Estimates of covariance functions for growth from birth to 630 days of age in Nelore cattle

Weight records of Brazilian Nelore cattle, from birth to 630 d of age, recorded every 3 mo, were analyzed using random regression models. Independent variables were Legendre polynomials of age at recording. The model of analysis included contemporary groups as fixed effects and age of dam as a linear and quadratic covariable. Mean trends were modeled through a cubic regression on orthogonal polynomials of age. Up to four sets of random regression coefficients were fitted for animals' direct and maternal, additive genetic, and permanent environmental effects. Changes in measurement error variances with age were modeled through a variance function. Orders of polynomial fit from three to six were considered, resulting in up to 77 parameters to be estimated. Models fitting random regressions modeled the pattern of variances in the data adequately, with estimates similar to those from corresponding univariate analysis. Direct heritability estimates decreased after birth and tended to be lowest at ages at which maternal effect estimates tended to be highest. Maternal heritability estimates increased after birth to a peak around 110 to 120 d of age and decreased thereafter. Additive genetic direct correlation estimates between weights at standard ages (birth, weaning, yearling, and final weight) were moderate to high and maternal genetic and environmental correlations were consistently high.

Association of ADIPOQ, OLR1 and PPARGC1A gene polymorphisms with growth and carcass traits in Nelore cattle

In beef cattle farming, growth and carcass traits are important for genetic breeding programs. Molecular markers can be used to assist selection and increase genetic gain. The ADIPOQ, OLR1 and PPARGC1A genes are involved in lipid synthesis and fat accumulation in adipose tissue. The objective of this study was to identify polymorphisms in these genes and to assess the association with growth and carcass traits in Nelore cattle. A total of 639 animals were genotyped by PCR-RFLP for rs208549452, rs109019599 and rs109163366 in ADIPOQ, OLR1 and PPARGC1A gene, respectively. We analyzed the association of SNPs identified with birth weight, weaning weight, female yearling weight, female hip height, male yearling weight, male hip height, loin eye area, rump fat thickness, and backfat thickness. The OLR1 marker was associated with rump fat thickness and weaning weight (P < 0.05) and the PPARGC1 marker was associated with female yearling weight.

Genetic analysis on accumulated productivity and calving intervals in Nelore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.

Background: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.

Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle.

Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina1 High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing 6.5% of the genome. Comparing our results with previous studies revealed an overlap in 1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.

Variation in myogenic differentiation 1 mRNA abundance is associated with beef tenderness in Nelore cattle.

The myogenic differentiation 1 gene (MYOD1) has a key role in skeletal muscle differentiation and composition through its regulation of the expression of several muscle-specific genes. We first used a general linear mixed model approach to evaluate the association of MYOD1 expression levels on individual beef tenderness phenotypes. MYOD1 mRNA levels measured by quantitative polymerase chain reactions in 136 Nelore steers were significantly associated (P ? 0.01) with Warner?Bratzler shear force, measured on the longissimus dorsi muscle after 7 and 14 days of beef aging. Transcript abundance for the muscle regulatory gene MYOD1 was lower in animals with more tender beef. We also performed a coexpression network analysis using whole transcriptome sequence data generated from 30 samples of longissimus muscle tissue to identify genes that are potentially regulated by MYOD1. The effect of MYOD1 gene expression on beef tenderness may emerge from its function as an activator of muscle-specific gene transcription such as for the serum response factor (C-fos serum response element-binding transcription factor) gene (SRF), which determines muscle tissue development, composition, growth and maturation.

Association analyses pointed the TIPARP as a potential candidate gene influencing residual feed intake variation in Nelore cattle.

2016

Genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle.

Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.

Covariance functions for body weight from birth to maturity in Nellore cows

The objective of this study was to estimate (co)variance functions using random regression models on Legendre polynomials for the analysis of repeated measures of BW from birth to adult age. A total of 82,064 records from 8,145 females were analyzed. Different models were compared. The models included additive direct and maternal effects, and animal and maternal permanent environmental effects as random terms. Contemporary group and dam age at calving (linear and quadratic effect) were included as fixed effects, and orthogonal Legendre polynomials of animal age (cubic regression) were considered as random co-variables. Eight models with polynomials of third to sixth order were used to describe additive direct and maternal effects, and animal and maternal permanent environmental effects. Residual effects were modeled using 1 (i.e., assuming homogeneity of variances across all ages) or 5 age classes. The model with 5 classes was the best to describe the trajectory of residuals along the growth curve. The model including fourth- and sixth-order polynomials for additive direct and animal permanent environmental effects, respectively, and third-order polynomials for maternal genetic and maternal permanent environmental effects were the best. Estimates of (co) variance obtained with the multi-trait and random regression models were similar. Direct heritability estimates obtained with the random regression models followed a trend similar to that obtained with the multi-trait model. The largest estimates of maternal heritability were those of BW taken close to 240 d of age. In general, estimates of correlation between BW from birth to 8 yr of age decreased with increasing distance between ages.

Validation of body condition score as a predictor of subcutaneous fat in Nelore (Bos indicus) cows

The aim of the present study was to determine the relationship among body weight (BW), body condition score (BCS) and rump fat thickness (RFAT) measured by ultrasonography, and validate the relationship between BCS and RFAT over the time. Two hundred sixty and six Nelore cows had their BW, BCS and RFAT evaluated at five different moments during the production cycle: M1) weaning: M2) parturition, M3) 42 days post-partum; M4) 82 days postpartum and M5) 112 days post-partum. A BCS value was attributed for each cow following a I to 5 points scale. Ultrasonographic images for RFAT measurement were obtained using a 3.5 MHz linear transducer. Images were immediately analyzed as soon as they were formed and frozen. Body condition scores and ultrasound measurements were collected on the same day by a single trained technician. The relationship between BCS and RFAT values was investigated by regression models. The analysis of similarity among the five obtained models was performed using the proc MIXED from SAS and the correlations among variables were analyzed with proc CORR from SAS. The BCS was able to predict RFAT in Nelore cows in all different moments evaluated. Also, it was shown that BCS presented high correlation (r=0.82 to 0.93) and relationship (R(2) = 0.73 to 0.92) with RFAT. However, both BCS and RFAT showed low correlation (r=0.37 to 0.50) and relationship (R(2) = 0.13 to 0.25) with BW. The BCS classification by visual method using a 1 to 5 point scale, was able to predict the RFAT in Nelore cows over the time. (C) 2008 Elsevier B.V. All rights reserved.

Genetic improvement and population structure of the Nelore breed in Northern Brazil

The objective of this work was to evaluate the population structure and the genetic and phenotypic progress of Nelore cattle in Northern Brazil. Pedigree information concerning animals born between 1942 and 2006 were analyzed. Population structure was performed using the Endog program. Out of the 140,628 animals studied, 67.7, 14.52 and 3.18% had complete pedigree record of the first, second and third parental generation, respectively. Inbreeding and average relatedness coefficients were low: 0.2 and 0.13%, respectively. However, these parameters may have been underestimated, since information on pedigree was incomplete. The effective number of founders was 370 and the genetic contribution of 10, 50 and 448 most influent ancestors explained 13.2, 28 and 50% of the genetic variability in the population, respectively. The genetic variability for growth traits and population structure demonstrates high probability of increasing productivity through selective breeding. Moreover, management strategies to reduce the currently observed age at first calving and generation intervals are important for Nelore cattle genetic improvement.

Trends of the genetic connectedness measures among Nelore beef cattle herds

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Field study on nematode resistance in Nelore-breed cattle

The present study evaluated Nelore cattle with different degrees of resistance to natural infections by gastrointestinal nematodes. One hundred weaned male cattle, 11-12 months of age, were kept on the same pasture and evaluated from October 2003 to February 2004. Faecal and blood samples were collected for parasitological, haematological and immunological tests. In February 2004, the 10 most resistant and the 10 most susceptible animals were selected based on individual means of nematode faecal egg counts (FEC). Such animals were slaughtered for worm burden determination and nematode species identification. The repeatability estimates for FEC (+/- S.D.), log-transformed FEC and packed-cell volume (PCV) in all animals were 0.3 (+/- 0.05), 0.26 (+/- 0.04) and 0.42 (+/- 0.05), respectively. The resistant group showed lower FEC and worm burdens than the susceptible group (P < 0.05). There were no significant differences between groups regarding mean body weight, weight gain, PCV and total serum protein values (P > 0.05). The resistant group showed higher total serum IgE levels (P < 0.05) and higher mean eosinophil blood counts. However, the latter was statistically significant only 42 days after the beginning of the study. Nematodes Cooperia punctata and Haemonchus placei were predominant and the correlation between Cooperia and Haemonchus burdens was 0.64 (P < 0.05), which indicated that animals presenting increased numbers of one of those genera probably had increased numbers of the other. The current study provides further evidence of IgE active role in nematode immunity and suggests that total serum IgE level might serve as an additional marker to select Nelore cattle that are responsive to H. placei and C. punctata infections. (C) 2007 Elsevier B.V. All rights reserved.

Estimativas de parâmetros genéticos de características de carcaça, medidas por ultrassonografia, e suas relações com escores visuais na raça Nelore

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Correlações entre escores visuais e características produtivas em prova de ganho de peso de bovinos da raça Nelore Mocha

The objective was evaluate the phenotypic correlations among visual scores, performance traits and scrotal circumference of the polled Nelore cattle performance tests. Animals of the fifth, sixth, seventh official performance test in pasture were analysed. At the end of each test period the following measures were taken: adjusted weight to 550 days, gain weight, visual score (body structure; precocity and muscle) and scrotal circumference. The musculature, precocity and body structure showed significant positive correlations (P <0.01) with gain weight, adjusted average daily weight to 550 days, scrotal circumference and chest circumference. However, only hip height showed a significant positive correlation with muscularity. Therefore, in polled Nelore cattle, regards to performance test in pasture, the visual scores show positive correlation with the performance traits and scrotal circumference, showing that visual scores is important tool in the polled Nelore Cattle performance test.