Radiative properties of the skin and haircoat of cattle and other animals

Radiative properties (reflectance rho, transmittance tau, and absorptance alpha) were determined for wavelengths from 300 to 850 nm in the haircoat and the skin of water buffalo, deer (Pantanal deer, Blastocerus dichotomus), and cattle of the Holstein, Simmental, Canchim, Brangus, and Nelore breeds. The results showed that white hairs have higher rho (0.60 to 0.67) than the other coat colors, but the gray coats (mixed white and dark hair) of the Nelore cattle presented higher rho than that of the white coats of the European breeds at wavelengths lower than 600 nm. The light gray colored skin of the Canchim cattle had higher rho (0. 66) than the non-pigmented skin of Holstein (0.53). Red skins presented rho values higher than those of dark gray and black skins. Buffalo skin (dark gray) presented an average rho of 0.23+/-0.02 and alpha of 0.77+/-0.02. The red haircoat of the deer presented rho lower (0.37) than that of cattle of the same color (0.58). However, there was little difference between deer and cattle with respect to reflectance and absorptance of the skin. As for the spectral transmittance of the skin, it was very low and about the same for both species, until 600 nm. In the range 600 to 850 nm, the tau values for cattle rose to 0. 17, while those for deer increased only to 0.12.

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Synaptonemal complex analysis of Nellore and Gyr breeds of Bos taurus indicus

A synaptonemal complex (SC) study of specimens of Nellore and Gyr breeds of Bos taurus indicus was performed with the main objective to identify and determinate the frequency of abnormalities of SC and the frequency of cells with abnormalities. All animals analyzed had 29 autosomal bivalents and one sexual bivalent. The Nellore breed had 30.00% of cells with SC abnormalities while the Gyr breed had only 11.11%. Statistical analyses showed that there were not significant differences for the number of cells with abnormalities among the breeds studied. The subspecies Bos taurus indicus had 16.92% of cells showing abnormalities, being 62.82% of these abnormalities in zygotene and 37.18% in pachytene. Some aspects regarding the frequency of cells with abnormalities and the fertility of Nellore and Gyr breeds are discussed.

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 polyno-mial 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. © 2001 American Society of Animal Science. All rights reserved.

Implementation of DNA markers to produce genomically - Enhanced EPDs in nellore cattle

Background: The sequencing and publication of the cattle genome and the identification of single nucleotide polymorphism (SNP) molecular markers have provided new tools for animal genetic evaluation and genomic-enhanced selection. These new tools aim to increase the accuracy and scope of selection while decreasing generation interval. The objective of this study was to evaluate the enhancement of accuracy caused by the use of genomic information (Clarifide® - Pfizer) on genetic evaluation of Brazilian Nellore cattle. Review: The application of genome-wide association studies (GWAS) is recognized as one of the most practical approaches to modern genetic improvement. Genomic selection is perhaps most suited to the improvement of traits with low heritability in zebu cattle. The primary interest in livestock genomics has been to estimate the effects of all the markers on the chip, conduct cross-validation to determine accuracy, and apply the resulting information in GWAS either alone [9] or in combination with bull test and pedigree-based genetic evaluation data. The cost of SNP50K genotyping however limits the commercial application of GWAS based on all the SNPs on the chip. However, reasonable predictability and accuracy can be achieved in GWAS by using an assay that contains an optimally selected predictive subset of markers, as opposed to all the SNPs on the chip. The best way to integrate genomic information into genetic improvement programs is to have it included in traditional genetic evaluations. This approach combines traditional expected progeny differences based on phenotype and pedigree with the genomic breeding values based on the markers. Including the different sources of information into a multiple trait genetic evaluation model, for within breed dairy cattle selection, is working with excellent results. However, given the wide genetic diversity of zebu breeds, the high-density panel used for genomic selection in dairy cattle (Ilumina Bovine SNP50 array) appears insufficient for across-breed genomic predictions and selection in beef cattle. Today there is only one breed-specific targeted SNP panel and genomic predictions developed using animals across the entire population of the Nellore breed (www.pfizersaudeanimal.com), which enables genomically - enhanced selection. Genomic profiles are a way to enhance our current selection tools to achieve more accurate predictions for younger animals. Material and Methods: We analyzed the age at first calving (AFC), accumulated productivity (ACP), stayability (STAY) and heifer pregnancy at 30 months (HP30) in Nellore cattle fitting two different animal models; 1) a traditional single trait model, and 2) a two-trait model where the genomic breeding value or molecular value prediction (MVP) was included as a correlated trait. All mixed model analyses were performed using the statistical software ASREML 3.0. Results: Genetic correlation estimates between AFC, ACP, STAY, HP30 and respective MVPs ranged from 0.29 to 0.46. Results also showed an increase of 56%, 36%, 62% and 19% in estimated accuracy of AFC, ACP, STAY and HP30 when MVP information was included in the animal model. Conclusion: Depending upon the trait, integration of MVP information into genetic evaluation resulted in increased accuracy of 19% to 62% as compared to accuracy from traditional genetic evaluation. GE-EPD will be an effective tool to enable faster genetic improvement through more dependable selection of young animals.

Effect of superstimulatory treatments on the expression of genes related to ovulatory capacity, oocyte competence and embryo development in cattle.

Multiple ovulation (superovulation) and embryo transfer has been used extensively in cattle. In the past decade, superstimulatory treatment protocols that synchronise follicle growth and ovulation, allowing for improved donor management and fixed-time AI (FTAI), have been developed for zebu (Bos indicus) and European (Bos taurus) breeds of cattle. There is evidence that additional stimulus with LH (through the administration of exogenous LH or equine chorionic gonadotrophin (eCG)) on the last day of the superstimulatory treatment protocol, called the 'P-36 protocol' for FTAI, can increase embryo yield compared with conventional protocols that are based on the detection of oestrus. However, inconsistent results with the use of hormones that stimulate LH receptors (LHR) have prompted further studies on the roles of LH and its receptors in ovulatory capacity (acquisition of LHR in granulosa cells), oocyte competence and embryo quality in superstimulated cattle. Recent experiments have shown that superstimulation with FSH increases mRNA expression of LHR and angiotensin AT(2) receptors in granulosa cells of follicles >8 mm in diameter. In addition, FSH decreases mRNA expression of growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) in oocytes, but increases the expression of both in cumulus cells, without diminishing the capacity of cumulus-oocyte complexes to generate blastocysts. Although these results indicate that superstimulation with FSH is not detrimental to oocyte competence, supplementary studies are warranted to investigate the effects of superstimulation on embryo quality and viability. In addition, experiments comparing the cellular and/or molecular effects of adding eCG to the P-36 treatment protocol are being conducted to elucidate the effects of superstimulatory protocols on the yield of viable embryos.

Resistance against gastrointestinal nematodes in Crioulo Lageano and crossbred Angus cattle in southern Brazil

Gastrointestinal nematode (GIN) infection is a major cause of production losses in cattle. This study was carried out to evaluate the natural resistance against nematode infection in Crioulo Lageano and crossbred Angus male calves. Crioulo Lageano is a local cattle breed in the state of Santa Catarina, in southern Brazil. Ten weaned calves of each breed were grazed together on pasture and naturally infected with nematodes between July 2009 and December 2010. Once every 28 days, we collected fecal and blood samples for parasitological and immunological tests, as well as recording body weights. After 19 samplings, all animals were slaughtered for quantification and identification of GINs. We found that the animals had been infected with the following nematode species, in decreasing order by the mean number of specimens: Trichostrongylus axei, Cooperia punctata, Ostertagia ostertagi, Haemonchus placei, Oesophagostomum radiatum, and Trichuris spp. There were no significant differences between the Crioulo Lageano and crossbred Angus groups in terms of worm burden or nematode fecal egg count, nor in terms of the mean levels of immunoglobulin (G and A) against C. punctata and H. placei antigens, except in IgA mean level in abomasal mucus against H. placei adult worms that was significantly higher in crossbred Angus cattle (p<0.05). At the end of the study, the crossbred Angus cattle were heavier than were the Crioulo Lageano cattle (mean live weight, 507.35 and 390.3. kg, respectively). Comparative parasitological and immunological evaluation revealed no difference between two breeds in terms of their natural resistance against GINs. © 2012 Elsevier B.V.

Physiology and endocrinology symposium: Influence of cattle genotype (Bos indicus vs. Bos taurus) on oocyte and preimplantation embryo resistance to increased temperature

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

Expression of genes related to quality of Longissimus dorsi muscle meat in Nellore (Bos indicus) and Canchim (5/8 Bos taurus×3/8 Bos indicus) cattle

This study was performed to compare CAPN1, CAPN2, CAST, TG, DGAT1 and LEP gene expressions and correlate them with meat quality traits in two genetic groups (Nellore and Canchim) in order to assess their expression profile and use their expression profile as genetic markers. We analyzed 30 young bulls (1. year old), 15 of each genetic group. Samples of the Longissimus dorsi muscle were collected for analysis of: total lipids (TL) and meat tenderness measured as Warner-Bratzler shear force (SF) and myofibrillar fragmentation (MFI) at day of slaughter and 7. days of aging. Gene expression profiles were obtained via RT-qPCR. TL and MFI showed differences between breeds, higher MFI in Canchim and higher TL in Nellore. Calpains showed no differential expression between groups, as did DGAT1, TG, and LEP. CAST was expressed more in the Nellore cattle. The only significant within-breed correlation (0.79) between gene expression and meat traits was found for DGAT1 and MFI in Canchim breed. Although the number of animals used in this study was small, the results indicate that the increased expression of CAST in Nellore may reflect tougher meat, but the lack of correlations with the meat traits indicates it is not a promising genetic marker. © 2013 Elsevier Ltd.

Genetic associations among average annual productivity, growth traits, and stayability: A parallel between Nelore and composite beef cattle

This study was conducted to examine the relationship among average annual productivity of the cow (PRODAM), yearling weight (YW), postweaning BW gain (PWG), scrotal circumference (SC), and stayability in the herd for at least 6 yr (STAY) of Nelore and composite beef cattle. Measurements were taken on animals born between 1980 and 2010 on 70 farms located in 7 Brazilian states. Estimates of heritability and genetic and environmental correlations were obtained by Bayesian approach with 5-trait animal models. Genetic trends were estimated by regressing means of estimated breeding values by year of birth. The heritability estimates were between 0.14 and 0.47. Estimates of genetic correlation among female traits (PRODAM and STAY) and growth traits ranged from-0.02 to 0.30. Estimates of genetic correlations ranged from 0.23 to 0.94 among growth traits indicating that selection for these traits could be successful in tropical breeding programs. Genetic correlations among all traits were favorable and simultaneous selection for growth, productivity, and stayability is therefore possible. Genetic correlation between PRODAM and STAY was 0.99 and 0.85 for Nelore and composite cattle, respectively. Therefore, PRODAM and STAY might be influenced by many of the same genes. The inclusion of PRODAM instead of STAY as a selection criterion seems to be more advantageous for tropical breeding programs because the generation interval required to obtain accurate estimates of genetic merit for PRODAM is shorter. Average annual genetic changes were greater in Nelore than in composite cattle. This was not unexpected because the breeding program of composite cattle included a large number of farms, different production environments, and genetic level of the herds and breeds. Thus, the selection process has become more difficult in this population. © 2013 American Society of Animal Science. All rights reserved.

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

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

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

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

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Accuracy of genotype imputation in Nelore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Prediction of genomic-enabled breeding values and genome-wide association study for feedlot average daily weight gain in Nelore cattle

Pós-graduação em Genética e Melhoramento Animal - FCAV