Efficient large-scale single-step evaluations and indirect genomic prediction of genotyped selection candidates.

BACKGROUND: Single-step genomic best linear unbiased prediction (ssGBLUP) models allow the combination of genomic, pedigree, and phenotypic data into a single model, which is computationally challenging for large genotyped populations. In practice, genotypes of animals without their own phenotype and progeny, so-called genotyped selection candidates, can become available after genomic breeding values have been estimated by ssGBLUP. In some breeding programmes, genomic estimated breeding values (GEBV) for these animals should be known shortly after obtaining genotype information but recomputing GEBV using the full ssGBLUP takes too much time. In this study, first we compare two equivalent formulations of ssGBLUP models, i.e. one that is based on the Woodbury matrix identity applied to the inverse of the genomic relationship matrix, and one that is based on marker equations. Second, we present computationally-fast approaches to indirectly compute GEBV for genotyped selection candidates, without the need to do the full ssGBLUP evaluation. RESULTS: The indirect approaches use information from the latest ssGBLUP evaluation and rely on the decomposition of GEBV into its components. The two equivalent ssGBLUP models and indirect approaches were tested on a six-trait calving difficulty model using Irish dairy and beef cattle data that include 2.6 million genotyped animals of which about 500,000 were considered as genotyped selection candidates. When using the same computational approaches, the solving phase of the two equivalent ssGBLUP models showed similar requirements for memory and time per iteration. The computational differences between them were due to the preprocessing phase of the genomic information. Regarding the indirect approaches, compared to GEBV obtained from single-step evaluations including all genotypes, indirect GEBV had correlations higher than 0.99 for all traits while showing little dispersion and level bias. CONCLUSIONS: In conclusion, ssGBLUP predictions for the genotyped selection candidates were accurately approximated using the presented indirect approaches, which are more memory efficient and computationally fast, compared to solving a full ssGBLUP evaluation. Thus, indirect approaches can be used even on a weekly basis to estimate GEBV for newly genotyped animals, while the full single-step evaluation is done only a few times within a year.

Impact of age at first calving on performance traits in Irish beef herds.

Reducing age at first calving (AFC) has been a challenge in beef herds. There is anecdotal evidence that herd owners choose to calve heifers older because of the perceived consequences of calving heifers at 24 mo of age compared to 36 mo on performance traits in beef herds. The objective of this study was to estimate the association of calving heifers at younger ages on subsequent performance traits, calving interval, longevity, cow weight, dystocia, and progeny weaning weight for parities 1 to 5. Available to the study after data edits were 219,818 calving interval records, 219,818 longevity records, 118,504 cow live-weight records, 230,998 dystocia records, and 230,998 weaning weight records. Linear mixed models were used to quantify performance of each trait in AFC groups for each parity. As parity increased, there was a favorable reduction in calving interval and dystocia (P < 0.001), while the likelihood of cows surviving reduced (P < 0.001). Both cow live weight and progeny weaning weight increased as parity increased. Age at first calving only had a significant association with dystocia within parity 1 (P < 0.001), where older heifers at first calving subsequently had lower risk of calving. Calving interval for parity 1 cows was observed to be longer by 6 d in cows that calved for the first time at 33 to 36 mo compared to cows calved for the first time at 22 to 24 mo (P < 0.001). No statistical difference was observed for longevity between cows with an AFC of 22 to 24 mo compared to cows with an AFC of 33 to 36 mo (P > 0.05). Cows that calved at a younger age did wean lighter calves for their first three lactations (P < 0.01) but had no association with weaning weight for parity 4 and 5 cows (P > 0.05). Cows with a lower AFC were lighter for parity 1 to 4 (P < 0.001); at parity 5, AFC had no association with cow live weight (P > 0.05). The performance of mature cows for calving interval, longevity, calving difficulty, cow live weight, and weaning weight was not impacted by AFC. In conclusion, calving cows for the first time at younger ages do pose risks and associated performance loss but this risk and loss should be minimized by good management.

Reducing the age at first calving (AFC) in beef cows is known to be economically and environmentally beneficial for beef herds. The age of heifers at first calving is influenced by genetics and management. Additionally, beef herd owners choose to delay the breeding of young heifers because of the anecdotal perception that there is a higher risk of calving difficulty and potential negative consequences on lifetime performance of cows that calve at a younger age. This study aimed to estimate the potential risks and consequences of reducing AFC on beef herds which is known to economically beneficial. It was observed that cows that calved at younger ages were more likely to receive assistance at calving at their first calving. This negative consequence could be negated by good management and breeding decisions. In addition, younger calving cows weaned lighter calves for their first three lactations and had lighter cow live weights for their first four lactations. Overall, the impact of AFC was biologically small on key performance traits in beef herds. Results from this study should provide confidence to beef herd owners to calve cows for the first time at 24 mo of age.

International single-step SNPBLUP beef cattle evaluations for Limousin weaning weight.

BACKGROUND: Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation using data (or proxy of them) from different countries. Genomic selection is increasingly adopted in beef cattle, but, to date, the benefits of including genomic information in international evaluations have not been explored. Our objective was to develop an international beef cattle single-step genomic evaluation and investigate its impact on the accuracy and bias of genomic evaluations compared to current pedigree-based evaluations. METHODS: Weaning weight records were available for 331,593 animals from seven European countries. The pedigree included 519,740 animals. After imputation and quality control, 17,607 genotypes at a density of 57,899 single nucleotide polymorphisms (SNPs) from four countries were available. We implemented two international scenarios where countries were modelled as different correlated traits: an international genomic single-step SNP best linear unbiased prediction (SNPBLUP) evaluation (ssSNPBLUPINT) and an international pedigree-based BLUP evaluation (PBLUPINT). Two national scenarios were implemented for pedigree and genomic evaluations using only nationally submitted phenotypes and genotypes. Accuracies, level and dispersion bias of EBV of animals born from 2014 onwards, and increases in population accuracies were estimated using the linear regression method. RESULTS: On average across countries, 39 and 17% of sires and maternal-grand-sires with recorded (grand-)offspring across two countries were genotyped. ssSNPBLUPINT showed the highest accuracies of EBV and, compared to PBLUPINT, led to increases in population accuracy of 13.7% for direct EBV, and 25.8% for maternal EBV, on average across countries. Increases in population accuracies when moving from national scenarios to ssSNPBLUPINT were observed for all countries. Overall, ssSNPBLUPINT level and dispersion bias remained similar or slightly reduced compared to PBLUPINT and national scenarios. CONCLUSIONS: International single-step SNPBLUP evaluations are feasible and lead to higher population accuracies for both large and small countries compared to current international pedigree-based evaluations and national evaluations. These results are likely related to the larger multi-country reference population and the inclusion of phenotypes from relatives recorded in other countries via single-step international evaluations. The proposed international single-step approach can be applied to other traits and breeds.

Exploring the Opinions of Irish Beef Farmers Regarding Dairy Beef Integration.

Background: There has been very little previous research in Ireland on the opinions of farmers regarding dairy beef integration. The need for increased dairy beef integration has assumed a greater importance in Ireland in recent years due to a rapid expansion in dairy production, and associated increase in numbers of male dairy calves born on Irish farms. The objective of this study was to explore beef farmers' views on a broad range of issues related to dairy beef integration, using a survey methodology. The survey was distributed to approximately 4,250 beef farmers via email and 1,203 participated in the study. Results: The sample was composed almost entirely of beef farmers, although a very small proportion also had a dairy enterprise on their farm. Eighty percent of the farmers were concerned with the increase in the number of male dairy calves in recent years. Fifty seven percent of farmers responded that they were not willing to rear dairy bred calves for beef. Limousin, Aberdeen Angus and Hereford were the breeds farmers would be most willing to rear for beef. Good health, breed, and conformation were ranked as the main factors calf rearers consider when buying calves. Expectation of poor profit margin, expectation of poor-quality calves, and price volatility/market uncertainty were the top ranked factors dissuading farmers from rearing dairy calves for beef. The main themes arising from the qualitative question related to beef price/ability to make a profit, breed, and calf quality. Conclusions: While it is concerning that the majority of respondents expressed an unwillingness to rear dairy bred calves for beef, approximately a quarter of beef farmers indicated a willingness to rear beef-sired dairy calves for beef. In the qualitative responses, farmers described how their concerns about calf quality and their ability to make a profit from dairy bred calves would make it difficult for them to rear these calves for beef. Future strategy will have to consider how these challenges can be overcome and the issues of who bears the risks and costs associated with greater integration will have to be carefully considered.

Validation of a beef cattle maternal breeding objective based on a cross-sectional analysis of a large national cattle database.

Despite the importance of validating any technology prior to recommendation for use, few studies exist in the scientific literature which have demonstrated the superior performance of high-ranking animals in a given total merit index; this is especially true for maternal cattle selection indexes. The objective of the present study was to demonstrate the impact of the Irish total merit maternal-based index and provide the benefits of using the Irish total merit maternal-based beef index as part of a breeding policy. The validation exercise was undertaken using 269,407 records (which included the cow's own records and her progeny records) from 92,300 females differing in a total merit index for maternal value; a comparison was also made with the Irish terminal index. Association analyses were undertaken within the framework of linear and threshold mixed models; the traits analyzed were fertility (e.g., calving interval), slaughter (e.g., harvest weight), live weight (e.g., weaning weight), and producer-recorded traits (e.g., docility). All traits were analyzed with the maternal index and terminal index fitted as covariate(s) separately. Depending on the independent variable analyzed, the other fixed effects included: parity of cow, heterosis and recombination loss of cow and/or progeny, gender of progeny, and the estimated breeding value of the sire; contemporary group was included as a random effect. The results demonstrate the effectiveness of using total merit indexes to improve performance in a whole range of different traits, despite the often antagonistic genetic correlations among traits that underpin the index. Cows excelling on the maternal index had less calving difficulty, superior fertility performance, lighter carcasses, and live weight, as well as being more easily managed. Additionally, progeny of higher maternal index cows were lighter at birth and more docile albeit with a small impact on slaughter traits. In contrast, higher terminal index cows had more calving difficulty, compromised fertility and had heavier carcasses themselves as well as their progeny. While the differences in phenotypic performance between groups on maternal index was, in most instances, relatively small, the benefits are: (1) expected to be greater when more genetically extreme groups of animals are evaluated and (2) expected to accumulate over time given the cumulative and permanent properties of breeding schemes.

Prediction of Warner-Bratzler shear force, intramuscular fat, drip-loss and cook-loss in beef via Raman spectroscopy and chemometrics.

Rapid prediction of beef quality remains a challenge for meat processors. This study evaluated the potential of Raman spectroscopy followed by chemometrics for prediction of Warner-Bratzler shear force (WBSF), intramuscular fat (IMF), ultimate pH, drip-loss and cook-loss. PLS regression models were developed based on spectra recorded on frozen-thawed day 2 longissimus thoracis et lumborum muscle and validated using test sets randomly selected 3 times. With the exception of ultimate pH, models presented notable performance in calibration (R2 ranging from 0.5 to 0.9; low RMSEC) and, despite variability in the results, promising predictive ability: WBSF (RMSEP ranging from 4.6 to 9 N), IMF (RMSEP ranging from 0.9 to 1.1%), drip-loss (RMSEP ranging from 1 to 1.3%) and cook-loss (RMSEP ranging from 1.5 to 2.9%). Furthermore, the loading values indicated that the physicochemical variation of the meat influenced the models. Overall, results indicated that Raman spectroscopy is a promising technique for routine quality assessments of IMF and drip-loss, which, with further development and improvement of its accuracy could become a reliable tool for the beef industry.

Investigating the use of visible and near infrared spectroscopy to predict sensory and texture attributes of beef M. longissimus thoracis et lumborum.

The aim of this study was to calibrate chemometric models to predict beef M. longissimus thoracis et lumborum (LTL) sensory and textural values using visible-near infrared (VISNIR) spectroscopy. Spectra were collected on the cut surface of LTL steaks both on-line and off-line. Cooked LTL steaks were analysed by a trained beef sensory panel as well as undergoing WBSF analysis. The best coefficients of determination of cross validation (R2CV) in the current study were for textural traits (WBSF = 0.22; stringiness = 0.22; crumbly texture = 0.41: all 3 models calibrated using 48 h post-mortem spectra), and some sensory flavour traits (fatty mouthfeel = 0.23; fatty after-effect = 0.28: both calibrated using 49 h post-mortem spectra). The results of this experiment indicate that VISNIR spectroscopy has potential to predict a range of sensory traits (particularly textural traits) with an acceptable level of accuracy at specific post-mortem times.

Online Prediction of Physico-Chemical Quality Attributes of Beef Using Visible-Near-Infrared Spectroscopy and Chemometrics.

The potential of visible-near-infrared (Vis-NIR) spectroscopy to predict physico-chemical quality traits in 368 samples of bovine musculus longissimus thoracis et lumborum (LTL) was evaluated. A fibre-optic probe was applied on the exposed surface of the bovine carcass for the collection of spectra, including the neck and rump (1 h and 2 h post-mortem and after quartering, i.e., 24 h and 25 h post-mortem) and the boned-out LTL muscle (48 h and 49 h post-mortem). In parallel, reference analysis for physico-chemical parameters of beef quality including ultimate pH, colour (L, a*, b*), cook loss and drip loss was conducted using standard laboratory methods. Partial least-squares (PLS) regression models were used to correlate the spectral information with reference quality parameters of beef muscle. Different mathematical pre-treatments and their combinations were applied to improve the model accuracy, which was evaluated on the basis of the coefficient of determination of calibration (R2C) and cross-validation (R2CV) and root-mean-square error of calibration (RMSEC) and cross-validation (RMSECV). Reliable cross-validation models were achieved for ultimate pH (R2CV: 0.91 (quartering, 24 h) and R2CV: 0.96 (LTL muscle, 48 h)) and drip loss (R2CV: 0.82 (quartering, 24 h) and R2CV: 0.99 (LTL muscle, 48 h)) with lower RMSECV values. The results show the potential of Vis-NIR spectroscopy for online prediction of certain quality parameters of beef over different time periods.

Genetic benefits of genomic selection breeding programmes considering foreign sire contributions.

BACKGROUND: In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme's wider dairy population. These features of a breeding programme contribute in different ways to the rate of genetic gain for the wider industry. METHODS: A deterministic recursive gene flow model across subpopulations of animals in a dairy industry was created to predict the commercial performance of replacement heifers and future artificial insemination bulls. Various breeding strategies were assessed by varying the reliability of breeding values, the genetic contributions from subpopulations, and the genetic trend and merit of the foreign subpopulation. RESULTS: A higher response in the true breeding goal measured in standard deviations (SD) of true merit (G) after 20 years of selection can be achieved when genetic contributions shift towards higher merit alternatives compared to keeping them fixed. A foreign annual genetic trend of 0.08 SD of the breeding goal, while the domestic genetic trend is 0.10 SD, results in the overall net present value of genetic gain increasing by 1.2, 2.3, and 3.4% after 20 years as the reliability of GS in the domestic population increased from 0.3 to 0.45, 0.60 and 0.75. With a foreign genetic trend of 0.10 SD, these increases are more modest; 0.9, 1.7, and 2.4%. Increasing the foreign genetic trend so that it is higher than the domestic trend erodes the benefits of increasing the reliability of domestic GS further. CONCLUSIONS: Having a foreign source of genetic material with a high rate of genetic progress contributes substantially to the benefits of domestic genetic progress while at the same time reducing the expected returns from investments to improve the accuracy of genomic prediction in the home country.

Effect of Breed and Gender on Meat Quality of M. longissimus thoracis et lumborum Muscle from Crossbred Beef Bulls and Steers.

The objective of this study was to determine whether sire breed and/or castration had an effect on meat quality of M. longissimus thoracis et lumborum (LTL) muscle from crossbred bulls and steers and to investigate the relationship amongst the traits examined. Warner-Bratzler shear force (WBSF), intramuscular fat (IMF)%, cook-loss%, drip-loss%, colour (L*, a*, b*) and ultimate pH (upH) were determined in the LTL muscle from eight beef sire breeds representative of the Irish herd (Aberdeen Angus, Belgian Blue, Charolais, Hereford, Limousin, Parthenaise, Salers and Simmental). The results indicate that IMF%, cook-loss% and drip-loss% were associated with breed (p < 0.05); while WBSF, IMF% and cook-loss% differ between genders (p < 0.05). Steer LTL had a greater IMF% and exhibited reduced WBSF and cook-loss% in comparison to the bull LTL (p < 0.05). This study provides greater insight into how quality traits in beef are influenced by breed and gender and will support the industry to produce beef with consistent eating quality.

Predicted carcass meat yield and primal cut yields in cattle divergent in genetic merit for a terminal index.

Several studies have clearly demonstrated the favorable impact of genetic selection on increasing beef cattle performance within the farm gate. Few studies, however, have attempted to quantify the value of genetic selection to downstream sectors of the beef industry, such as the meat processing sector. The objective of the current study was to characterize detailed carcass attributes of animals divergent in genetic merit for a terminal index as well as individual measures of genetic merit for carcass weight, conformation, and fat. The data used consisted of 53,674 young bulls and steers slaughtered between the years 2010 and 2013 in multiple Irish processing plants. All animals had a genetic evaluation as well as phenotypic measures of carcass characteristics. A terminal index, based on pedigree index for calving performance, feed intake, and carcass traits, calculated from the Irish national genetic evaluations, was obtained for each animal. Animals were categorized into four terminal index groups based on genetic merit estimates derived prior to the expression of the carcass phenotype by the animal. The association between genetic merit for terminal index with predicted phenotypic carcass red meat yield, carcass fat, carcass bone, and carcass composition, as well as between genetic merit for carcass weight, conformation, and fat with predicted phenotypic carcass red meat yield and composition were all quantified using linear mixed models. A greater terminal index value was associated with, on average, heavier phenotypic weights of each wholesale cut category. A greater terminal index value was also associated with a greater weight of meat and bone, but reduced carcass fat. Relative to animals in the lowest 25% genetic merit group, animals in the highest 25% genetic merit group had, on average, a greater predicted yield of very high value cuts (4.52 kg), high value cuts (13.13 kg), medium value cuts (6.06 kg), low value cuts (13.25 kg) as well as more total meat yield (37 kg). The results from the present study clearly signify a benefit to meat processers from breeding programs for terminal characteristics; coupled with the previously documented benefits to the producer, the benefits of breeding programs across the entire food production chain are obvious.

Factors associated with the weight of individual primal cuts and their inter-relationship in cattle.

Input parameters for decision support tools are comprised of, amongst others, knowledge of the associated factors and the extent of those associations with the animal-level feature of interest. The objective of the present study was to quantify the association between animal-level factors with primal cut yields in cattle and to understand the extent of the variability in primal cut yields independent carcass weight. The data used consisted of the weight of 14 primal carcass cuts (as well as carcass weight, conformation, and fat score) on up to 54,250 young cattle slaughtered between the years 2013 and 2017. Linear mixed models, with contemporary group of herd-sex-season of slaughter as a random effect, were used to quantify the associations between a range of model fixed effects with each primal cut separately. Fixed effects in the model were dam parity, heterosis coefficient, recombination loss, a covariate per breed representing the proportion of Angus, Belgian Blue, Charolais, Jersey, Hereford, Limousin, Simmental, and Holstein-Friesian and a three-way interaction between whether the animal was born in a dairy or beef herd, sex, and age at slaughter, with or without carcass weight as a covariate in the mixed model. The raw correlations among all cuts were all positive varying from 0.33 (between the bavette and the striploin) to 0.93 (between the topside and knuckle). The partial correlation among cuts, following adjustment for differences in carcass weight, varied from -0.36 to 0.74. Age at slaughter, sex, dam parity, and breed were all associated (P < 0.05) with the primal cut weight. Knowledge of the relationship between the individual primal cuts, and the solutions from the models developed in the study, could prove useful inputs for decision support systems to increase performance.

A dual targeted ß-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility.

Bovine fertility remains a critical issue underpinning the sustainability of the agricultural sector. Phenotypic records collected on >7,000 bulls used in artificial insemination (AI) were used to identify 160 reliable and divergently fertile bulls for a dual strategy of targeted sequencing (TS) of fertility-related ß-defensin genes and whole exome sequencing (WES). A haplotype spanning multiple ß-defensin genes and containing 94 SNPs was significantly associated with fertility and functional analysis confirmed that sperm from bulls possessing the haplotype showed significantly enhanced binding to oviductal epithelium. WES of all exons in the genome in 24 bulls of high and low fertility identified 484 additional SNPs significantly associated with fertility. After validation, the most significantly associated SNP was located in the FOXJ3 gene, a transcription factor which regulates sperm function in mice. This study represents the first comprehensive characterisation of genetic variation in bovine ß-defensin genes and functional analysis supports a role for ß-defensins in regulating bull sperm function. This first application of WES in AI bulls with divergent fertility phenotypes has identified a novel role for the transcription factor FOXJ3 in the regulation of bull fertility. Validated genetic variants associated with bull fertility could prove useful for improving reproductive outcomes in cattle.

In vitro characterisation of fresh and frozen sex-sorted bull spermatozoa.

This study sought to compare the in vitro characteristics of fresh and frozen non-sorted (NS) and sex-sorted (SS) bull spermatozoa. Experiment 1: Holstein-Friesian ejaculates (n=10 bulls) were split across four treatments and processed: (1) NS fresh at 3×106 spermatozoa, (2) X-SS frozen at 2×106 spermatozoa, (3) X-SS fresh at 2×106 spermatozoa and (4) X-SS fresh at 1×106 spermatozoa. NS frozen controls of 20×106 spermatozoa per straw were sourced from previously frozen ejaculates (n=3 bulls). Experiment 2: Aberdeen Angus ejaculates (n=4 bulls) were split across four treatments and processed as: (1) NS fresh 3×106 spermatozoa, (2) Y-SS fresh at 1×106 spermatozoa, (3) Y-SS fresh at 2×106 spermatozoa and (4) X-SS fresh at 2×106 spermatozoa. Controls were sourced as per Experiment 1. In vitro assessments for progressive linear motility, acrosomal status and oxidative stress were carried out on Days 1, 2 and 3 after sorting (Day 0=day of sorting. In both experiments SS fresh treatments had higher levels of agglutination in comparison to the NS fresh (P<0.001), NS frozen treatments had the greatest PLM (P<0.05) and NS spermatozoa exhibited higher levels of superoxide anion production compared with SS spermatozoa (P<0.05). Experiment 1 found both fresh and frozen SS treatments had higher levels of viable acrosome-intact spermatozoa compared with the NS frozen treatments (P<0.01).

The impact of storage temperature and sperm number on the fertility of liquid-stored bull semen.

In Ireland, liquid bull semen is stored at unregulated ambient temperatures, typically at 5×106 spermatozoa per dose, and inseminated within 2.5 days of collection. In Experiment 1, the effect of storage temperature (5, 15, 22, 32°C and fluctuations (Flux) between these temperatures) on progressive motility, viability, acrosomal status, DNA fragmentation and osmotic resistance was assessed. In Experiment 2, the field fertility of liquid semen at 5, 4 and 3×106 spermatozoa per dose, up to Day 2 after collection, was assessed in comparison to frozen-thawed semen at 20×106 spermatozoa per dose (n=35328 inseminations). In Experiment 1, storage at 15°C resulted in the highest progressive motility (PP6 spermatozoa per dose on Day 2 of storage was reduced in comparison to frozen-thawed semen (P<0.01). In conclusion, liquid semen is versatile between storage temperatures of 5 and 22°C, but demonstrates reduced fertility on Day 2 of storage at lower sperm numbers in comparison to frozen-thawed semen.

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.

Evidence for genetic variance in resistance to tuberculosis in Great Britain and Irish Holstein-Friesian populations.

BACKGROUND: Here, we jointly summarise scientific evidence for genetic variation in resistance to infection with Mycobacterium bovis, the primary agent of bovine tuberculosis (TB), provided by two recent and separate studies of Holstein-Friesian dairy cow populations in Great Britain (GB) and Ireland. METHODS: The studies quantified genetic variation within archived data from field and abattoir surveillance control programmes within each country. These data included results from the single intradermal comparative tuberculin test (SICTT), abattoir inspection for TB lesions and laboratory confirmation of disease status. Threshold animal models were used to estimate variance components for responsiveness to the SICTT and abattoir confirmed M. bovis infection. The link functions between the observed 0/1 scale and the liability scale were the complementary log-log in the GB, and logit link function in the Irish population. RESULTS AND DISCUSSION: The estimated heritability of susceptibility to TB, as judged by responsiveness to the SICTT, was 0.16 (0.012) and 0.14 (0.025) in the GB and Irish populations, respectively. For abattoir or laboratory confirmation of infection, estimates were 0.18 (0.044) and 0.18 (0.041) from the GB and the Irish populations, respectively. CONCLUSIONS: Estimates were all significantly different from zero and indicate that exploitable variation exists among GB and Irish Holstein Friesian dairy cows for resistance to TB. Epidemiological analysis suggests that factors such as variation in exposure or imperfect sensitivity and specificity would have resulted in underestimation of the true values.

Setting priorities for non-regulatory animal health in Ireland: results from an expert Policy Delphi study and a farmer priority identification survey.

Agriculture is a very important contributor to the Irish economy. In Ireland, national animal health services have been a government, rather than an industry, responsibility. In 2009, Animal Health Ireland (AHI) was established to provide a partnership approach to national leadership of non-regulatory animal health issues (those not subject to national and/or EU regulation). The objectives of this study were to elicit opinion from experts and farmers about non-regulatory animal health issues facing Irish livestock industries, including prioritisation of animal health issues and identification of opportunities to maximise the effective use of AHI resources. The study was conducted with experts using Policy Delphi methodology over three rounds, and with farmers using a priority identification survey. Non-regulatory bovine diseases/conditions were prioritised by both experts and farmers based on impact and international competitiveness. For each high-priority disease/condition, experts were asked to provide an assessment based on cost, impact, international perception, impediment to international market access and current resource usage effectiveness. Further information was also sought from experts about resource allocation preferences, methods to improve education and coordination, and innovative measures to improve prevention and management. There was close agreement between responses from experts and dairy farmers: each gave highest priority to 3 diseases with a biosecurity risk (subsequently termed 'biosecure diseases') (bovine viral diarrhoea [BVD], infectious bovine rhinotracheitis [IBR], paratuberculosis) and 4 diseases/conditions generally without a biosecurity risk ('non-biosecure diseases/conditions') (fertility, udder health/milk quality, lameness, calf health). Beef farmers also prioritised parasitic conditions and weanling pneumonia. The adverse impact of biosecure diseases is currently considered relatively minor by experts, but would increase substantially in time. There are already substantial costs to farms and agribusiness from non-biosecure diseases/conditions. Experts preferred an equal allocation of resources between these biosecure and non-biosecure diseases/conditions, with emphasis on adopting/adapting international models, education and awareness-raising. The results from this study provide robust insights about non-regulatory animal health priorities in Ireland, as perceived by experts and farmers, using methodologies that are both transparent and inclusive. They have already been extremely influential in shaping national policy, as a foundation for interdisciplinary (and multi-agency) cooperation, as a contribution to efforts to encourage stakeholder responsibility-taking, and to ongoing development of postgraduate and undergraduate veterinary education in Ireland.