Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle

For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.

Longitudinal genetic dynamics of weaning index and implications for cow-calf production efficiency

In beef cattle, the selection for higher weights at young ages has been questioned with the argument that this criterion may increase the adult weight of cows, resulting in higher costs. Therefore, selection criteria should be employed to increase weights at young ages with minimal impact on the adult weight of cows. Additionally, the relationship between measures of cow production efficiency and other well-established selection criteria in breeding programs remains poorly understood. The objective of this study was to longitudinally evaluate the relationship between the weaning index (WIndex) as a measure of efficiency and growth traits of the cows. Possible changes over time in WIndex due to selection applied for yearling weight (YW) were also investigated. The WIndex was proposed to maximize genetic response in the weaning weight of the calf while maintaining genetic gain in BW of the cow at zero. A random regression model was adopted to estimate correlations between WIndex, BW, hip height (HH), and body condition score (BCS) using records of Nelore cows from three lines. Genetic trends were calculated for the control line (NeC) and lines selected for greater YW (NeS and NeT). The age of 3 years was the most critical for the weaning efficiency of the cows. At this stage, young cows are still growing and wean lighter calves than their adult counterparts. The genetic correlation estimates between WIndex and BW (-0.58 to 0.04), HH (-0.05 to -0.34), and BCS (-0.51 to -0.17) were close to zero or negative. BW and HH were strongly correlated genetically across all ages (0.73-0.76). In general, HH exhibited a weak and negative genetic relationship with BCS. The genetic correlation between BW and BCS was stronger for advanced ages (0.45-0.68). In lines selected for YW, important increases in WIndex were observed. However, NeS has been selected since the 1980s until the present for YW, and thus, it showed a more pronounced trend of increasing BW and, consequently, a more modest trend of increasing WIndex compared to NeT. In contrast, WIndex exhibited a trend close to zero for NeC. In this context, monitoring HH and BCS can be useful to avoid losses in the weaning efficiency of cows. Furthermore, we suggest that one way to mitigate efficiency losses in calf production could involve stabilizing the BW of cows and increasing the weaning weight of calves using the WIndex.

Genetic evaluation of lactation persistency in the Gyr breed by using a two-trait random regression model

ContextLactation persistency (LP) is an economically important characteristic to include in the selection objectives of the Gyr breed. Two persistency measures were tested to establish their contribution to the genetic evaluation of milk production in this genotype. The second measure of persistency studied would be the more appropriate measure to use in the genetic evaluation of lactation persistency.AimThe aim of this work was to study LP in Gyr cows by using a random regression model (RRM) in two-trait analysis.MethodsTest-day milk yields (TDMY) of the first two lactations of Gyr cows were analysed. RRM was performed by Bayesian inference using the GIBBS3F90 program. Fourth-order Legendre polynomials were used to describe the random additive genetic and permanent environmental effects of the animal. The fixed effects included in the model were contemporary group and, as covariates, age of cow at calving and the regression function according to the TDMY class of lactation as the average trajectories of lactation curve, distinguished by calving order. Two persistency measures (PSi, i.e. PS1 and PS2) were used in the analyses. Rank correlations were calculated between the predicted breeding values for PSi, 305-day lactation milk yield (MY305), and the regression coefficients a0 and a1, to determine the percentage of matching animals between rankings when different selection intensities are applied on the basis ofthe ranking for MY305.Key resultsThe heritability estimates for PS1, PS2 and for MY305 were 0.19, 0.12 and 0.41 respectively, in the first lactation, and 0.43, 0.27 and 0.38 in the second lactation. The genetic correlation between MY305 and PS1 was negative and of low magnitude. The rank correlation between breeding values for PSi, obtained for bulls with at least five daughters with production records, was higher than 0.80 in the two lactation periods.ConclusionsThe results indicated that PS2 is the more suitable of the two persistency measures used in this work, for inclusion in genetic evaluations of lactation persistency in Brazilian Gyr cows.ImplicationsPS2 must be included as a selection criteria in a breeding program for the Gyr breed.

Contemporary group alternatives for genetic evaluation of milk yield in small populations of dairy cattle

In the present study, different random regression models, focussed on the nature of the effect of the contemporary group, fixed or random, were compared for genetic evaluation of test-day milk yield in dairy Gir breed, whose herds are characterised by relatively reduced numbers of cows. Cows were assigned to the same contemporary group if they were tested in the same herd, year and month. In one of the evaluated models, the contemporary group was investigated as a fixed effect and a clustering procedure was adopted to group herd-year subclasses in order to, at the end of the process, all contemporary groups contained at least three cows. The models were compared by the quality of fit, the accuracy of the predicted breeding values and their estimates of genetic parameters. The clustering procedure did not significantly improve the accuracy of predicted breeding values. Moreover, the fit to the data for this model was negatively affected. Therefore, this strategy should not be further implemented. The model including the herd-calving period effect and contemporary group treated as random effect showed similar characteristics to its equivalent, where the contemporary group was modelled as a fixed effect. However, the fit to the data for this model was slightly worse. Thus, the results suggest a random regression model including the herd-calving period effect and the fixed effect of contemporary group for the genetic evaluations of production traits in dairy Gir cattle. These findings could be extended to small dairy cattle populations whose herds are small-sized.

Inbreeding depression in Zebu cattle traits

The productivity of herds may be negatively affected by inbreeding depression, and it is important to know how intense is this effect on the livestock performance. We performed a comprehensive analysis involving five Zebu breeds reared in Brazil to estimate inbreeding depression in productive and reproductive traits. Inbreeding depression was estimated for 13 traits by including the individual inbreeding rate as a linear covariate in the standard genetic evaluation models. For all breeds and for almost all traits (no effect was observed on gestation length), the performance of the animals was compromised by an increase in inbreeding. The average inbreeding depression was -0.222% and -0.859% per 1% of inbreeding for linear regression coefficients scaled on the percentage of mean (β_m ) and standard deviation (β_σ ), respectively. The means for β_m (and β_σ ) were -0.269% (-1.202%) for weight/growth traits and -0.174% (-0.546%) for reproductive traits. Hence, inbreeding depression is more pronounced in weight/growth traits than in reproductive traits. These findings highlight the need for the management of inbreeding in the respective breeding programmes of the breeds studied here.

Genetic parameters and investigation of genotype × environment interactions in Nellore × Hereford crossbred for resistance to cattle ticks in different regions of Brazil

Data from 6,156 Nellore × Hereford crossbred cattle, distributed in 18 herds located in the Brazilian states of Mato Grosso do Sul (MS), São Paulo (SP), Paraná (PR) and Rio Grande do Sul (RS), were analysed in order to investigate genetic variation for resistance to the cattle tick through the estimation of variance components and genetic parameters for counting ticks (Rhipicephalus (Boophilus) microplus) in natural infestation, and also a possible genotype × environment interaction. The tick count data (CC) were transformed to log10(CC + 1) and grouped into two regions, defined by cluster analysis and analysed using the method of restricted maximum likelihood. The statistical model included the additive genetic effect as random and fixed effects of the contemporary group (CG) and genetic group (GG) as classificatory and the age of the animal at the time of counting (linear effect) and individual heterozygosity (linear effect, ranging from 0 to 1) as covariates. In the studied regions, the effect of heterosis found was inversely proportional; in other words, the count of ticks decreased with the increase of heterozygosity. The observed heritability estimation for resistance to tick infestation were 0.12 ± 0.04 and 0.11 ± 0.04 for groups A (RS and south PR) and B (MS, SP and north PR), respectively. The results of this study suggest that selection for animals resistant to ticks would be possible using the tick count to estimate the genetic value of animals, but with a slow genetic progress. The genetic correlation for tick count between the two groups (A and B) was 0.84 ± 0.27 and genotype × environment interaction for this trait was not observed in the studied population.

Genotype by environment interaction for post-weaning weight gain, scrotal circumference, and muscling score of composite beef cattle in different regions of Brazil

The objectives of this study were to characterize and define homogenous production environments of composite beef cattle in Brazil in terms of climatic and geographic variables by using multivariate exploratory techniques; to evaluate the presence of genotype by environment interaction (GxE) for post-weaning weight gain (PWG), yearling scrotal circumference (SC), and yearling muscling (MUS). Hierarchical and nonhierarchical cluster analysis was used to group farms located in regions with similar environmental variables into clusters. Six clusters of farms were formed. The effect of sire-cluster interaction was tested by single-trait analysis. Genetic parameters were estimated by multi-trait analysis considering the same trait to be different in each cluster. The effect of sire-cluster interaction was significant (P <0.01) for PWG and MUS. Estimates of genetic correlations among clusters ranged from 0.31 to 0.93 for PWG, 0.64 to 0.89 for SC, and 0.18 to 0.80 for MUS. These results indicate the need for a genetic analysis on a regional basis or inclusion of the GxE effect in the statistical model to permit appropriate evaluation of the animals.

Genetic associations of visual scores with subsequent rebreeding and days to first calving in Nellore cattle

Records of Nellore animals born from 1990 to 2006 were used to estimate genetic correlations of visual scores at yearling (conformation, C; finishing precocity, P; and muscling, M) with primiparous subsequent rebreeding (SR) and days to first calving (DC), because the magnitude of these associations is still unknown. Genetic parameters were estimated by multiple-traits Bayesian analysis, using a nonlinear (threshold) animal models for visual scores and SR and a linear animal models for weaning weight (WW) and DC. WW was included in the analysis to account for the effects of sequential selection. The posterior means of heritabilities estimated for C, P, M, SR and DC were 0.24 ± 0.01, 0.31 ± 0.01, 0.30 ± 0.01, 0.18 ± 0.02 and 0.06 ± 0.02, respectively. The posterior means of genetic correlations estimated between SR and visual scores were low and positive, with values of 0.09 ± 0.02 (C), 0.19 ± 0.03 (P) and 0.18 ± 0.05 (M). On the other hand, negative genetic correlations were found between DC and C (-0.11 ± 0.09), P (-0.19 ± 0.09) and M (-0.16 ± 0.09). The primiparous rebreeding trait has genetic variability in Nellore cattle. The genetic correlations between visual scores, and SR and DC were low and favourable. The genetic changes in C, P and M were 0.02, 0.03 and 0.03/year, respectively. For SR and DC, genetic trends were 0.01/year and -0.01 days/year, respectively, indicating that the increase in genetic merit for reproductive traits was small over time. Direct selection for visual scores together with female reproductive traits is recommended to increase the fertility of beef cows.

Effect of pregnancy on the genetic evaluation of dairy cattle

We investigated the effect of stage of pregnancy on estimates of breeding values for milk yield and milk persistency in Gyr and Holstein dairy cattle in Brazil. Test-day milk yield records were analyzed using random regression models with or without the effect of pregnancy. Models were compared using residual variances, heritabilities, rank correlations of estimated breeding values of bulls and cows, and number of nonpregnant cows in the top 200 for milk yield and milk persistency. The estimates of residual variance and heritabilities obtained with the models with or without the effect of pregnancy were similar for the two breeds. Inclusion of the effect of pregnancy in genetic evaluation models for these populations did not affect the ranking of cows and sires based on their predicted breeding values for 305-day cumulative milk yield. In contrast, when we examined persistency of milk yield, lack of adjustment for the effect of pregnancy overestimated breeding values of nonpregnant cows and cows with a long days open period and underestimated breeding values of cows with a short days open period. We recommend that models include the effect of days of pregnancy for estimation of adjustment factors for the effect of pregnancy in genetic evaluations of Dairy Gyr and Holstein cattle.

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.

High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean-type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species' range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear beta-fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co-distributed taxa.

The effect of heparin, caffeine and calcium ionophore A23187 on in vitro induction of the acrosome reaction in frozen-thawed bovine and caprine spermatozoa

The effect of heparin (5 IU), caffeine (5 mM) and calcium-ionophore A23187 (0.1 mM) on motility and in vitro induction of the acrosome reaction in glass wool filtered frozen-thawed bull and goat semen was studied. The motile spermatozoa fraction was obtained after glass wool filtration of frozen-thawed semen. The seminal plasma was removed from filtered semen by centrifugation, and the sperm pellet was resuspended in Sperm-TALP medium. Samples of treated and untreated control semen of both species were incubated at 37 degrees C. At 1, 15 and 30 min of incubation the proportions of progressively motile and acrosome-reacted spermatozoa were assessed. Trypan blue and Giemsa stain was used to differentiate live and dead spermatozoa having undergone acrosome reaction. Glass wool filtration enhanced the proportion of motile spermatozoa from 43% to 62% in the bovine and from 41% to 60% in the caprine. Whereas the effect of incubation with caffeine, heparin and calcium-ionophore on spermatozoan motility was negligible, the treatment of semen with calcium-ionophore resulted in a significantly improved percentage of live spermatozoa with true acrosome reaction at all stages of incubation, both in the bovine and the caprine.

Nonsurgical embryo collection in goats treated with prostaglandin F2alpha and oxytocin

Embryos were collected transcervically from 38 unanesthetized goats in a standing position. Goats of the Boer breed were superovulated by injecting them with 16 mg of pFSH containing 40% LH. Collection took place 6 d after the last mating. A luteolytic dose of PGF2alpha was injected 16, 8, or 0 h before flushing the uterine lumen. One half of each group received an additional injection of oxytocin just before flushing. The flushing catheter was introduced transcervically, and 24 flushings were performed, with a 2-h pause between the first 12 and the last 12 flushings. Injection of PGF2alpha 16 or 8 h before transcervical embryo collection resulted in a significant increase (P < .001, chi-square test) in embryo recovery (-16 h: 91% with oxytocin, 85% without; -8 h: 91% with oxytocin, 80% without) compared with an injection at the time of collection (52% with oxytocin, 66% without). The recovery rate which was estimated as the percentage of embryos recovered relative to the number of corpora lutea counted endoscopically, was comparable to that achieved by surgical collection. There were no differences among groups with regard to embryo morphology. Embryos were transferred, and healthy kids were born. The nonsurgical collection of caprine embryos may be considered a viable alternative to conventional surgical procedures.