Genotype by environment interaction for 450-day weight of Nelore cattle analyzed by reaction norm models

Genotype by environment interactions (GEI) have attracted increasing attention in tropical breeding programs because of the variety of production systems involved. In this work, we assessed GEI in 450-day adjusted weight (W450) Nelore cattle from 366 Brazilian herds by comparing traditional univariate single-environment model analysis (UM) and random regression first order reaction norm models for six environmental variables: standard deviations of herd-year (RRMw) and herd-year-season-management (RRMw-m) groups for mean W450, standard deviations of herd-year (RRMg) and herd-year-season-management (RRMg-m) groups adjusted for 365-450 days weight gain (G450) averages, and two iterative algorithms using herd-year-season-management group solution estimates from a first RRMw-m and RRMg-m analysis (RRMITw-m and RRMITg-m, respectively). The RRM results showed similar tendencies in the variance components and heritability estimates along environmental gradient. Some of the variation among RRM estimates may have been related to the precision of the predictor and to correlations between environmental variables and the likely components of the weight trait. GEI, which was assessed by estimating the genetic correlation surfaces, had values < 0.5 between extreme environments in all models. Regression analyses showed that the correlation between the expected progeny differences for UM and the corresponding differences estimated by RRM was higher in intermediate and favorable environments than in unfavorable environments (p < 0.0001).     

Dynamics of Haematobia irritans irritans (Diptera: Muscidae) infestation on Nelore cattle in the Pantanal, Brazil

From June 1993 to May 1995, horn fly counts were conducted twice a month on untreated Nelore cattle raised extensively in the Pantanal. Horn fly population showed a bimodal fluctuation and peaks were observed every year after the beginning (November/December) and at the end (May/June) of the rainy season, which coincided with mid-late spring and mid-late fall, respectively. Horn flies were present on cattle throughout the year in at least 64% of the animals. Mean horn fly numbers on animals did not exceed 85 flies/cow during peaks and were under 35 flies/cow in most of the remaining periods. The highest infestations (population peaks) were short and dropped suddenly within two weeks. Less than 15% of the animals in both herds could be considered as "fly-susceptible" - showing consistently higher infestations, or "fly-resistant" - showing consistently lower infestations.     

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.     

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

We quantified the potential increase in accuracy of expected breeding value for weights of Nelore cattle, from birth to mature age, using multi-trait and random regression models on Legendre polynomials and B-spline functions. A total of 87,712 weight records from 8144 females were used, recorded every three months from birth to mature age from the Nelore Brazil Program. For random regression analyses, all female weight records from birth to eight years of age (data set I) were considered. From this general data set, a subset was created (data set II), which included only nine weight records: at birth, weaning, 365 and 550 days of age, and 2, 3, 4, 5, and 6 years of age. Data set II was analyzed using random regression and multi-trait models. The model of analysis included the contemporary group as fixed effects and age of dam as a linear and quadratic covariable. In the random regression analyses, average growth trends were modeled using a cubic regression on orthogonal polynomials of age. Residual variances were modeled by a step function with five classes. Legendre polynomials of fourth and sixth order were utilized to model the direct genetic and animal permanent environmental effects, respectively, while third-order Legendre polynomials were considered for maternal genetic and maternal permanent environmental effects. Quadratic polynomials were applied to model all random effects in random regression models on B-spline functions. Direct genetic and animal permanent environmental effects were modeled using three segments or five coefficients, and genetic maternal and maternal permanent environmental effects were modeled with one segment or three coefficients in the random regression models on B-spline functions. For both data sets (I and II), animals ranked differently according to expected breeding value obtained by random regression or multi-trait models. With random regression models, the highest gains in accuracy were obtained at ages with a low number of weight records. The results indicate that random regression models provide more accurate expected breeding values than the traditionally finite multi-trait models. Thus, higher genetic responses are expected for beef cattle growth traits by replacing a multi-trait model with random regression models for genetic evaluation. B-spline functions could be applied as an alternative to Legendre polynomials to model covariance functions for weights from birth to mature age.     

Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

Background

Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds.

Results

We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings.

Conclusions

The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0109-5) contains supplementary material, which is available to authorized users.     

Delphi-consensus weights for ischemic and bleeding events to be included in a composite outcome for RCTs in thrombosis prevention

Background and Objectives

To weight ischemic and bleeding events according to their severity to be used in a composite outcome in RCTs in the field of thrombosis prevention.

Method

Using a Delphi consensus method, a panel of anaesthesiology and cardiology experts rated the severity of thrombotic and bleeding clinical events. The ratings were expressed on a 10-point scale. The median and quartiles of the ratings of each item were returned to the experts. Then, the panel members evaluated the events a second time with knowledge of the group responses from the first round. Cronbach''s a was used as a measure of homogeneity for the ratings. The final rating for each event corresponded to the median rating obtained at the last Delphi round.

Results

Of 70 experts invited, 32 (46%) accepted to participate. Consensus was reached at the second round as indicated by Cronbach''s a value (0.99 (95% CI 0.98-1.00)) so the Delphi was stopped. Severity ranged from under-popliteal venous thrombosis (median = 3, Q1 = 2; Q3 = 3) to ischemic stroke or intracerebral hemorrhage with severe disability at 7 days and massive pulmonary embolism (median = 9, Q1 = 9; Q3 = 9). Ratings did not differ according to the medical specialty of experts.

Conclusions

These ratings could be used to weight ischemic and bleeding events of various severity comprising a composite outcome in the field of thrombosis prevention.     

Analysis of genetic correlations of hip height with selection indices and mature weight in Nelore cattle

Body size is directly related to the productive and reproductive performance of beef cattle raised under free-range conditions. In an attempt to better plan selection criteria, avoiding extremes in body size, this study estimated the heritabilities and genetic correlations of yearling hip height (YH) and mature hip height (MH) with selection indices obtained at weaning (WI) and yearling (YI) and mature weight (MW). Data from 102,373 Nelore animals born between 1984 and 2010, which belong to 263 farms that participate in genetic evaluation programmes of beef cattle conducted in Brazil and Paraguay, were used. The (co)variance components and genetic parameters were estimated by Bayesian inference in multi-trait analysis using an animal model. The mean heritabilities for YH, MH and MW were 0.56?±?0.06, 0.47?±?0.02 and 0.42?±?0.02, respectively. The genetic correlation of YH with WI (0.13?±?0.01) and YI (0.11?±?0.01) was practically zero, whereas a higher correlation was observed with MW (0.22?±?0.03). Positive genetic correlations of medium magnitude were estimated between MH and WI and YI (0.23?±?0.01 and 0.43?±?0.02, respectively). On the other hand, a high genetic correlation (0.68?±?0.03) was observed between the indicator traits of mature body size (MH and MW). Considering the top 20 % of sire (896 sires) in terms of breeding values for the yearling index, the rank sire correlations between breeding values for MH and MW was 0.62. In general, the results indicate that selection based on WI and YI should not lead to important changes in YH. However, an undesired correlated response in mature cow height is expected, particularly when selection is performed using YI. Therefore, changes in the body structure of Nelore females can be obtained when MH and MW is used as a selection criterion for cows.     

Fertility effects of chromosome rearrangement (insertion 16) in Charolais cattle from Brazil

Insertion 16, a structural chromosome abnormality originated by three breaks in one autosome, was detected with familial recurrence in a Charolais cattle population. Due to the peculiar nature of Insertion 16, its effect on the fertility of the carriers was verified by various parameters. A total of 115 animals was karyotyped to learn the segregational behavior of the chromosome abnormality, and 1,354 females were studied to evaluate the reproductive efficiency of the propositi, a pair of chimeric bulls for insertion 16. Their fertility was observed and compared with that of three normal bulls. Analysis of the results revealed that insertion 15 segregates in the offspring of only one heterozygous proposita, without sex preference, and that the percentage of conceptions in the cows inseminated by the propositi was similar to the controls'; however, for each conception with the semen of the propositus in which the insertion segregated, 0.16 more inseminations were necessary than for the controls. Similarly, the deviation in the percentage of nonreturns after the first insemination (15.9%) and the frequency of abnormal oestrous cycles (10.3%) indicate reduced fertility in the propositus, which is related to early embryo mortality.     

Phenotypic and genetic parameters compared during repeated measures of longissimus muscle area and subcutaneous fat thickness in Nelore cattle

Real-time ultrasound is currently used for in vivo carcass evaluation of beef cattle. We estimated heritability and repeatability coefficients for ultrasound-measured carcass traits in Nelore cattle. We measured longissimus muscle area, backfat thickness, and rump fat thickness in male and female animals ranging in age from 10 to 26 months. The variance components were estimated by single-trait analysis using the derivative-free restricted maximum likelihood method, under an animal model. The complete data file included 3077 records of 1172 animals born between 2003 and 2008. Two analyses were performed using a repeatability model: a) all records of longissimus muscle area, backfat thickness, and rump fat thickness of animals aged 10 to 26 months, and b) considering two age periods (11 to 17 and 18 to 24 months). The heritability estimates ranged from 0.33 to 0.46 for longissimus muscle area, from 0.20 to 0.26 for backfat, and from 0.26 to 0.29 for rump fat, demonstrating that direct selection for these traits can provide genetic gain. The repeatability estimates were moderate, ranging from 0.42 to 0.73. The highest repeatability estimates were obtained for longissimus muscle area in both the first (0.70) and second (0.73) analyses. The repeatability estimates suggest that ultrasound measures are precise; higher precision was obtained for longissimus muscle area than for subcutaneous fat thickness. The latter could be obtained during periods of greater feed availability to increase precision.     

Genetic signatures of parental contribution in black and white populations in Brazil

Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups.     

Sample path analysis of contribution and reward in cooperative groups

Explaining cooperative behavior is one of the major challenges in both biology and human society. The individual reward in cooperative group depends on how we share the rewards in the group. Thus, the group size dynamics in a cooperative group and reward-allocation rule seem essential to evaluate the emergence of cooperative groups. We apply a sample path-based analysis called an extension of Little's formula to general cooperative group. We show that the expected reward is insensitive to the specific reward-allocation rule and probabilistic structure of group dynamics, and the simple productivity condition guarantees the expected reward to be larger than the average contribution. As an example, we take social queues to see the insensitivity result in detail.     

Molecular and geographic analyses of vampire bat-transmitted cattle rabies in central Brazil

Background

Vampire bats are important rabies virus vectors, causing critical problems in both the livestock industry and public health sector in Latin America. In order to assess the epidemiological characteristics of vampire bat-transmitted rabies, the authors conducted phylogenetic and geographical analyses using sequence data of a large number of cattle rabies isolates collected from a wide geographical area in Brazil.

Methods

Partial nucleoprotein genes of rabies viruses isolated from 666 cattle and 18 vampire bats between 1987 and 2006 were sequenced and used for phylogenetic analysis. The genetic variants were plotted on topographical maps of Brazil.

Results

In this study, 593 samples consisting of 24 genetic variants were analyzed. Regional localization of variants was observed, with the distribution of several variants found to be delimited by mountain ranges which served as geographic boundaries. The geographical distributions of vampire-bat and cattle isolates that were classified as the identical phylogenetic group were found to overlap with high certainty. Most of the samples analyzed in this study were isolated from adjacent areas linked by rivers.

Conclusion

This study revealed the existence of several dozen regional variants associated with vampire bats in Brazil, with the distribution patterns of these variants found to be affected by mountain ranges and rivers. These results suggest that epidemiological characteristics of vampire bat-related rabies appear to be associated with the topographical and geographical characteristics of areas where cattle are maintained, and the factors affecting vampire bat ecology.

     

Relative contribution of euphausiid prey species and timing of breeding to Cassin's auklet Ptychoramphus aleuticus growth: within-season effects

Within-season variation in life-history parameters is characteristic of long-lived seabirds breeding in dynamic marine environments. Zooplanktivorous Cassin's auklets Ptychoramphus aleuticus breeding in central California feed primarily on euphausiid crustaceans, and switch from provisioning their offspring with Euphausia pacifica early in the nestling period to Thysanoessa spinifera later in the nestling period. I examined the effects of seasonal variation in nestling diet composition and meal mass, and timing of breeding and breeding attempt number (only/first or second breeding attempt) on the growth rate of individual nestlings on Southeast Farallon Island, California. For individual years, there were variable seasonal trends in growth, but no trends were apparent when all years were combined. Along with the predicted seasonal shift in prey use, there was a concurrent decrease in meal mass. In multivariate models, there were significant and positive effects of the mass proportions of E. pacifica and T. spinifera in the diet, meal mass and breeding attempt number on nestling growth, while the effect of hatching date on growth was negative. The relative influence of T. spinifera on growth was stronger than that of E. pacifica , the effects of hatching date on growth were likely dependent on the effects of breeding attempt, and breeding attempt exerted the strongest effect on nestling growth of all parameters examined. These suggest that the seasonal switch in prey use is advantageous (whether intentional or otherwise). Results illustrate the importance of adequate availability of both E. pacifica and T. spinifera to auklets in the Gulf of the Farallones. This study represents a unique approach in the investigation of linkages between individual nestling growth rate and diet and breeding phenology parameters by focusing on a fine temporal scale.     

Anti-Toxoplasma gondii antibodies in cattle and pigs in a highly endemic area for human toxoplasmosis in Brazil

Sera from 77 cattle and 61 pigs from herds of Campos dos Goytacazes and neighborhood, north of Rio de Janeiro state, Brazil, were analyzed for the presence of antibodies anti-Toxoplasma gondii via ELISA. The seropositivity was confirmed at 49.4% (38 of 77) for cattle and at 11.5% (7 of 61) for pigs. Pigs bred under free-ranging systems presented with 20.6% (7 of 34) seropositivity and no pigs bred under indoor systems were positive (n = 27). The seropositivity verified for cattle and pigs confirmed the extensive distribution of the parasite in this region. In the face of these data, we discuss the potential risk for human infection by consumption of raw or undercooked meat in this geographic region of Brazil. This is the first report of seropositivity for anti-T. gondii antibodies in cattle in the north of Rio de Janeiro State, Brazil.     

Genetic parameters for direct and maternal effects on body weights of Draa goats

Genetic parameters and (co)variance components were estimated for weights at birth and at 30, 90 and 180 days of age for Draa goat maintained at Ouarzazate station over a period of 18 years (1988–2005). Records of 1498 kids, the progeny of 46 sires and 404 dams were used in the study. Analyses were carried out by restricted maximum likelihood. Six different animal models including or ignoring maternal genetic or permanent environmental effects were fitted for all traits. The Model 2 with only permanent environmental maternal effects seemed most suitable. Estimates of direct heritability from this model were 0.16 for birth weight and 0.07, 0.11 and 0.11 for weights at 30, 90 and 180 days, respectively. Maternal heritability estimates varied from 0.00 to 0.24 for all traits according to the model used (Models 4–6). Bivariate analysis by Model 2 was also used to estimate genetic correlations between traits. The estimates of genetic and phenotypic correlations among weights were positive and intermediate to high in value. Despite the low estimated heritabilities of body weight traits of Draa goat, there is a small genetic variability that may be exploited to improve growth performance.     

Compilation of classical and contemporary terminology used to describe morphological aspects of ovarian dynamics in cattle

Veterinarians and scientists involved in applied and basic research in cattle require a lexicon of terms that is used uniformly so that diagnoses and inference of results between and among studies can be correctly interpreted and substantiated or negated and therapy and hypotheses can be formulated without unnecessary confusion and redundancy in treatments and experiments. This review provides a compilation of many of the classical and contemporary terms used in association with ovarian dynamics primarily during the estrous cycle in cattle, which can also apply to other reproductive states. While many classical terms used to describe healthy and diseased conditions associated with follicles and corpora lutea are still applicable today, there are some that have become antiquated (e.g., cystic corpus luteum, cystic ovarian degeneration, luteolysis, and granulosa cell tumor), due, in part, to advanced technology (e.g., ultrasonography) and a more thorough understanding of ovarian function. In this regard, older terms have been revised (e.g., corpus luteum with a cavity, follicular and luteinized-follicular cysts, structural and functional luteal regression, and granulosa-theca cell tumor) and newer terms have been coined (e.g., follicle deviation) and advocated herein. Defining and adopting terminology used in bovine reproduction that is clear, precise and understandable and available in a single source, is expected to make the exchange of clinical and research information and outcomes more effective, safe, and economical.     

Relative contribution of contemporary pollen and seed dispersal to the effective parental size of seedling population of California valley oak (Quercus lobata, Née)

For plant populations, gene movement through pollen and seed dispersal governs the size of local genetic neighbourhoods and shapes the opportunities for natural selection and genetic drift. A critical question is how together these two processes influence the evolutionary dynamics of local populations. To assess the respective contributions of pollen and seed flow, we propose a novel indirect assessment of the separate male and female gametic contributions to total effective parental size ( N _e), based on parental correlations estimated via kinship coefficients, that can be applied to data sets that include unambiguous genotypes for male and female gametic contributions. Using the endemic Californian valley oak ( Quercus lobata ) as our study species, we apply this method to a set of microsatellite genotypes for two distinct ecological sets of naturally recruiting seedlings with acorns attached. We found that the effective numbers of contributing male parents ( N _ep) exceed effective numbers of female parents ( N _em) for seedlings established beneath adult trees ( N _ep = 8.1 and N _em = 1.1), as well as for seedlings established away from adult trees ( N _ep = 15.4 and N _em = 2.7), illustrating that seed dispersal enhances pollen dispersal and increases the effective number of seed sources in open seedling patches. The resulting effective parental size of seedling populations translates into smaller effective numbers of parents for undispersed vs. dispersed seedlings ( N _e = 3.6 and N _e = 6.7, respectively). This study introduces a novel statistic method and provides important new evidence that, on a short-term temporal scale, seed dispersal shapes the local neighbourhood size of new recruits.