Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle

Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (F ROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Prospecting major genes in dairy buffaloes

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

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Environmental and Farm Management Factors Associated with Tuberculosis on Cattle Farms in Northeastern Michigan

Objective—To identify major environmental and farm management factors associated with the occurrence of tuberculosis (TB) on cattle farms in northeastern Michigan. Design—Case-control study. Sample Population—17 cattle farms with infected cattle and 51 control farms. Procedure—Each case farm (laboratory confirmed diagnosis of Mycobacterium bovis infection) was matched with 2 to 4 control farms (negative whole-herd test results within previous 12 months) on the basis of type of farm (dairy or beef) and location. Cattle farm data were collected from in-person interviews and mailed questionnaires. Wildlife TB data were gathered through state wildlife surveillance. Environmental data were gathered from a satellite image-based geographic information system. Multivariable conditional logistic regression for matched analysis was performed. Results—Major factors associated with increased farm risk of TB were higher TB prevalence among wild deer and cattle farms in the area, herd size, and ponds or creeks in cattle housing areas. Factors associated with reduced farm risk of TB were greater amounts of natural open lands in the surrounding area and reducing deer access to cattle housing areas by housing cattle in barns, barnyards, or feedlots and use of electrified wire or barbed wire for livestock fencing. Conclusions and Clinical Relevance—Results suggest that certain environmental and management factors may be associated with risk of TB on cattle farms.

Manipulation of follicle development to ensure optimal oocyte quality and conception rates in cattle

Over the last several decades, a number of therapies have been developed that manipulate ovarian follicle growth to improve oocyte quality and conception rates in cattle. Various strategies have been proposed to improve the responses to reproductive biotechnologies following timed artificial insemination (TAI), superovulation (SOV) or ovum pickup (OPU) programmes. During TAI protocols, final follicular growth and size of the ovulatory follicle are key factors that may significantly influence oocyte quality, ovulation, the uterine environment and consequently pregnancy outcomes. Progesterone concentrations during SOV protocols influence follicular growth, oocyte quality and embryo quality; therefore, several adjustments to SOV protocols have been proposed depending on the animal category and breed. In addition, the success of in vitro embryo production is directly related to the number and quality of cumulus oocyte complexes harvested by OPU. Control of follicle development has a significant impact on the OPU outcome. This article discusses a number of key points related to the manipulation of ovarian follicular growth to maximize oocyte quality and improve conception rates following TAI and embryo transfer of in vivo-and in vitro-derived embryos in cattle.

Luteal function and follicular growth following follicular aspiration during the peri-luteolysis period in bos indicus and crossbred cattle

Follicular estradiol triggers luteolysis in cattle. Therefore, the control of follicle growth and steroidogenesis is expected to modulate luteal function and might be used as an anti-luteolytic strategy to improve embryo survival. Objectives were to evaluate follicular dynamics, plasma concentrations of estradiol and luteal lifespan in Bos indicus and crossbred cows subjected to sequential follicular aspirations. From D13 to D25 of a synchronized cycle (ovulation = D1), Nelore or crossbred, non-pregnant and non-lactating cows were submitted to daily ultrasound-guided aspiration of follicles >6 mm (n = 10) or to sham aspirations (n = 8). Diameter of the largest follicle on the day of luteolysis (7.4 +/- 1.0 vs 9.7 +/- 1.0 mm; mean +/- SEM), number of days in which follicles >6 mm were present (2.3 +/- 0.4 vs 4.6 +/- 0.5 days) and daily mean diameter of the largest follicle between D15 and D19 (6.4 +/- 0.2 vs 8.5 +/- 0.3 mm) were smaller (p <0.01) in the aspirated group compared with the control group, respectively. Aspiration tended to reduce (p< 0.10) plasma estradiol concentrations between D18 and D20 (2.95 +/- 0.54 vs 4.30 +/- 0.55 pg/ml). The luteal lifespan was similar (p > 0.10) between the groups (19.6 +/- 0.4 days), whereas the oestrous cycle was longer (p <0.01) in the aspirated group (31.4 +/- 1.2 vs 21.2 +/- 1.3 days). Hyperechogenic structures were present at the sites of aspiration and were associated with increase in concentration of progesterone between luteolysis and oestrus. It is concluded that follicular aspiration extended the oestrous cycle and decreased the average follicular diameter on the peri-luteolysis period but failed to delay luteolysis.

Study of using marker assisted selection on a beef cattle breeding program by model comparison

A data set of a commercial Nellore beef cattle selection program was used to compare breeding models that assumed or not markers effects to estimate the breeding values, when a reduced number of animals have phenotypic, genotypic and pedigree information available. This herd complete data set was composed of 83,404 animals measured for weaning weight (WW), post-weaning gain (PWG), scrotal circumference (SC) and muscle score (MS), corresponding to 116,652 animals in the relationship matrix. Single trait analyses were performed by MTDFREML software to estimate fixed and random effects solutions using this complete data. The additive effects estimated were assumed as the reference breeding values for those animals. The individual observed phenotype of each trait was adjusted for fixed and random effects solutions, except for direct additive effects. The adjusted phenotype composed of the additive and residual parts of observed phenotype was used as dependent variable for models' comparison. Among all measured animals of this herd, only 3160 animals were genotyped for 106 SNP markers. Three models were compared in terms of changes on animals' rank, global fit and predictive ability. Model 1 included only polygenic effects, model 2 included only markers effects and model 3 included both polygenic and markers effects. Bayesian inference via Markov chain Monte Carlo methods performed by TM software was used to analyze the data for model comparison. Two different priors were adopted for markers effects in models 2 and 3, the first prior assumed was a uniform distribution (U) and, as a second prior, was assumed that markers effects were distributed as normal (N). Higher rank correlation coefficients were observed for models 3_U and 3_N, indicating a greater similarity of these models animals' rank and the rank based on the reference breeding values. Model 3_N presented a better global fit, as demonstrated by its low DIC. The best models in terms of predictive ability were models 1 and 3_N. Differences due prior assumed to markers effects in models 2 and 3 could be attributed to the better ability of normal prior in handle with collinear effects. The models 2_U and 2_N presented the worst performance, indicating that this small set of markers should not be used to genetically evaluate animals with no data, since its predictive ability is restricted. In conclusion, model 3_N presented a slight superiority when a reduce number of animals have phenotypic, genotypic and pedigree information. It could be attributed to the variation retained by markers and polygenic effects assumed together and the normal prior assumed to markers effects, that deals better with the collinearity between markers. (C) 2012 Elsevier B.V. All rights reserved.

Interaction of dietary vitamin D-3 and sunlight exposure on B. indicus cattle: Animal performance, carcass traits, and meat quality

Attempts to improve beef tenderness through supplementation with dietary vitamin D-3 have been challenged by null results and negative impacts on animal performance and carcass traits. Because vitamin D-3 is also synthesised by the animal via ultraviolet radiation from sunlight, the effectiveness of supplementation with dietary vitamin D-3 may be modulated by the degree of exposure of the animal to sunlight. Hence, this work aimed to verify whether dietary vitamin D-3 modifies meat quality without negatively affecting animal performance and carcass traits in B. indicus beef cattle that were either exposed to or protected from natural sunlight. Forty-two (411 +/- 38 kg) Nellore-type castrated males were fed a high-concentrate diet for 45 days after assignment to a treatment group. The treatments comprised combinations of three levels of vitamin D3 [ViTD - none (V0) or 2 x 10(6) IU of vitamin D-3 administered for either 2 (V2) or 8 (V8) consecutive days pre-slaughter] and two shading conditions (SHADE - unshaded or shaded). The post-mortem (pm) measurements were taken in the Longissimus thoracis et lumborum muscle. The animal performance and carcass traits were unaffected by ViTD or SHADE The V2 treatment increased the Myofibrillar Fragmentation Index in shaded animals compared to unshaded ones. Animals under shade had higher muscle calcium concentration. There was no effect of either ViTD or SHADE on the shear force. The L* values were higher at 24 h pm than at 0 and 1 h pm, with no differences among the animals in the ViTD or SHADE groups. Higher a* values were observed among animals in the V8 group than in the V0 group, and higher b* values were observed among animals in the V8 group than in the V2 or V0 groups, which were not different. In conclusion, ViTD and SHADE did not affect animal performance, carcass traits or shear force, whereas animals receiving a lower ViTD dosage and SHADE exhibited altered myofibrillar fragmentation. ViTD affected the colour parameters, and changes in the lightness of the beef related to the time pm were found in meat from animals under SHADE. (c) 2012 Elsevier B.V. All rights reserved.

Estimation methods of non-additive effects for characteristics of weight and scrotal circumference in crossbred beef cattle

The objective of this study was to investigate, in a population of crossbred cattle, the obtainment of the non-additive genetic effects for the characteristics weight at 205 and 390 days and scrotal circumference, and to evaluate the consideration of these effects in the prediction of breeding values of sires using different estimation methodologies. In method 1, the data were pre-adjusted for the non-additive effects obtained by least squares means method in a model that considered the direct additive, maternal and non-additive fixed genetic effects, the direct and total maternal heterozygosities, and epistasis. In method 2, the non-additive effects were considered covariates in genetic model. Genetic values for adjusted and non-adjusted data were predicted considering additive direct and maternal effects, and for weight at 205 days, also the permanent environmental effect, as random effects in the model. The breeding values of the categories of sires considered for the weight characteristic at 205 days were organized in files, in order to verify alterations in the magnitude of the predictions and ranking of animals in the two methods of correction data for the non-additives effects. The non-additive effects were not similar in magnitude and direction in the two estimation methods used, nor for the characteristics evaluated. Pearson and Spearman correlations between breeding values were higher than 0.94, and the use of different methods does not imply changes in the selection of animals.

Prediction of retail beef yield, trim fat and proportion of high-valued cuts in Nellore cattle using ultrasound live measurements

The objective of this study was to develop equations to predict retail product and fat trim (weights and percentages) for Nellore (Bos indicus) cattle. Live ultrasound measurements of the longissimus muscle area, backfat thickness at the 12th rib and rump fat depth and shrunk body weight were obtained from 218 Nellore steers to predict weights and percentages of carcass retail product, pistola retail product and fat trimmings. After slaughter, carcasses were deboned and weighed and percentages of retail cuts were obtained directly. Measurements taken directly in the carcasses explained 97% and 36% of variation in carcass retail product weight and percentage, and 94% and 36% of variation in pistola retail weight and percentage, respectively. Live measurements explained 93% of carcass retail product weight and 39% of carcass retail product percentage. Lower accuracies were observed for pistola retail product weight (R-2=0.87) and percentage (R-2=0.33). Accuracies for fat trimmings weight and percentage were 79% and 55%, respectively. Ultrasound rump fat thickness showed greater correlations with retail product and fat trimmings (weights and percentages) when compared with ultrasound backfat thickness. The weight and percentage of retail products and of trimmable fat can be estimated in Nellore steers from live animal measurements, with similar accuracy to equations developed based on carcass measurements obtained at slaughter.

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 19992003 to the 20042008 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.

Intracellular Reactive Oxygen Species Production by Polymorphonuclear Leukocytes in Bovine Leukemia Virus-Infected Dairy Cows

The present study assesses the oxidative burst activity from polymorphonuclear leukocytes (PMNLs) from bovine leukemia virus (BLV)-infected cows. Fifteen clinically healthy cows were divided into serologically positive cows without any hematological alteration, serologically positive animals with persistent lymphocytosis (PL) and healthy serologically negative cows. The oxidative burst activity from the PMNLs was evaluated by now cytometry using 2',7'-dichlorofluorescein diacetate as a probe. PMNLs from each cow were incubated with heat-killed Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) to stimulate oxidative burst activity. The results of the present work showed no significant difference in the oxidative burst activity without any stimulus and elicited by S. caucus. Conversely, a decrease in the oxidative burst index induced by E. coli in PMNLs was observed in BLV-infected cows.

Genetic associations between flight speed and growth traits in Nellore cattle

The aim of the present study was to estimate genetic parameters for flight speed and its association with growth traits in Nellore beef cattle. The flight speed (FS) of 7,402 yearling animals was measured, using a device composed of a pair of photoelectric cells. Time interval data (s) were converted to speed (m/s) and faster animals were regarded as more reactive. The growth traits analyzed were weaning weight (WW), ADG from weaning to yearling age, and yearling scrotal circumference (SC). The (co)variance components were estimated using REML in a multitrait analysis applying an animal model. The model included random direct additive genetic and residual effects, fixed effects of contemporary groups, age of dam (classes), and age of animal as covariable. For WW, the model also included maternal genetic and permanent environmental random effects. The direct heritability estimate for FS was 0.26 +/- 0.05 and direct heritability estimates for WW, SC, and ADG were 0.30 +/- 0.01, 0.48 +/- 0.02, and 0.19 +/- 0.01, respectively. Estimates of the genetic correlation between FS and the growth traits were -0.12 +/- 0.07 (WW), -0.13 +/- 0.08 (ADG), and -0.11 +/- 0.07 (SC). Although the values were low, these correlations showed that animals with better temperaments (slower FS) tended to present better performance. It is possible to infer that long-term selection for weight and scrotal circumference can promote a positive genetic response in the temperament of animals. Nevertheless, to obtain faster genetic progress in temperament, it would be necessary to perform direct selection for such trait. Flight speed is an easily measured indicator of temperament and can be included as a selection criterion in breeding programs for Nellore cattle.

Quantification of B cells and T lymphocyte subsets in bovine leukemia virus infected dairy cows

The aim of the present trial was to determine the frequencies and absolute number of B and T lymphocytes subpopulations in bovine leukemia virus (BLV)-infected dairy cows with distinct lymphocyte profile known as non-leukemic (AL) and persistent lymphocytosis (PL). Thus, 15 animals were selected and divided uniformly in three groups (negative, AL, PL). The BLV infection was detected by agar gel immunodiffusion and enzyme-linked immunosorbent-assay. The lymphocytes subsets were evaluated using monoclonal antibodies by flow cytometry. The results of the present study pointed out to an increase in B lymphocytes, and also an augment in CD5(+) and CD11b(+) cells in animals showing PL. Consequently, it can be observed a decrease in the percentage of T cells subsets in these animals. Conversely, no significant alterations in the absolute number of the T lymphocytes, T CD4(+) cells and T CD8(+) lymphocytes were found in BLV-infected dairy cows with PL. Therefore, the correlation between the absolute numbers of B- and T cell subsets in the peripheral blood applied to each group showed a significant and positive strong correlation between numbers of B cells and T cells or T CD8(+) cells in the PL animals, although the same cannot be predicted for T CD4(+) lymphocytes. No such correlation was encountered for the AL and negative-control animals.

A longitudinal study of Neospora caninum infection on three dairy farms in Brazil

Neospora caninum is an apicomplexan protozoan parasite that is one of the most important infectious causes of abortion in both dairy and beef cattle in many countries. The objectives of this longitudinal study were to determine the prevalence, rates of vertical and horizontal transmission of N. caninum and hazard for culling of N. caninum-seropositive animals in three Brazilian dairy herds. Blood samples from all animals were collected nine times at each of the three farms over a two-year period. Serum was tested for antibodies against N. caninum using the indirect fluorescent antibody test with a cutoff value of 1:100. The percentage of N. caninum-positive samples at each sampling time ranged at Farm 1 from 3.32% to 11.71%, at Farm 11 from 3.90% to 22.06% and at Farm III from 3.90% to 22.06%. The number of positive serological reactions varied in relation to the number of repeated samples taken from individual animals at each farm. In all herds, there was a high degree (P < 0.05) of association between the N. caninum serological status of dams and daughters. The seropositive conversion rate was estimated as 0.37%, 3.00% and 6.94% per 100 cow-years at Farms I, II and III, respectively. The seronegative conversion rate was estimated as 31.58% and 11.11% per 100 cow-years at Farms 1 and III, respectively. In all herds, there was no difference (P > 0.05) in the culling rate between the cattle that were seropositive cattle and seronegative for N. caninum infection. The results from this study confirm the importance of vertical transmission in the epidemiology of N. caninum. Although a few positive seroconversions indicated horizontal transmission, it does not appear to be the major route of infection for N. caninum. (C) 2012 Elsevier B.V. All rights reserved.