such as weaning weight, weight gain from weaning to yearling, scrotal circumference, muscle score, and an empiric index for animal classification for the Special Certificate of Identification and Production (CEIP). Data on 12,728 animals, raised in Southeastern Brazil, with ages from 490 to 610 days were analyzed. Estimates of heritability for FRAME_GMA and FRAME_BIF in multi-trait analysis were 0.28 and 0.24, respectively. Genetic correlation coefficients between frame scores and the growth trait were of medium magnitude, which indicates that genetic selection for weight resulted in undesirable responses, increasing the animals' frames. Small changes should be expected in the frame of animals that have been submitted to a genetic selection regarding muscle score and scrotal circumference. The low magnitude of phenotypic and genetic correlation between frame scores and the empirical selection index that classifies animals for CEIP, a Brazilian official certificate that recognizes the value of seedstock that is not registered at breeders associations, but is genetically evaluated, does not indicate important responses in giving a CEIP to animals that have been directly or indirectly selected for frame. Other studies must be performed to determine estimates of the genetic parameters for frame scores in other beef cattle populations.

Estimation of genetic parameters for a new model for defining body structure scores (frame scores) in Nellore cattle

Models for estimation of frame scores in Nellore beef cattle (FRAME_GMA) were developed, comparing them with frame scores estimated using equations proposed by the Beef Improvement Federation (FRAME_BIF, USA). Correlation among frame scores obtained by these two methodologies, along with the independent variables considered in the estimation models, were also studied. A data set with 12,728 animals, with ages between 490 and 610 days, was used. The models that best adjusted to FRAME_GMA included hip height, weight and interaction between height and weight. Estimates of heritability for FRAME_GMA and FRAME_BIF were 0.26 +/- 0.03 and 0.23 +/- 0.03, respectively, in single trait analysis, and 0.28 and 0.24, respectively, in multi-trait analysis. Phenotypic Pearson and Spearman correlation coefficients between FRAME_GMA and FRAME_BIF for males were 0.87 and 0.83, respectively, being lower than those found for females (0.92 for both coefficients). Genetic correlation between the frame scores did not differ between genders, with values of 0.92 for the Pearson coefficient and 0.91 for the Spearman coefficient. We concluded that FRAME_GMA was better adapted to this data set than FRAME_BIF. Other studies need to be made to evaluate the applicability of this proposed model to other populations of Nellore beef cattle and for other age groups.

Genetic correlation between heifer pregnancy and scrotal circumference measured at 15 and 18 months of age in Nellore cattle

Data of pregnancy diagnosis from 24,945 Nellore heifers, raised under tropical conditions in Brazil and exposed to breeding at about 14 months of age, were analyzed simultaneously with 13,742 (analysis 1), 36,091 (analysis 2), 8,405 (analysis 3), and 8,405 (analysis 4) scrotal circumference (SC) records of contemporary young bulls in order to estimate heritability (h(2)) for yearling heifer pregnancy (HP) and for SC measured at around 15 (SC15) and 18 (SC18) months of age and to estimate genetic correlation between HP and SC15 (SC18). Heifer pregnancy was considered as a categorical trait, with the value 1 (success) assigned to heifers that were detected as pregnant by rectal palpation approximately 60 days after the end of a 90-day breeding season and the value 0 (failure) otherwise. In analyses 1 and 3, SC was measured at around 15 months of age and in analysis 2 and 4 it was measured at around 18 months of age. Only 8,848 animals from datasets 1 and 2 were common in both files, which means the same animals measured at different ages. Datasets used in analyses 3 and 4 included the same animals, measured at 15 and at 18 months of age, respectively. Heritability estimates for HP were similar in all analyses, with values ranging from 0.66 +/- 0.08 to 0.67 +/- 0.008. For SC15, the estimates were 0.57 +/- 0.05 in analysis 1 and 0.60 +/- 0.07 in analysis 3. For SC18, the estimates were 0.53 +/- 0.03 in analysis 2 and 0.64 +/- 0.06 in analysis 4. The estimates of genetic correlation between HP and SC15 were 0.15 +/- 0.10 in analysis 1 and 0.11 +/- 0.11 in analysis 3. For the correlation between HP and SC18, the values were 0.27 +/- 0.10 in analysis 2 and 0.16 +/- 0.11 in analysis 4. Based on standard errors and confidence intervals, the best heritability and genetic correlation estimates were obtained from analysis 2, which included more data and a better pedigree structure. Pearson correlation between HP and SC breeding values was similar to the genetic correlation estimates obtained from two-trait models, when all animals in the pedigree file were considered for its calculation. If only sires were considered for the calculation, Pearson correlation was higher but the pattern was the same as from two-trait analyses. The high heritability estimates obtained in the present study confirm that expected progeny difference (EPD) for HP can be used to select bulls for the production of precocious daughters and that the low genetic correlation between SC and HP indicates a greater efficacy of selection based on heifer pregnancy EPD than of selection based on scrotal circumference EPD. The results of the present study, although not conclusive, indicate that SC measured at around SC18 would have a higher genetic correlation with HP than would SC measured at around SC15.

Heritability and Genetic Correlation Estimates for Performance and Carcass and Body Composition Traits in a Male Broiler Line

The current research was conducted to estimate the heritability coefficients and the genetic correlations for performance and carcass and body composition traits in a single sire broiler line. The performance traits analyzed were BW at 38 d, ultrasound records of pectoral muscle depth, feed intake, feed conversion ratio, and BW at 42 d. The carcass traits analyzed were eviscerated BW, breast weight, and leg weight, and the body composition traits analyzed were abdominal fat content, heart weight, gizzard weight, liver weight, and intestine weight. The number of observations varied between 4,120 and 29,040 for each trait. The (co)variance components, heritability, and genetic correlation estimates were obtained by restricted maximum likelihood. The numerator relationship matrix had 42,912 animals. Based on the heritability estimates obtained, the analyzed traits seemed to be able to respond to selection, at variable intensities. The genetic correlation estimates between a great number of performance traits, as well as between a great number of carcass traits, were suggestive of a close genetic relationship between these traits. The genetic correlation estimates between body composition traits were variable. A large genetic association between a great number of performance and carcass traits seemed to exist. The genetic correlation estimates between performance and body composition traits were variable, and important associations between carcass and body composition traits did not seem to exist.

Additive genetic relationships between heifer pregnancy and scrotal circumference in Nellore cattle1

To estimate heritability (h2) for yearling heifer pregnancy and to estimate the genetic correlation between heifer pregnancy and scrotal circumference, 18,145 records of Nellore heifers exposed to breeding at an age of approximately 14 mo and 25,466 records of contemporary young bulls were analyzed. Heifer pregnancy was considered as a categorical trait, with the value 1 (success) assigned to heifers that were pregnant after rectal palpation approximately 60 d after the end of a 90-d breeding season and the value 0 (failure) otherwise. A single-trait animal model for heifer pregnancy and a two-trait animal model including heifer pregnancy and scrotal circumference were used. Contemporary groups were defined in two ways: including (CG2) or not including (CG1) weaning management of the heifer. Heritability estimates obtained by Method R in single-trait analyses were 0.68 +/- 0.09 and 0.61 +/- 0.10 using CG1 and CG2 definitions, respectively. Heritability estimates for two-trait analyses were 0.69 +/- 0.09 (CG1) and 0.63 +/- 0.08 (CG2) for heifer pregnancy and 0.57 +/- 0.03 (both CG) for scrotal circumference. The genetic correlation estimates between the two traits were 0.20 +/- 0.12 (CG1) and 0.20 +/- 0.13 (CG2). Based on the results of this study, EPD for heifer pregnancy can be used to select bulls for the production of precocious daughters and will be more effective than selecting on scrotal circumference EPD in Nellore cattle. However, scrotal circumference can be incorporated in a two-trait analysis to increase the accuracy of prediction for heifer pregnancy EPD for young bulls. Using contemporary group without heifer weaning management gave higher h2 and, for two-trait analysis, converged more quickly.

Genetic evaluation of the probability of pregnancy at 14 months for Nellore heifers

To estimate the heritability for the probability that yearling heifers would become pregnant, we analyzed the records of 11,487 Nellore animals that participated in breeding seasons at three farms in the Brazilian states of São Paulo and Mato Grosso do Sul. All heifers were exposed to a bull at the age of about 14 mo. The probability of pregnancy was analyzed as a categorical trait, with a value of 1 (success) assigned to heifers that were diagnosed pregnant by rectal palpation about 60 d after the end of the breeding season of 90 d and a value of 0 (failure) assigned to those that were not pregnant at that time. The estimate of heritability, obtained by Method R, was 0.57 with standard error of 0.01. The EPD was predicted using a maximum a posteriori threshold method and was expressed as deviations from 50% probability. The range in EPD was -24.50 to 24.55%, with a mean of 0.78% and a SD of 7.46%. We conclude that EPD for probability of pregnancy can be used to select heifers with a higher probability of being fertile. However, it is mainly recommended for the selection of bulls for the production of precocious daughters because the accuracy of prediction is higher for bulls, depending on their number of daughters.