Genome-wide association study for milking speed in Fleckvieh cattle.

Milking speed is an important trait influencing udder health of dairy cows as well as labor efficiency. Yet, it has received little attention in genomic association studies. The main objective of this study was to determine regions and genes on the genome with a potential effect on milking speed in Fleckvieh (dual purpose Simmental) cattle. Genome-wide association studies were conducted using de-regressed breeding values of bulls as phenotypes. Six SNP on 4 autosomes were significantly associated with milking speed for additive effects. Significant regions on BTA4 and BTA19 correspond with findings for other dairy cattle breeds. Based on the observation of Fleckvieh breed managers, variation of milking speed in batches of daughters of some bulls is much higher than in daughter groups of other bulls. This difference in within family variation may be caused by transmission of alternative alleles of bulls being heterozygous for a gene affecting milking speed. To check on this, we considered standard deviation of yield deviations in milking speed of half-sib daughters as a new trait and performed GWAS for dominance effects. One signal on BTA5 passed the genome wide Bonferroni threshold that corresponded to the significant signal from standard GWAS on de-regressed breeding values. The key conclusion of this study is that several strong genomic signals were found for milking speed in Fleckvieh cattle and that the strongest of them are supported by similar findings in Brown Swiss and Holstein Friesian cattle. Milking speed is a complex trait whose sub-processes have not yet been elucidated in detail. Hence, it remains a challenge to link the associated regions on the genome with causal genes and their functions.

From farmers to livestock keepers: a typology of cattle production systems in south-western Burkina Faso.

Cattle production is an essential livelihood strategy in south-western Burkina Faso. Although having a distinct cultural role and known to be resistant against African animal trypanosomosis, the Lobi taurine cattle breed is endangered due to its low market value. As the first step in preservation efforts, our study aimed to develop a typology of production systems at the farm level. We used a structured questionnaire and focus group discussions for collecting data on household characteristics, socioeconomic activities, livestock, and access to services. The sample comprised 169 households in three communities. The analytical strategy included factor analysis of mixed data and hierarchical clustering. We identified four distinct types of cattle production systems: (1) sedentary Lobi farms, (2) sedentary crossbreed farms, (3) semi-transhumant Fulani zebu farms, and (4) transhumant Fulani zebu farms. Significant factors in developing this typology were the farmers' ethnic group, crop diversity, cattle herd size, cattle herd composition, number of small ruminants, and livestock management strategies. Across all production systems, men were considered being primary decision-makers in cattle production, with women, herders, and children being responsible for specific tasks. All identified production systems are increasingly confronting disease pressure and scarcity of water and land. Future efforts in preservation and breeding will need to respond to these trends in the agroecosystem, integrate risk management measures, and resonate with the specific needs of the different household members involved in cattle rearing.

Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls.

Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.

A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern.

A specific white spotting phenotype, termed finching or line-backed spotting, is known for all Pinzgauer cattle and occurs occasionally in Tux-Zillertaler cattle, two Austrian breeds. The so-called Pinzgauer spotting is inherited as an autosomal incompletely dominant trait. A genome-wide association study using 27 white spotted and 16 solid-coloured Tux-Zillertaler cattle, based on 777k SNP data, revealed a strong signal on chromosome 6 at the KIT locus. Haplotype analyses defined a critical interval of 122 kb downstream of the KIT coding region. Whole-genome sequencing of a Pinzgauer cattle and comparison to 338 control genomes revealed a complex structural variant consisting of a 9.4-kb deletion and an inversely inserted duplication of 1.5 kb fused to a 310-kb duplicated segment from chromosome 4. A diagnostic PCR was developed for straightforward genotyping of carriers for this structural variant (KITPINZ ) and confirmed that the variant allele was present in all Pinzgauer and most of the white spotted Tux-Zillertaler cattle. In addition, we detected the variant in all Slovenian Cika, British Gloucester and Spanish Berrenda en negro cattle with similar spotting patterns. Interestingly, the KITPINZ variant occurs in some white spotted animals of the Swiss breeds Evolèner and Eringer. The introgression of the KITPINZ variant confirms admixture and the reported historical relationship of these short-headed breeds with Austrian Tux-Zillertaler and suggests a mutation event, occurring before breed formation.

Genetic associations of lactose and its ratios to other milk solids with health traits in Austrian Fleckvieh cows.

The genetic correlations (ra) of milk lactose percentage (LP), lactose yield (LY), and ratios of LP to other milk solids with udder, metabolic, and fertility disorders have not been assessed in dairy cattle so far. To evaluate the potential role of milk lactose as indicator of cow health, 142,285 lactation records of 84,289 Austrian Fleckvieh cows were analyzed with univariate and bivariate animal models. Milk traits were on a 150-d basis and health traits were coded as binary (0/1). Other than LP and LY, 3 new phenotypes were defined and included in the present study, namely the lactose-to-fat, lactose-to-protein, and lactose-to-solids ratios. The most heritable trait was LP (0.566 ± 0.008) and heritability of LY was much lower (0.145 ± 0.005). Heritability estimates close to 0.50 were assessed for the ratios. The frequency of health disorders was higher in multiparous cows yielding milk with low LP (≤4.553%) compared with cows yielding milk with high LP (≥5.045%). Heritabilities of health traits were in the expected ranges, with the highest estimate for ovarian cysts (CYS; 0.037 ± 0.004) and the lowest for retained placenta (0.005 ± 0.001). Mastitis (MAS) genetically correlated with LY (0.518 ± 0.057); considering that the amount of synthesized lactose is the key regulator of milk volume, this result confirmed that high-producing cows are more genetically susceptible to MAS than low-producing animals. Similar to MAS, ketosis (KET) was also positively genetically associated with LY (0.420 ± 0.077) and a weak and unfavorable ra between KET and lactose-to-protein ratio was estimated (0.159 ± 0.077). The ra of LY with milk fever (MFV) and CYS were approximately 0.20. The ra of LP with MAS, KET, and MFV were negative (-0.142 on average), supporting the idea that LP is a potential health indicator. Genetic correlations between health traits ranged from zero (retained placenta with MAS and CYS) to 0.463 ± 0.090 (MAS and MFV). Results of the present study suggest that LP has potentiality to be used as indicator trait to improve udder health in Austrian Fleckvieh population.

Fast Data Sorting with Modified Principal Component Analysis to Distinguish Unique Single Molecular Break Junction Trajectories.

A simple and fast analysis method to sort large data sets into groups with shared distinguishing characteristics is described and applied to single molecular break junction conductance versus electrode displacement data. The method, based on principal component analysis, successfully sorts data sets based on the projection of the data onto the first or second principal component of the correlation matrix without the need to assert any specific hypothesis about the expected features within the data. This is an improvement on the current correlation matrix analysis approach because it sorts data automatically, making it more objective and less time consuming, and our method is applicable to a wide range of multivariate data sets. Here the method is demonstrated on two systems. First, it is demonstrated on mixtures of two molecules with identical anchor groups and similar lengths, but either a π (high conductance) or a σ (low conductance) bridge. The mixed data are automatically sorted into two groups containing one molecule or the other. Second, it is demonstrated on break junction data measured with the π bridged molecule alone. Again, the method distinguishes between two groups. These groups are tentatively assigned to different geometries of the molecule in the junction.

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed.

The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.

The use of mid-infrared spectrometry to estimate the ration composition of lactating dairy cows.

The composition of cow milk is strongly affected by the feeding regimen. Because milk components are routinely determined using mid-infrared (MIR) spectrometry, MIR spectra could also be used to estimate an animal's ration composition. The objective of this study was to determine whether and how well amounts of dry matter intake and the proportions of concentrates, hay, grass silage, maize silage, and pasture in the total ration can be estimated using MIR spectra at an individual animal level. A total of 10,200 milk samples and sets of feed intake data were collected from 90 dairy cows at 2 experimental farms of the Agricultural Research and Education Centre in Raumberg-Gumpenstein, Austria. For each run of analysis, the data set was split into a calibration and a validation data set in a 40:60 ratio. Estimated ration compositions were calculated using a partial least squares regression and then compared with the respective observed ration compositions. In separate analyses, the factors milk yield and concentrate intake were included as additional predictors. To evaluate accuracy, the coefficient of determination (R2) and ratio to performance deviation were used. The highest R2 values (for kg of dry matter intake/for % of ration) for the individual feedstuffs were as follows: pasture, 0.63/0.66; grass silage, 0.32/0.43; concentrate intake, 0.39/0.34; maize silage, 0.32/0.33; and hay, 0.15/0.16. Estimation of groups of feedstuffs (forages, energy-dense feedstuffs) mostly resulted in R2 values >0.50. Including the parameters milk yield or concentrate intake improved R2 values by up to 0.21, with an average improvement of 0.04. The results of this study indicate that not all ration components may be estimated equally accurately. Even if some estimates are good on average, there may be strong deviations between estimated and observed values in individual data sets, and therefore individual estimates should not be overemphasized. Further research including pooled samples (e.g., bulk milk, farm samples) or variations in ration composition is called for.

Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle.

Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied. A total of 474 bulls and 1,688 cows were genotyped with the Illumina BovineHD (HD; San Diego, CA) and BovineSNP50 (50K) chip, respectively. Genotypes of cows were imputed to HD using FImpute v2.2. After quality check of data, 496,606 markers remained. The HD markers present on the GeneSeek SGGP-20Ki (15,727; Lincoln, NE), 50K (22,152), and GeneSeek GGP-75Ki (65,018) were subset and used to assess the effect of lower SNP density on accuracy of prediction. Deregressed breeding values were used as pseudophenotypes for model training. Data were split into reference and validation to mimic a forward prediction scheme. The reference population consisted of animals whose birth year was ≤2004 and consisted of either only bulls (TR1) or a combination of bulls and dams (TR2), whereas the validation set consisted of younger bulls (born after 2004). Genomic BLUP was used to estimate genomic breeding values (GEBV) and reliability of GEBV (R2PEV) was based on the prediction error variance approach. Reliability of GEBV ranged from ∼0.46 (FY and PY) to 0.56 (MY) with TR1 and from 0.51 (PY) to 0.65 (MY) with TR2. When averaged across all traits, R2PEV were substantially higher (R2PEV of TR1 = 0.50 and TR2 = 0.57) compared with reliabilities of parent averages (0.35) computed from pedigree data and based on diagonals of the coefficient matrix (prediction error variance approach). Reliability was similar for all the 4 marker panels using either TR1 or TR2, except that imputed HD cow data set led to an inflation of reliability. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information. A reduced panel of ∼15K markers resulted in reliabilities similar to using HD markers. Reliability of GEBV could be increased by enlarging the limited bull reference population with cow information.

Heritability and factors associated with number of harness race starts in the Spanish Trotter horse population.

BACKGROUND: Longevity/durability is a relevant trait in racehorses. Genetic analysis and knowledge of factors that influence number of harness race starts would be advantageous for both horse welfare and the equine industry. OBJECTIVES: To perform a genetic analysis on harness racing using number of races as a measure of longevity/durability and to identify factors associated with career length in Spanish Trotter Horses (STH). STUDY DESIGN: Longitudinal study. METHODS: Performance data (n = 331,970) on the STH population for harness racing at national level between 1990 and 2014 were used. A grouped data model was fitted to assess factors influencing the risk of ending harness racing career and to estimate the heritability and breeding values for total number of harness races starts as an indicator of horses' longevity and durability. The model included sex, age at first race and first start earnings as time-independent effects, and the calendar year, driver, trainer, racetrack category and season of competition as time-dependent effects. RESULTS: Across the whole dataset, the average number of harness races horses achieved in Spain was 54.7 races, and this was associated with the horses' sex, age at first race and first start earnings, calendar year, driver, racetrack category, and season. The heritability estimated (0.17 ± 0.01) for number of harness race starts indicates that a beneficial response to direct genetic selection can be expected. MAIN LIMITATIONS: Data on horses' health status were not available. CONCLUSIONS: Horses' total number of harness race starts is a promising tool for genetic analysis and the evaluation of racing longevity and durability. The estimated heritability provides evidence to support the application of genetic selection of total career number of races to improve longevity/durability of STH.

Direct and maternal genetic effects on growth, reproduction, and ultrasound traits in zebu Brahman cattle in Colombia.

Covariance components and genetic parameters were estimated for birth weight (BiW); adjusted weights at 4, 7, 12, and 18 mo; and ADG between 0 and 4 mo, between 4 and 7 mo, between 7 and 12 mo, and between 12 and 18 mo. Additionally, reproductive traits, calving interval, and age at first calving were analyzed, together with traits measured by ultrasound: loin eye area, deep fat mean, back fat, and rump fat. Analyses were performed using an animal model, considering the fixed effects of the farm ( = 37), year and month of birth, sex, calving number (1 to 7), season (dry and rainy seasons), region (North Coast, Andean Region, and Oriental Savannas), and conception (natural mating or AI), whereas the age of the cows at calving was considered a polynomial covariate with linear and quadratic effects. Three different models were used to find the one with the best fit for each trait: a single-trait model with an additive direct genetic effect, a single-trait model with additive direct and maternal genetic effects, and finally, a multitrait model with an additive direct genetic effect. For the growth traits, the heritability was between 0.24 and 0.47, with the lowest value for weight at 7 mo and the greatest value for BiW, and the maternal heritability was found to be between 0.15 and 0.21 but did not decrease later on. The correlation between direct and maternal effects was high and negative (-0.59 to -0.76). With ultrasound traits, a model with only direct effects was used. The heritability was between 0.13 and 0.28 for back fat and loin eye area, respectively. The heritabilities for deep fat mean and rump fat were similar, being 0.19 and 0.21, respectively. The reproductive traits showed high residual variance. In particular, the heritability of calving interval was low (0.06). The results showed that the growth traits have an important genetic component, which is a favorable indicator for obtaining improvement progress in the zebu Brahman breed for beef production in tropical regions of Colombia. The maternal effects influenced the weight performance from 4 to 18 mo and should be taken into account in genetic analyses. In general, the direct heritability of medium magnitude estimated for growth and traits measured by ultrasound suggests that individual selection for these traits will be effective.

Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle.

Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (Fst ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.

The use of coancestry based on shared segments for maintaining genetic diversity.

We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP-by-SNP basis and with pedigree-based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree-based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes.

Altered mitochondrial response to activation of T-cells in neonate.

UNLABELLED: Mitochondrial functions have a major impact on T-cell functionality. In this study we characterized whether mitochondrial function in the neonatal T-cells differs from that in the adult T-cells during short T-cell activation. METHODS: We used flow cytometry methods to test mitochondrial mass and to monitor mitochondrial Ca²âº levels, mitochondrial potential and superoxide generation in parallel with cytoplasmic Ca²âº levels during phythohaemagglutinine-induced activation of CD4+ and CD8+ T-cells of 12 term neonates and 11 healthy adults. RESULTS: Baseline mitochondrial mass of CD4+ and CD8+ cells was lower in the neonate than in the adult. In comparison with the adult, neonatal resting CD4+ T-cells had lower cytoplasmic Ca²âº levels and this was associated with normal activation induced Ca²âº-response. During short-term activation cytoplasmic Ca²âº-response was lower in neonatal than in adult CD8+ T-cells. Mitochondrial Ca²âº uptake was increased in CD4+ neonatal T cells while it decreased in CD8+ T-cells. Mitochondrial depolarization was increased in CD4+ and decreased in CD8+ neonatal T-cells compared to adults. Superoxide generation was higher and equal in neonatal CD4+ and CD8+ cells, respectively, compared to the adult ones. CONCLUSION: Our data suggest that neonatal T-cells exhibit marked differences in mitochondrial function and superoxide generation compared to adult T-cells.

First trimester termination of pregnancy: methods in comparison between two European university hospitals.

PURPOSE OF INVESTIGATION: To compare methods, epidemiological features, and legislations of first trimester termination of pregnancy in two European Union University Hospital: Szeged, Hungary, (UHS) and Rome, Italy (UHR). MATERIALS AND METHODS: The study included 195 women in UHS and 197 women in UHR undergoing a termination of pregnancy, The method used in UHR was electric vacuum aspiration, while in UHS it is chosen according to the patients' features. RESULTS: Mean gestational week at the time of interruption was 8.21 ± 0.12 SD for UHS and 9.00 ± 0.08 SD for UHR (p = 0.000 1). Previous artificial termination of pregnancy was 0.40 ± 0.05 SD for UHR, and 0.77 ± 0.07 SD for UHS (p = 0.0001). Foreign women were 32.5% in UHR and 0.5% in UHS. Incidence of side effects was 1% for UHS and 0.5% for UHR. Parity was 2.54 ± 0.12 SD for UHR and 3.00 ± 0.14 SD for UHS (p = 0.01). CONCLUSIONS: The methods for interruption resulted safe and effective. Antibiotic prophylaxis, routinely provided in UHR, turned out to be effective to pre- vent post-operative infections. Cervical priming with Laminaria is safe, but patient's hospitalization is required. Different legislations may account for some epidemiological differences between the two hospitals.

GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach.

GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

Electrochemical control of a non-covalent binding between ferrocene and beta-cyclodextrin.

The forces required for the detachment of ferrocene (Fc) from ß-cyclodextrin (ßCD) in a single host (ßCD)-guest (Fc) complex were investigated using force spectroscopy under electrochemical conditions. The redox state of the guest Fc moiety as well as the structure of the supporting matrix was found to decisively affect the nanomechanical properties of the complex.

Evaluation of the length of competitive life in Hungarian sport horses.

The aim of this study was to analyse the duration of the competitive life of jumping horses in Hungary to assess the potential for genetic evaluation and to get information about the risk factors affecting jumping performance of sport horses. The data set included lifetime performance in jumping competitions for 8475 horses born from 1992 onwards with records between 1996 and 2011 (32.7% were right-censored). Longevity was measured as the number of years spent in the competition. Discrete time survival model included fixed effects of gender, age at first competition, and the time-dependent effect of competition level. All fixed effects were highly significant (p < 0.001). The highest risk of ending the race career was estimated for horses competing in the lowest level (category 1) events. The smallest risk was found in horses competing in the highest category. The culling risk for stallions was 15% higher, for geldings 20% lower when compared to mares. As the age at the first competition result increased, the risk ratio also increased. Risk ratios of horses starting as 8 years old or older were 56% higher than those of 5-year-old horses. The longest time in sport tracks belonged to horses starting their career as 4 years old. Their culling risk was 20% lower than those of 5-year-old horses. The heritability of the length of competitive life was 0.17. Breeding values were predicted for each animals, and 47 showed an accuracy greater than 0.60. The clear benefit of the analysis was shown by comparison of offspring to extreme stallion groups.

The Survival Kit: software to analyze survival data including possibly correlated random effects.

The Survival Kit is a Fortran 90 Software intended for survival analysis using proportional hazards models and their extension to frailty models with a single response time. The hazard function is described as the product of a baseline hazard function and a positive (exponential) function of possibly time-dependent fixed and random covariates. Stratified Cox, grouped data and Weibull models can be used. Random effects can be either log-gamma or normally distributed and can account for a pedigree structure. Variance parameters are estimated in a Bayesian context. It is possible to account for the correlated nature of two random effects either by specifying a known correlation coefficient or estimating it from the data. An R interface of the Survival Kit provides a user friendly way to run the software.

Genetic evaluation of ovulatory disorders in Austrian Fleckvieh cows: a comparison between linear models and survival analysis.

The objective of this study was to compare linear models and survival analysis for genetic evaluation of ovulatory disorders, which included veterinary treatments of silent heat/anestrus and cystic ovaries. Data of 23 450 daughters of 274 Austrian Fleckvieh sires were analyzed. For linear model analyses, ovulatory disorders were defined as a binary response (presence or absence) in the time periods from calving to 150 days after calving and from calving to 300 days after calving. For survival analysis, ovulatory disorders were defined either as the number of days from calving to the day of the first treatment for an ovulatory disorder (uncensored record) or from calving to the day of culling, or the last day of the period under investigation (until 150 or 300 days after calving; censored record). Estimates of heritability were very similar (0.016 to 0.020) across methods and periods. Correlations between sire estimated breeding value from linear model and survival analysis were 0.98, whereas correlations between different time periods were somewhat lower (0.95 and 0.96). The results showed that the length of time period had a larger effect on genetic evaluation than methodology.