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.

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.

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.

Effect of early shearing during gestation on the productive and reproductive behavior of female sheep offspring in their first 18 months of age.

The research has shown the interesting contributions of shearing in mid-gestation on the performance of lambs from birth to weaning. Other studies have reported that shearing at early pregnancy influences the development of the placenta and lamb live weight at birth. However, there was a lack of information on the effect of early-prepartum shearing on the behavior of the offspring from weaning onward. This study evaluated the effect of shearing ewes at 50 days of gestation on the growth, reproductive behavior and response to a gastrointestinal parasite challenge in the female offspring from weaning to 18 months old. Fifty-seven Polwarth female lambs were used, 22 being singles and 35 twins born to ewes either shorn at 50 days of pregnancy (PS, n = 23) or shorn at 62 days postpartum (U, control, n = 34) resulting in four subgroups: single lambs born to PS ewes (n = 8), born to U ewes (n = 14), twin lambs born to PS ewes (n = 15) or born to U ewes (n = 20). All progeny were managed together under improved pasture with a minimum forage allowance of 6% live weight on dry basis. Body weight, body condition score and fecal eggs count were recorded every 14 days from weaning to 18 months of age. Concentrations of progesterone were measured weekly (from 4 to 10 months of age and from 14 to 18 months of age) to establish the onset of puberty. Ovulation rate at an induced and a natural heat (545 ± 1.0 and 562 ± 1.0 day old) was recorded. Prepartum shearing did not affect the age at puberty or the ovulation rate of female offspring, but those born as singles were more precocious ( P = 0.03) and heavier ( P = 0.02) at puberty than twin born lambs. Both the average value of parasite egg count ( P = 0.0 7) and the Famacha index ( P = 0.02) for the entire study period were lower in lambs born to prepartum shorn ewes than those born to postpartum shorn ewes. In conclusion, shearing at 50 days of gestation did not affect the growth or the reproductive behavior of female offspring. However, female lambs born from ewe shorn during gestation showed a better response to the parasitic challenge, and further research is required to confirm this.

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.

Genome-wide association study for growth traits in Nelore cattle.

The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology. The analyses were processed with the BLUPF90 family of programs. When applied to a genome-wide association studies, the single-step GBLUP methodology is an iterative process that estimates weights for the SNPs. The weights of SNPs were included in all analyses by iteratively applying the single-step GBLUP methodology and repeated twice so that the effect of the SNP and the effect of the animal were recalculated in order to increase the weight of SNPs with large effects and to reduce the weight of those with small effects. The genome-wide association results are reported based on the proportion of variance explained by windows of 50 adjacent SNPs. Considering the two iterations, only windows with an additive genetic variance >1.5% were presented in the results. Associations were observed with birth weight on BTA 14, with weight gain from birth to weaning on BTA 5 and 29, with weight gain from weaning to yearling on BTA 11, and with yearling height on BTA 8, showing the genes TMEM68 (transmembrane protein 8B) associated with birth weight and yearling height, XKR4 (XK, Kell blood group complex subunit-related family, member 4) associated with birth weight, NPR2 (natriuretic peptide receptor B) associated with yearling height, and REG3G (regenerating islet-derived 3-gamma) associated with weight gain from weaning to yearling. These genes play an important role in feed intake, weight gain and the regulation of skeletal growth.

Growth, meat and feed efficiency traits of lambs born to ewes submitted to energy restriction during mid-gestation.

The objective of this study was to evaluate the effects of the energy restriction of gestation of adult ewes from day 45 to day 115 on lamb live performance parameters, carcass and meat traits. In experiment I, dietary energy was restricted at 70% of the metabolizable energy (ME) requirements, after which ewes were re-fed ad libitum until lambing. In experiment II, dietary energy was restricted at 60% of the ME requirements, and ewes were re-fed to ME requirements until lambing. All ewes grazed together from the end of the restriction periods to weaning. Lambs were weaned and lot fed until slaughter. Feed intake, weight gain and feed efficiency were recorded, and body fat thickness and ribeye area (REA) were measured in the longissimus thoracis muscle. After slaughter, carcass weight and yield, fat depth, carcass and leg length, and frenched rack and leg weights and yields were determined. Muscle fiber type composition, Warner-Bratzler shear force, pH and color were determined in the longissimus lumborum muscle. In experiment I, energy restriction followed by ad libitum feeding affected lamb birth weight (P0.05) were observed on later BW, REA, BF or carcass traits. Lambs born to non-restricted-fed ewes had higher (P<0.05) weight and yield of the frenched rack cut and their meat tended (P=0.11) to be tender compared with that of lambs from restricted ewes. The percentage of oxidative muscle fibers was lower for lambs born to non-restricted ewes (P<0.05); however, no effects of ewe treatment were observed on other muscle fiber types. For experiment II, energy restriction followed by ME requirements feeding, affected (P<0.01) pre-weaning live weight gain, weaning and final weights. Lambs from restricted ewes had higher (P<0.05) feed intake as % of leg weight and a trend to be less efficient (P=0.16) than lambs from unrestricted dams. Ribeye area and BF were not influenced by treatment. Treatment significantly affected slaughter weight, but had no effects on carcass yield and traits or on meat traits. The results obtained in both experiments indicate submitting ewes to energy restriction during gestation affects the performance of their progeny but the final outcome would depend on the ewe's re-feeding level during late gestation and the capacity of the offspring to compensate the in utero restriction after birth.

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 (FROH ) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED ). The better results of FROH suggest that FROH 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.

Genetic parameter estimates for prenatal and postnatal mortality in Nellore cattle.

The aim of this study was to estimate genetic parameters for prenatal (PRE) and postnatal (POS) mortality in Nellore cattle. A total of 13 141 (PRE) and 17 818 (POS) records from Nellore females were used. PRE and POS were recorded using binary scale scores: a score of '1' was given to calves that were born alive (PRE) and those that were alive at weaning (POS), and a score of '0' was given to calves that were not alive at or around birth (PRE), as well as to those weighed at birth but not at weaning (POS). The relationship matrix included 698 sires, 107 paternal grandsires and 69 maternal grandsires. Data were analysed using Bayesian inference and a sire-maternal grandsire threshold model, including contemporary groups as random effects, and the classes of dam age at the beginning of mating season (for PRE), and dam age at calving and birthweight (linear covariable) (for POS), as fixed effects. For both traits, the covariance between direct and maternal effects (rD,M ) was estimated (rD,M ≠ 0) or fixed at zero (rD,M  = 0). PRE and POS rates were 3.00 and 4.04%, respectively. Estimates of direct and maternal heritability were 0.07 and 0.17, respectively, for PRE, and 0.02 and 0.07, respectively, for POS, assuming rD,M  = 0. For rD,M  ≠ 0, these estimates were 0.07 and 0.12, respectively, for PRE, and 0.03 and 0.07, respectively, for POS. The correlation estimates between direct and maternal effects were -0.71 (PRE) and -0.33 (POS). PRE and POS show low genetic variability, indicating that these traits probably suffer major environmental influences. Additionally, our study shows that the maternal genetic component affects preweaning calf mortality twice as much (or more) as the direct genetic component. A large number of offspring per sire is necessary in progeny tests to genetically decrease calf mortality.

Accuracies of genomic prediction of feed efficiency traits using different prediction and validation methods in an experimental Nelore cattle population.

Animal feeding is the most important economic component of beef production systems. Selection for feed efficiency has not been effective mainly due to difficult and high costs to obtain the phenotypes. The application of genomic selection using SNP can decrease the cost of animal evaluation as well as the generation interval. The objective of this study was to compare methods for genomic evaluation of feed efficiency traits using different cross-validation layouts in an experimental beef cattle population genotyped for a high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA). After quality control, a total of 437,197 SNP genotypes were available for 761 Nelore animals from the Institute of Animal Science, Sertãozinho, São Paulo, Brazil. The studied traits were residual feed intake, feed conversion ratio, ADG, and DMI. Methods of analysis were traditional BLUP, single-step genomic BLUP (ssGBLUP), genomic BLUP (GBLUP), and a Bayesian regression method (BayesCπ). Direct genomic values (DGV) from the last 2 methods were compared directly or in an index that combines DGV with parent average. Three cross-validation approaches were used to validate the models: 1) YOUNG, in which the partition into training and testing sets was based on year of birth and testing animals were born after 2010; 2) UNREL, in which the data set was split into 3 less related subsets and the validation was done in each subset a time; and 3) RANDOM, in which the data set was randomly divided into 4 subsets (considering the contemporary groups) and the validation was done in each subset at a time. On average, the RANDOM design provided the most accurate predictions. Average accuracies ranged from 0.10 to 0.58 using BLUP, from 0.09 to 0.48 using GBLUP, from 0.06 to 0.49 using BayesCπ, and from 0.22 to 0.49 using ssGBLUP. The most accurate and consistent predictions were obtained using ssGBLUP for all analyzed traits. The ssGBLUP seems to be more suitable to obtain genomic predictions for feed efficiency traits on an experimental population of genotyped animals.

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 (σam). 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 σam. Model 2 included Lc and σam was set to zero. Model 3 did not include Lc. Model 4 did not include Lc and σam 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 σam. 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 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.

Multivariate analysis of test-day and total milk yield in goats.

The objective of this study was to estimate genetic parameters for 305-day cumulative milk yield (MY305) and its association with test-day milk yield (TDMY) in Saanen and Alpine goats in order to provide information that allows the use of TDMY as selection criteria. This was done using standard multi-trait and reduced rank models. Data from 1157 lactations, including the first three kiddings, and 5435 test-day records from 683 Saanen and 449 Alpine goats were used. MY305 was analyzed together with TDMY by multi-trait analysis, from the first to tenth test-day, using records of the first three lactations as repeated measures. Three multi-trait models were used: a standard (SM) and two reduced rank models that fitted the first two (PC2) and three (PC3) genetic principal components. Akaike and Schwarz Bayesian information criteria were used to compare models. Heritability for TDMY estimated with the SM ranged from 0.20 to 0.66, whereas the range calculated from the PC2 model was 0.16 to 0.63. Genetic correlations between TDMY and MY305 were positive and moderate to high, ranging from 0.56 to 0.98 when estimated with the SM, and 0.91 to 1.00 when estimated with the PC2. The standard multi-trait model produced estimates that were more accurate than the reduced rank models. Although the SM provided the worst fit according to the two model selection criteria, it was the best in this dataset.

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.

Genetic associations between scrotal circumference and female reproductive traits in Nelore cattle.

The objective of this study was to estimate genetic associations between scrotal circumference obtained at 12 (SC12; mean of 21.46 ± 2.74 cm), 15 (SC15; mean of 25.31 ± 3.19 cm), and 18 mo of age (SC18; mean of 26.77 ± 2.95 cm) and reproductive traits measured directly in heifers (age at first calving [AFC]: mean of 1,062.06 ± 114.79 d; heifer pregnancy at 16 mo of age [HP]: mean of 15.4 ± 0.36%; and subsequent rebreeding of primiparous heifers [HR]: mean of 27.1 ± 0.44%) using Bayesian inference to evaluate the possible inclusion of these traits as selection criteria in beef cattle breeding programs. Genetic gains comparisons were also estimated. A total of 53,683 data of Nelore animals born between 1990 and 2006, obtained from the livestock archive of Agropecuária Jacarezinho Ltda. (Valparaíso, São Paulo, Brazil), were analyzed. Two-trait analysis provided heritability estimates of 0.35 ± 0.08, 0.40 ± 0.04, 0.37 ± 0.03, 0.21 ± 0.01, 0.55 ± 0.03, and 0.17 ± 0.03 for SC12, SC15, SC18, AFC, HP, and HR, respectively. The genetic correlations between scrotal circumference and AFC, HP, and HR were -0.42 ± 0.12, 0.43 ± 0.13, and -0.13 ± 0.17, respectively, for SC12; -0.25 ± 0.07, 0.26 ± 0.07, and -0.11 ± 0.10, respectively, for SC15; and -0.22 ± 0.06, 0.39 ± 0.06, and 0.11 ± 0.09, respectively, for SC18. The direct selection response for HP was 0.12%, but when HP is indirectly selected based on the scrotal circumferences, the gains on these correlated responses were higher (0.16, 0.16, and 0.22%) for selection based on SC12, SC15, and SC18, respectively. These findings suggest that the selection of animals for larger scrotal circumference, particularly at 12 mo of age, should result in higher rates of HP and younger AFC of Nelore females.

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.