Genome-wide association study of economically important traits in Charolais and Limousin beef cows.

Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.

A mating advice system in dairy cattle incorporating genomic information.

This study investigated the effects of alternative mating programs that incorporate genomic information on expected progeny herd performance and inbreeding, as well as methods to include un-genotyped animals in such mating programs. A total of 54,535 Holstein-Friesian cattle with imputed high-density genotypes (547,650 SNP after edits) were available. First, to quantify the accuracy of imputing un-genotyped animals (often an issue in populations), a sub-population of 729 genotyped animals had their genotypes masked, and their allele dosages were imputed, using linear regression exploiting information on genotyped relatives. The reference population for imputation included all genotyped animals, excluding the 729 selected animals and their sires, dams, and grandsires, and had either (1) their sires' genotypes, (2) their dams' genotypes (3) both their sires' and their dams' genotypes, or (4) both their sires' and maternal grandsires' genotypes introduced into the reference population. The correlations between true genotypes and the imputed allele dosages ranged from 0.58 (sire only) to 0.68 (both sire and dam). A herd of 100 cows was then simulated (1,000 replicates) from the sub-population of 729 imputed animals. The top 10 bulls from the genotyped population, based on their total genetic merit index (TMI) were selected to be used as sires. Three mating allotment methods were investigated: (1) random mating, (2) sequential mating based on maximizing only the expected TMI of the progeny, and (3) linear programming to maximize a generated index constructed to maximize genetic merit and minimize expected progeny inbreeding as well as intra- and inter-progeny variability in genetic merit. Relationships among candidate parents were calculated using either the pedigree relationship matrix or the genomic relationship matrix; the latter was constructed using either the true genotypes of both parents or the true genotypes of the sire plus the imputed allele dosages of the dam. Using the genomic co-ancestry estimates resulted in lower average herd expected genomic inbreeding levels compared with using the pedigree-based co-ancestry estimates. Additionally, if the dams were not genotyped, using their imputed allele dosages also resulted in lower average herd expected inbreeding levels compared with using the pedigree co-ancestry estimates. The inter-progeny coefficient of variation for selected traits, milk and fertility, estimated breeding values were reduced by 12 to 65% using the linear programing method compared with sequential mating.

Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans.

Infection of cattle with bovine paratuberculosis (i.e., Johne's disease) is caused by Mycobacterium avium ssp. paratuberculosis (MAP) and results in a chronic incurable gastroenteritis. This disease, which has economic ramifications for the cattle industry, is increasing in detected prevalence globally; subclinically infected animals can silently shed the bacterium into the environment for years, exposing contemporaries and hampering disease-control programs. The objective of the present study was to first quantify the genetic parameters for humoral response to MAP in dairy cattle. This was followed by a genome-based association analysis and subsequent downstream bioinformatic analyses from imputed whole genome sequence SNP data. After edits, ELISA test records were available on 136,767 cows; analyses were also undertaken on a subset of 33,818 of these animals from herds with at least 5 MAP ELISA-positive cows, with at least 1 of those positive cows being homebred. Variance components were estimated using univariate animal and sire linear mixed models. The heritability calculated from the animal model for humoral response to MAP using alternative phenotype definitions varied from 0.02 (standard error = 0.003) to 0.05 (standard error = 0.008). The genome-based associations were undertaken within a mixed model framework using weighted deregressed estimated breeding values as a dependent variable on 1,883 phenotyped animals that were ≥87.5% Holstein-Friesian. Putative susceptibility quantitative trait loci (QTL) were identified on Bos taurus autosome 1, 3, 5, 6, 8, 9, 10, 11, 13, 14, 18, 21, 23, 25, 26, 27, and 29; mapping the most significant SNP to genes within and overlapping these QTL revealed that the most significant associations were with the 10 functional candidate genes KALRN, ZBTB20, LPP, SLA2, FI3A1, LRCH3, DNAJC6, ZDHHC14, SNX1, and HAS2. Pathway analysis failed to reveal significantly enriched biological pathways, when both bovine-specific pathway data and human ortholog data were taken into account. The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility. Furthermore, the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation. The novel molecular similarities identified between bovine paratuberculosis and human inflammatory bowel disease suggest potential for human therapeutic interventions to be translated to veterinary medicine and vice versa.

Genetic relationships between detailed reproductive traits and performance traits in Holstein-Friesian dairy cattle.

The objective of the study was to estimate the genetic relationships between detailed reproductive traits derived from ultrasound examination of the reproductive tract and a range of performance traits in Holstein-Friesian dairy cows. The performance traits investigated included calving performance, milk production, somatic cell score (i.e., logarithm transformation of somatic cell count), carcass traits, and body-related linear type traits. Detailed reproductive traits included (1) resumed cyclicity at the time of examination, (2) multiple ovulations, (3) early ovulation, (4) heat detection, (5) ovarian cystic structures, (6) embryo loss, and (7) uterine score, measured on a 1 (little or no fluid with normal tone) to 4 (large quantity of fluid with a flaccid tone) scale, based on the tone of the uterine wall and the quantity of fluid present in the uterus. (Co)variance components were estimated using a repeatability animal linear mixed model. Genetic merit for greater milk, fat, and protein yield was associated with a reduced ability to resume cyclicity postpartum (genetic correlations ranged from -0.25 to -0.15). Higher genetic merit for milk yield was also associated with a greater genetic susceptibility to multiple ovulations. Genetic predisposition to elevated somatic cell score was associated with a decreased likelihood of cyclicity postpartum (genetic correlation of -0.32) and a greater risk of both multiple ovulations (genetic correlation of 0.25) and embryo loss (genetic correlation of 0.32). Greater body condition score was genetically associated with an increased likelihood of resumption of cyclicity postpartum (genetic correlation of 0.52). Genetically heavier, fatter carcasses with better conformation were also associated with an increased likelihood of resumed cyclicity by the time of examination (genetic correlations ranged from 0.24 to 0.41). Genetically heavier carcasses were associated with an inferior uterine score as well as a greater predisposition to embryo loss. Despite the overall antagonistic relationship between reproductive performance and both milk and carcass traits, not all detailed aspects of reproduction performance exhibited an antagonistic relationship.

Genetic parameters of ovarian and uterine reproductive traits in dairy cows.

The objective of the study was to estimate genetic parameters of detailed reproductive traits derived from ultrasound examination of the reproductive tract as well as their genetic correlations with traditional reproductive traits. A total of 226,141 calving and insemination records as well as 74,134 ultrasound records from Irish dairy cows were used. Traditional reproductive traits included postpartum interval to first service, conception, and next calving, as well as the interval from first to last service; number of inseminations, pregnancy rate to first service, pregnant within 42 d of the herd breeding season, and submission in the first 21 d of the herd breeding season were also available. Detailed reproductive traits included resumed cyclicity at the time of ultrasound examination, incidence of multiple ovulations, incidence of early postpartum ovulation, heat detection, ovarian cystic structures, embryo loss, and uterine score; the latter was a subjectively assessed on a scale of 1 (little fluid with normal uterine tone) to 4 (large quantity of fluid with a flaccid uterine tone). Variance (and covariance) components were estimated using repeatability animal linear mixed models. Heritability for all reproductive traits were generally low (0.001-0.05), with the exception of traits related to cyclicity postpartum, regardless if defined traditionally (0.07; calving to first service) or from ultrasound examination [resumed cyclicity at the time of examination (0.07) or early postpartum ovulation (0.10)]. The genetic correlations among the detailed reproductive traits were generally favorable. The exception was the genetic correlation (0.29) between resumed cyclicity and uterine score; superior genetic merit for cyclicity postpartum was associated with inferior uterine score. Superior genetic merit for most traditional reproductive traits was associated with superior genetic merit for resumed cyclicity (genetic correlations ranged from -0.59 to -0.36 and from 0.56 to 0.70) and uterine score (genetic correlations ranged from -0.47 to 0.32 and from 0.25 to 0.52). Genetic predisposition to an increased incidence of embryo loss was associated with both an inferior uterine score (0.24) and inferior genetic merit for traditional reproductive traits (genetic correlations ranged from -0.52 to -0.42 and from 0.33 to 0.80). The results from the present study indicate that selection based on traditional reproductive traits, such as calving interval or days open, resulted in improved genetic merit of all the detailed reproductive traits evaluated in this study. Additionally, greater accuracy of selection for calving interval is expected for a relatively small progeny group size when detailed reproductive traits are included in a multitrait genetic evaluation.

Ovarian structures and uterine environment are associated with phenotypic and genetic merit for performance in lactating dairy cows.

The objective of this study was to estimate the association between detailed reproductive phenotypes for cows categorized as divergent for phenotypic and genetic performance. The hypothesis was that higher yielding animals, either phenotypically or genetically, would have compromised ovarian and uterine reproductive performance. Detailed reproductive traits including multiple ovulations, cystic ovarian structures, corpus luteum (CL) presence, and uterine environment were available on 9675 ultrasound records from 8174 dairy lactating cows, calved between 10 and 70 days. Cows were categorized, within parity, into low, average, or high for each of the performance traits. There was a greater likelihood of multiple ovulations in cows with greater phenotypic yields (odds ratio: 1.53-1.81) and greater genetic merit for yield (odds ratio: 1.31-1.59) relative to lower performing contemporaries. After adjustment for genetic merit, a similar trend of increased odds (odds ratio: 1.29-1.87) of multiple ovulations in higher yielding cows was observed compared with the lowest yielding category. There was no association between either phenotypic milk composition or genetic merit for milk composition with the likelihood of multiple ovulations. The likelihood of cystic ovarian structures was highest in cows with greatest phenotypic milk yields (odds ratio: 2.75-3.24), greater genetic merit for milk yield (odds ratio: 1.30-1.51), and even after adjustment for genetic merit there was a greater likelihood of cystic ovarian structures in cows with the highest milk yields (odds ratio: 2.71-2.95), compared with cows in the lowest category for each of the milk traits. Cows with average phenotypic milk yields were more likely to have a CL, compared with the lowest yielding category (odds ratio: 1.20-1.23), and these associations remained after adjustment for genetic merit of the trait. The likelihood of CL presence was highest in cows with the lowest genetic merit for milk. Lower fat:protein ratio was associated with an increased likelihood of CL presence compared with cows with greater fat:protein ratio and cows with the highest phenotypic milk composition were more likely to have a CL compared with cows in the lowest composition category. Genetic predisposition to higher somatic cell score was associated with a reduced risk of multiple ovulations (odds ratio: 0.69; 95% CI: 0.55-0.87) but an increased likelihood of CL presence (odds ratio: 2.66; 95% CI: 2.09-3.37) and poorer uterine health score (odds ratio: 1.36; 95% CI: 1.20-1.55). There was a lower likelihood of multiple ovulations, cystic ovarian structures, and poorer uterine health and an increased likelihood of CL presence in cows with superior genetic merit for reproductive performance and survival.

Risk factors associated with detailed reproductive phenotypes in dairy and beef cows.

The objective of this study was to identify detailed fertility traits in dairy and beef cattle from transrectal ultrasonography records and quantify the associated risk factors. Data were available on 148 947 ultrasound observations of the reproductive tract from 75 949 cows in 843 Irish dairy and beef herds between March 2008 and October 2012. Traits generated included (1) cycling at time of examination, (2) cystic structures, (3) early ovulation, (4) embryo death and (5) uterine score; the latter was measured on a scale of 1 (good) to 4 (poor) characterising the tone of the uterine wall and fluid present in the uterus. After editing, 72,773 records from 44,415 dairy and beef cows in 643 herds remained. Factors associated with the logit of the probability of a positive outcome for each of the binary fertility traits were determined using generalised estimating equations; linear mixed model analysis was used for the analysis of uterine score. The prevalence of cycling, cystic structures, early ovulation and embryo death was 84.75%, 3.87%, 7.47% and 3.84%, respectively. The occurrence of the uterine heath score of 1, 2, 3 and 4 was 70.63%, 19.75%, 8.36% and 1.26%, respectively. Cows in beef herds had a 0.51 odds (95% CI=0.41 to 0.63, P<0.001) of cycling at the time of examination compared with cows in dairy herds; stage of lactation at the time of examination was the same in both herd types. Furthermore, cows in dairy herds had an inferior uterine score (indicating poorer tone and a greater quantity of uterine fluid present) compared with cows in beef herds. The likelihood of cycling at the time of examination increased with parity and stage of lactation, but was reduced in cows that had experienced dystocia in the previous calving. The presence of cystic structures on the ovaries increased with parity and stage of lactation. The likelihood of embryo/foetal death increased with parity and stage of lactation. Dystocia was not associated with the presence of cystic structures or embryo death. Uterine score improved with parity and stage of lactation, while cows that experienced dystocia in the previous calving had an inferior uterine score. Heterosis was the only factor associated with increased likelihood of early ovulation. The fertility traits identified, and the associated risk factors, provide useful information on the reproductive status of dairy and beef cows.

Risk factors associated with multiple ovulation and twin birth rate in Irish dairy and beef cattle.

The objective of this study was to quantify the phenotypic and genetic risk factors associated with multiple ovulations and twin births in cattle. Prevalence and cow- and herd-level risk factors associated with ovulation rate were determined using 40,617 ultrasonographic records of the reproductive tract from 27,907 dairy and beef cows from 738 commercial herds. Prevalence of twin births was estimated from the Irish national database containing 23,658,351 calving events from 8,546,695 cows from 125,251 dairy and beef herds; factors associated with twin births were determined using a random subsample of 505,200 calving events from 280,638 cows in 81,329 herds. The mean prevalence of multiple ovulations was 6.83% while the prevalence of twin births was 1.74%. Occurrence of both multiple ovulations and twin births was associated with the month of scan (P < 0.0001) and month of calving (P < 0.0001), respectively, and peaked in November for multiple ovulations and October for twin births. The likelihood of multiple ovulations increased with interval postpartum and peaked between 45 to 185 d postcalving, after which the likelihood declined. The likelihood of both multiple ovulations (P < 0.0001) and twin births (P < 0.0001) increased with increasing cow parity. A greater proportion of Holstein, Friesian, Simmental, Hereford, and Charolais breed fractions were associated with a greater likelihood of multiple ovulations. There was no difference between breed proportion of the cow and incidence of twin births, where all breed proportions examined, litter difference existed among breeds in their association with risk of twin births. Although multiple ovulations were lowly heritable (0.028 ± 0.003), their occurrence was repeatable (0.326 ± 0.342) while twin birth rate in cattle was lowly heritable (0.017 ± 0.004) and repeatable (0.018 ± 0.011). The genetic SD of the presence of multiple ovulations and twin births was 0.04 and 0.02, respectively, indicating considerable genetic variation, especially for multiple ovulations. A moderate genetic correlation (0.66 ± 0.16) existed between multiple ovulations and twin births.

Revision arthroplasty in the haemophiliac patient.

Arthroplasty in the haemophiliac patient is associated with higher rates of infection and is traditionally performed in a younger age group. Despite this there is little evidence in the literature regarding revision arthroplasty in this cohort of patients. We describe the case of a periprosthetic fracture in a haemophiliac patient requiring revision arthroplasty, who did not consent to receiving blood products due to religious beliefs, with a successful outcome.

Assessment of the antioxidant potential of natural food and plant extracts in fresh and previously frozen pork patties.

Antioxidant activities of aloe vera, fenugreek, ginseng, mustard, rosemary, sage, soya protein, tea catechins and whey protein concentrate (35% protein) were evaluated in pork patties prepared from both fresh and previously frozen (-20°C) pork. Chemical analysis showed test ingredients to be more effective in reducing lipid oxidation in patties made from previously frozen pork. Tea catechins, rosemary and sage were identified as being the most effective antioxidants with potency decreasing in the following order: tea catechins>rosemary>sage. Optimum addition rates of these ingredients suggested levels of 0.25, 0.10, 0.05% for tea catechins, rosemary and sage, respectively. Soya protein (0.10%) increased meat redness in fresh pork patties producing significantly (P<0.05) higher Hunter 'a' values over the controls on days 0, 3 and 6. However, fenugreek (0.01%) was more effective in increasing Hunter 'a' values in patties manufactured from previously frozen pork. No significant (P>0.05) differences in Hunter 'L' and 'b' values were found between test and control samples on storage. The pH values of tea catechins, sage and soya protein fluctuated over time. Fresh pork patties with mustard and ginseng caused an initial decrease followed by a subsequent increase in pH values. Fenugreek caused an initial increase in pH values followed by a decrease from day 3 onwards.

Evaluation of the antioxidant potential of natural food/plant extracts as compared with synthetic antioxidants and vitamin E in raw and cooked pork patties.

Antioxidant potential for previously identified optimum levels of aloe vera (AV), fenugreek (FGK), ginseng (G), mustard (M), rosemary (R), sage (S), soya protein (SPI), tea catechins (TC) and whey protein concentrate (WPC) were evaluated in raw and cooked patties manufactured from frozen pork. The optimum levels determined were: AV (0.25%), FGK (0.01%), G (0.25%), M (0.10%), R (0.10%), S (0.05%), SPI (0.10%), TC (0.25%) and WPC (4%). Test ingredients were evaluated against synthetic antioxidants butylated hydroxyanisole/butylated hydroxytoluene (BHA/BHT) (0.01%) and a supplemented meat containing natural antioxidant, α-tocopherol (1000 mg α-tocopheryl acetate/kg feed). Ranking the decreasing antioxidant effectiveness of added ingredients in raw patties on day 9 showed that: Control>G>SPI>FGK>AV>M>WPC>S>α-tocopherol>R>TC>BHA/BHT. Cooking resulted in a four-fold increase in TBARS values over raw patties with TC being the most effective antioxidant having significantly (P<0.001) lower TBARS values than the cooked control on days 3, 6 and 9. Ranking of decreasing antioxidant effectiveness of added ingredients showed that: M>SPI>G>FGK>α-tocopherol>AV>control>S>BHA/BHT>R>WPC>TC. BHA/BHT had the most beneficial effect on cooked meat redness with Hunter 'a' values being significantly (P<0.05) higher than the control on days 3, 6 and 9. Ranking of Hunter 'a' values for added test ingredients showed that FGK>WPC>control>R>BHA/BHT>α-tocopherol>TC>AV>SPI>M>G>S on day 9. Hunter 'L' and 'b' values showed no significant trend over the storage period in either raw or cooked patties. The pH values of both raw and cooked pork control patties and products containing added test antioxidants were variable and while a number of trends were observed, no significant differences were recorded between samples.

Dissociable deficits in the decision-making cognition of chronic amphetamine abusers, opiate abusers, patients with focal damage to prefrontal cortex, and tryptophan-depleted normal volunteers: evidence for monoaminergic mechanisms.

We used a novel computerized decision-making task to compare the decision-making behavior of chronic amphetamine abusers, chronic opiate abusers, and patients with focal lesions of orbital prefrontal cortex (PFC) or dorsolateral/medial PFC. We also assessed the effects of reducing central 5-hydroxytryptamine (5-HT) activity using a tryptophan-depleting amino acid drink in normal volunteers. Chronic amphetamine abusers showed suboptimal decisions (correlated with years of abuse), and deliberated for significantly longer before making their choices. The opiate abusers exhibited only the second of these behavioral changes. Importantly, both sub-optimal choices and increased deliberation times were evident in the patients with damage to orbitofrontal PFC but not other sectors of PFC. Qualitatively, the performance of the subjects with lowered plasma tryptophan was similar to that associated with amphetamine abuse, consistent with recent reports of depleted 5-HT in the orbital regions of PFC of methamphetamine abusers. Overall, these data suggest that chronic amphetamine abusers show similar decision-making deficits to those seen after focal damage to orbitofrontal PFC. These deficits may reflect altered neuromodulation of the orbitofrontal PFC and interconnected limbic-striatal systems by both the ascending 5-HT and mesocortical dopamine (DA) projections.