Unknown parent groups and truncated pedigree in single-step genomic evaluations of Murrah buffaloes.

Missing pedigrees may produce bias in genomic evaluations. Thus, strategies to deal with this problem have been proposed as using unknown parent groups (UPG) or truncated pedigrees. The aim of this study was to investigate the impact of modeling missing pedigrees under single-step genomic best linear unbiased prediction (ssGBLUP) evaluations for productive and reproductive traits in dairy buffalo using different approaches: (1) traditional BLUP without UPG (BLUP), (2) traditional BLUP including UPG (BLUP/UPG), (3) ssGBLUP without UPG (ssGBLUP), (4) ssGBLUP including UPG in the A and A22 matrices (ssGBLUP/A_UPG), (5) ssGBLUP including UPG in all elements of the H matrix (ssGBLUP/H_UPG), (6) BLUP with pedigree truncation for the last 3 generations (BLUP/truncated), and (7) ssGBLUP with pedigree truncation for the last 3 generations (ssGBLUP/truncated). Unknown parent groups were not used in the scenarios with truncated pedigree. A total of 3,717, 4,126, and 3,823 records of the first lactation for accumulated 305-d milk yield (MY), age at first calving (AFC), and lactation length (LL), respectively, were used. Accuracies ranged from 0.27 for LL (BLUP) to 0.46 for MY (BLUP), bias ranged from -0.62 for MY (ssGBLUP) to 0.0002 for AFC (BLUP/truncated), and dispersion ranged from 0.88 for MY (BLUP/A_UPG) to 1.13 for LL (BLUP). Genetic trend showed genetic gains for all traits across 20 years of selection, and the impact of including genomic information, UPG, or pedigree truncation under GEBV accuracies ranged among the evaluated traits. Overall, methods using UPG, truncation pedigree, and genomic information exhibited potential to improve GEBV accuracies, bias, and dispersion for all traits compared with other methods. Truncated scenarios promoted high genetic gains. In small populations with few genotyped animals, combining truncated pedigree or UPG with genomic information is a feasible approach to deal with missing pedigrees.

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.

Multibreed genetic evaluation in bovines using simulated data employing a composite population.

Genetic evaluations in Brazil are performed within each animal breed; however, with the wide range of extant genetic groups in the country and the increased use of genetic crossing as a form of rapid meat production, more elaborate programs that can jointly evaluate animals of different genetic groups are needed. Genetic evaluation of a composite breed is difficult because of the variation in the genetic composition of a given herd, as well as the inclusion of non-additive genetic effects among breeds that can be important for selecting traits in certain breed combinations. Newer models include additive and non-additive effects; however, few studies have investigated these aspects in tropical breeds. The aim of this study was to simulate genetic values to compare different models. Non-inclusion of maternal effects in models leads to overestimation of variance and direct heritability. Estimates of the biological additive effects are influenced by the maternal effects; however, estimates of the non-additive effects are minimally influenced by the maternal effects and are well estimated in any situation. The studied models effectively predict the direct genetic values.

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 association of productive and reproductive traits with stayability in Nellore cattle: analysis using Bayesian models.

We evaluated the genetic association of growth traits [weight adjusted to 205 days of age (W205), 365 days of age (W365), and 550 days of age (W550); weight gain between 205 days of age and 365 days of age (WG1) and between 365 days of age and 550 days of age (WG2)] and reproductive traits [age at first calving (AFC); first calving interval (FCI)] with stayability in the herd (STAY), using Bayesian inference in linear and threshold models. We defined STAY as the probability of a cow calving three or more times before the age of 76 months, given that she had calved at least once. We assigned binary codes (0, failure; 1, success) to each female. We used a sire model for analysis and formed different contemporary groups for the investigated traits. We analyzed the results by applying a two-trait sire model that included STAY (threshold trait) and linear traits (W205, W365, W550, WG1, WG2, AFC, and FCI). We used Gibbs sampling to estimate variance components and heritabilities. In all the analyses, we found that the mean heritability estimates for STAY were of moderate magnitude (0.20-0.25). The mean heritabilities for W205, W365, W550, WG1, WG2, AFC, and FCI were 0.20, 0.23, 0.39, 0.08, 0.14, 0.12, and 0.11, respectively. We observed wide variation in the posterior distributions of genetic correlations; however, with the exception of those obtained for the reproductive traits, the mean estimates were of low magnitude. Selection for WG2 can results in favorable correlated response in STAY.

Polymorphisms in the GHRL gene and their associations with traits of economic interest in beef cattle.

The hormone ghrelin is produced in the stomach wall, has an orexigenic function, stimulates growth hormone secretion, and affects the energy balance of the animal. Therefore, the ghrelin gene (GHRL) is considered to be a good candidate marker for the identification of traits of great economic importance in cattle, such as those associated with feed intake, growth, and carcass quality. The use of molecular genetic markers associated with such traits permits the earlier and more accurate identification of superior animals, thus reducing the interval between generations, and increasing the genetic gain. Six SNPs were found in the GHRL gene, located in intron 3, intron 4, and exon 5. The positions of the SNPs on the gene and the substitutions were: g.2184A>G, g.2347T>C, g.4469T>C, g.4548A>G, g.4663T>C, and g.4729T>C (GenBank accession No. JX565585). After analysis of linkage disequilibrium, association tests were performed between four SNPs with the traits year weight for males, yearling weight for females, dry matter intake, loin eye area, and rump fat thickness (P ≤ 0.05). Therefore, GHRL is an important candidate gene that may be used to identify genetic variations that influence traits of economic importance in beef cattle.

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

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

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

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

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).

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.

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil.

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.

Trends of the genetic connectedness measures among Nelore beef cattle herds.

Validity of comparisons between expected breeding values obtained from best linear unbiased prediction procedures in genetic evaluations is dependent on genetic connectedness among herds. Different cattle breeding programmes have their own particular features that distinguish their database structure and can affect connectedness. Thus, the evolution of these programmes can also alter the connectedness measures. This study analysed the evolution of the genetic connectedness measures among Brazilian Nelore cattle herds from 1999 to 2008, using the French Criterion of Admission to the group of Connected Herds (CACO) method, based on coefficients of determination (CD) of contrasts. Genetic connectedness levels were analysed by using simple and multiple regression analyses on herd descriptors to understand their relationship and their temporal trends from the 1999-2003 to the 2004-2008 period. The results showed a high level of genetic connectedness, with CACO estimates higher than 0.4 for the majority of them. Evaluation of the last 5-year period showed only a small increase in average CACO measures compared with the first 5 years, from 0.77 to 0.80. The percentage of herds with CACO estimates lower than 0.7 decreased from 27.5% in the first period to 16.2% in the last one. The connectedness measures were correlated with percentage of progeny from connecting sires, and the artificial insemination spread among Brazilian herds in recent years. But changes in connectedness levels were shown to be more complex, and their complete explanation cannot consider only herd descriptors. They involve more comprehensive changes in the relationship matrix, which can be only fully expressed by the CD of contrasts.

Genetic parameter estimates and response to selection for weight and testicular traits in Nelore cattle.

We estimated genetic parameters for various phases of body and testicular growth until 550 days of age in Nelore cattle, using Bayesian inference, including correlation values and error estimates. Weight and scrotal records of 54,182 Nelore animals originating from 18 farms participating in the Brazilian Nelore Breeding Program (PMGRN) were included. The following traits were measured: weight at standard ages of 120 (W120), 210 (W210), 365 (W365), 450 (W450), and 550 (W550) days; weight gain between 120/210 (WG1), 210/365 (WG2), 365/450 (WG3), 450/550 (WG4), 120/365 (WG5), 120/450 (WG6), 120/550 (WG7), 210/450 (WG8), 210/550 (WG9), and 365/550 (WG10) days of age; scrotal circumference at 365 (SC365), 450 (SC450) and 550 (SC550) days of age, and testicular growth between 365/450 (TG1), 450/550 (TG2) and 365/550 (TG3) days of age. The model included contemporary group (current farm, year and two-month period of birth, sex, and management group) and age of dam at calving, divided into classes as fixed effects. The model also included random effects for direct additive, maternal additive and maternal permanent environmental, and residual effects. The direct heritability estimates ranged from 0.23 to 0.39, 0.13 to 0.39 and 0.32 to 0.56 for weights at standard ages, weight gains and testicular measures, respectively. The genetic correlations between weights (0.69 to 0.94) and scrotal circumferences (0.91 to 0.97) measured at standard ages were higher than those between weight gain and testicular growth (0.18 to 0.97 and 0.36 to 0.77, respectively). The weights at standard ages responded more effectively to selection, and also gave strong correlations with the other traits.

Association between IGF2 and CYP21 gene polymorphisms and characteristics of economic interest in Nellore cattle.

We analyzed two single nucleotide polymorphisms (SNPs) of the IGF2 and CYP21 genes in Nellore cattle participating in the Brazilian Animal Breeding Program. The SNPs were found in exon 6 of the IGF2 (insulin-like growth factor 2) gene (RFLP/MboII) as well as in the promoter region of the CYP21 (steroid 21-hydroxylase) gene (RFLP/HpaII) of these animals. The TC heterozygotes were significantly more frequent than CC and TT homozygotes in the RFLP/MboII polymorphism. The T allele was significantly more frequent than the C allele in RFLP/HpaII polymorphism. This population was found to be in Hardy-Weinberg equilibrium for these SNPs. Association of these polymorphisms with expected progeny differences of reproductive and productive traits was investigated, but proved to be significant only for DP550 (expected progeny differenced for weight at 365 days - IGF2 - RFLP/MboII) and DP450 (expected progeny differenced for weight at 450 days - CYP21 - RFLP/HpaII). This is the first study on the occurrence of these two polymorphisms in this Zebu breed of cattle. A total of 147 Nellore animals participating in the Breeding Program of the Nellore Breed (PMGRN) under the management of the National Association of Breeders and Researchers (ANCP) in the city of Ribeirão Preto were analyzed.

Application of proteomic to investigate the different degrees of meat tenderness in Nellore breed.

This study describes the association between meat tenderness and abundance of soluble muscle proteins in Nellore bulls (Bos indicus) using a proteomic approach. We evaluated shear force (SF) of Longissimus thoracis muscle 24 h after slaughter and selected three experimental groups of animals with moderately tender (TE; SF = 3.9 ± 0.7 kg), moderately tough (TO; SF = 5.6 ± 0.7 kg) and very tough meat (TO+; SF = 7.9 ± 1.4 kg). Proteome was investigated by two-dimensional electrophoresis (2D-PAGE) in combination with electrospray ionization-tandem mass spectrometry (ESI-MS/MS). The metabolic proteins triosephosphate isomerase (TPI1) and phosphoglucomutase 1 (PGM1), the structural protein profilin 1 (PFN1), and cytosol aminopeptidase (LAP3) were up-regulated (P < 0.05) in the TE meat group when compared to the TO and TO+ groups. Actin structural proteins (ACTA1, ACTB, and ACTG1), the oxidative stress protein peroxiredoxin (PRDX6, PRDX2, PRDX1, and PARK7), heat shock protein isoforms, and co-chaperones (CDC37 and STIP1) were up-regulated (P < 0.05) in the TO and TO+ meat groups. In addition, we also identified proteins PFN1, LAP3, PRDX1, PRDX2, HSPD1, and ARHGDIA to be associated with beef tenderness. The results reported herein demonstrated that meat tenderness in Nellore cattle depends on the modulation and expression of a set of proteins involved in different biological pathways. SIGNIFICANCE: The manuscript entitled "Application of proteomic to investigate the different degrees of meat tenderness in Nellore breed" describes a classical proteomics work using two-dimensional gel electrophoresis (2D-PAGE), followed by mass spectrometry coupled to electrospray ionization ion trap (ESI-MS/MS) in order to understand the biochemical engineering involved in the process of meat tenderness. We evaluated shear force (SF) of Longissimus thoracis muscle samples of Nellore cattle (n = 90) and select three experimental groups of animals with moderately tender (TE; SF = 3.9 ± 0.7), moderately tough (TO; SF = 5.6 ± 0.7) and very tough meat (TO+; SF = 7.9 ± 1.4). The proteomic approach allowed observing that meat tenderness is influenced by structural proteins (ACTA1, ACTG1, ACTB, MYL1 and PFN1), co-chaperones (CDC37 and STIP1), heat shock proteins (HSP90AA1, HSP90AB1, HSPD1, HSPA1L, HSPA1A and HSPB1), regulatory protein (ARHGDIA), metabolic proteins (TPI1 and PGM1) and oxidative stress proteins (PRDX1, PRDX2, PRDX6, PARK7). Our results suggest that meat tenderness in Nellore depends on the modulation and expression of a set of proteins involved in different biological pathways.

Additive genetic relationship of longevity with fertility and production traits in Nellore cattle based on bivariate models.

Survival or longevity is an economically important trait in beef cattle. The main inconvenience for its inclusion in selection criteria is delayed recording of phenotypic data and the high computational demand for including survival in proportional hazard models. Thus, identification of a longevity-correlated trait that could be recorded early in life would be very useful for selection purposes. We estimated the genetic relationship of survival with productive and reproductive traits in Nellore cattle, including weaning weight (WW), post-weaning growth (PWG), muscularity (MUSC), scrotal circumference at 18 months (SC18), and heifer pregnancy (HP). Survival was measured in discrete time intervals and modeled through a sequential threshold model. Five independent bivariate Bayesian analyses were performed, accounting for cow survival and the five productive and reproductive traits. Posterior mean estimates for heritability (standard deviation in parentheses) were 0.55 (0.01) for WW, 0.25 (0.01) for PWG, 0.23 (0.01) for MUSC, and 0.48 (0.01) for SC18. The posterior mean estimates (95% confidence interval in parentheses) for the genetic correlation with survival were 0.16 (0.13-0.19), 0.30 (0.25-0.34), 0.31 (0.25- 0.36), 0.07 (0.02-0.12), and 0.82 (0.78-0.86) for WW, PWG, MUSC, SC18, and HP, respectively. Based on the high genetic correlation and heritability (0.54) posterior mean estimates for HP, the expected progeny difference for HP can be used to select bulls for longevity, as well as for post-weaning gain and muscle score.

Prospecting candidate SNPs for backfat in Canchim beef cattle.

Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.

Genetic correlations between categorical morphological traits in Nelore cattle by applying Bayesian analysis under a threshold animal model.

In this study, Bayesian analysis under a threshold animal model was used to estimate genetic correlations between morphological traits (body structure, finishing precocity and muscling) in Nelore cattle evaluated at weaning and yearling. Visual scores obtained from 7651 Nelore cattle at weaning and from 4155 animals at yearling, belonging to the Brazilian Nelore Program, were used. Genetic parameters for the morphological traits were estimated by two-trait Bayesian analysis under a threshold animal model. The genetic correlations between the morphological traits evaluated at two ages of the animal (weaning and yearling) were positive and high for body structure (0.91), finishing precocity (0.96) and muscling (0.94). These results indicate that the traits are mainly determined by the same set of genes of additive action and that direct selection at weaning will also result in genetic progress for the same traits at yearling. Thus, selection of the best genotypes during only one phase of life of the animal is suggested. However, genetic differences between morphological traits were better detected during the growth phase to yearling. Direct selection for body structure, finishing precocity and muscling at only one age, preferentially at yearling, is recommended as genetic differences between traits can be detected at this age.

Effect of single nucleotide polymorphisms of CAPN1 and CAST genes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses with Bos taurus.

The objectives of this work were to study the segregation of single nucleotide polymorphisms of the calpain 1, large subunit (CAPN1) and calpastatin (CAST) genes in Nellore (Bos indicus) and Nellore xBos taurus beef cattle, as well as to evaluate their effects on meat traits. For this, 300 animals, including 114 Nellore, 67 Angus x Nellore, 44 Rubia Gallega x Nellore, 41 Canchim, 19 Brangus three-way crosses and 15 Braunvieh three-way crosses, were genotyped for the CAPN4751 [AF_248054.2:g.6545C>T (GenBank accession AF248054.2)] and CAST/DdeI [AF_159246.1:g.2959A>G (GenBank accession AF159246.1)] polymorphisms and phenotyped for Ribeye Area, Backfat Thickness, Intramuscular Fat, Shear Force (SF) and Myofibrillar Fragmentation Index (MFI). In relation to the CAPN4751 polymorphism, a frequency of 10.5% was observed for the C allele in the Nellore breed. In the total sample of studied animals, a significant association was found between genotypes and meat tenderness, assessed by SF (P = 0.005) and MFI (P = 0.008), with genotype CT being more favourable than TT. For the CAST/DdeI polymorphism, a frequency of 55.7% was found for the A allele in the Nellore breed. In the total sample, a significant association was observed between genotypes and meat tenderness - SF (P = 0.004) and MFI (P = 0.006), with genotype AA being more favourable than AG. The relationship between genotypes and aged meat tenderness in confluence with the distribution of favourable alleles shows great potential for application of the CAPN4751 and CAST/DdeI polymorphisms in the genetic improvement of the Nellore breed, whilst contributing to the validation, in this breed and in its crosses with B. taurus, of the association results previously described in the literature.

Detection of Babesia bigemina in cattle of different genetic groups and in Rhipicephalus (Boophilus) microplus tick.

Babesia bigemina infections were investigated in four genetic groups of beef cattle and in Rhipicephalus (Boophilus) microplus engorged female ticks. Blood samples and engorged female ticks were collected from 15 cows and 15 calves from each of the following genetic groups: Nelore, Angus x Nelore, Canchim x Nelore, and Simmental x Nelore. Microscopic examination of blood smears and tick hemolymph revealed that merozoites of B. bigemina (6/60) as well as kinetes of Babesia spp. (9/549) were only detected in samples (blood and ticks, respectively) originated from calves. PCR-based methods using primers for specific detection of B. bigemina revealed 100% infection in both calves and cows, regardless the genetic group. Tick infection was detected by nested-PCR amplifications showing that the frequency of B. bigemina was higher (P<0.01) in female ticks collected from calves (134/549) than in those collected from cows (52/553). The frequency of B. bigemina was similar in ticks collected from animals, either cows or calves, of the four genetic groups (P>0.05).