Imputation accuracy and carrier frequency of deleterious recessive defects in Australian dairy cattle.

Widespread genotyping has enabled the identification of putative recessive mutations that affect fertility through early embryonic fetal loss, or compromise neonate or calf viability. The use of artificial insemination in the global dairy population can rapidly spread these harmful mutations, and testing for multiple mutations can become relatively expensive if not all tests are available on the same SNP panel. However, it is possible to provide heifer and cow predicted carrier status to farmers at no additional cost if the animals are genotyped with a standard SNP panel. Additionally, for defects where the causal mutation is unknown, but a haplotype of markers has been associated with the defect, the carrier status can be predicted based on that haplotype. The aims of this study were 3-fold: 1) to determine the accuracy of imputation of putative causal mutations for recessive deleterious conditions in Australian dairy cattle, 2) to impute carrier status for known recessive deleterious conditions in all genotyped Australian Holstein, Jersey and Red breed cows, and 3) to determine the changes in carrier frequencies across time for these recessive deleterious mutations. We used the F1 statistic, combining precision and recall, to assess the accuracy of carrier status prediction. We showed that known deleterious mutations can be accurately imputed in Australian Holstein and Jersey cattle that are not directly genotyped for the causal mutation, with F1 ranging between 0.88 and 0.99. For recessive deleterious conditions not included on the standard Australian SNP panel, carrier status could be predicted using a marker haplotype, with F1 ranging from 0.91 to 0.92. Most putative causals and haplotypes were either stable with a low carrier percentage or had a declining carrier percentage. However, several recessive mutations showed a relatively high or increasing percentage, highlighting the importance of detecting carriers to reduce the number of at risk matings. Furthermore, the high carrier percentage of the recently identified Bovine Lymphocyte Intestinal Retention Defect (BLIRD) mutation emphasizes the importance of detection of novel mutations.

Erratum to "Evaluation of updated Feed Saved breeding values developed in Australian Holstein dairy cattle" (JDS Commun. 3:114-119).

[This corrects the article DOI: 10.3168/jdsc.2021-0150.].

Evaluation of updated Feed Saved breeding values developed in Australian Holstein dairy cattle.

Although selection for increased milk production traits has led to a genetic increase in body weight (BW), the genetic gain in milk production has exceeded the gain in BW, so gross feed efficiency has improved. Nonetheless, greater gains may be possible by directly selecting for a measure of feed efficiency. Australia first introduced Feed Saved (FS) estimated breeding value (EBV) in 2015. Feed Saved combines residual feed intake (RFI) genomic EBV and maintenance requirements calculated from mature BW EBV. The FS EBV was designed to enable the selection of cows for reduced energy requirements with similar milk production. In this study, we used a reference population of 3,711 animals in a multivariate analysis including Australian heifers (AUSh), Australian cows (AUSc), and overseas cows (OVEc) to update the Australian EBV for lifetime RFI (i.e., a breeding value that incorporated RFI in growing and lactating cows) and to recalculate the FS EBV in Australian Holstein bulls (AUSb). The estimates of genomic heritabilities using univariate (only AUSc or AUSh) to trivariate (including the OVEc) analyses were similar. Genomic heritabilities for RFI were estimated as 0.18 for AUSc, 0.27 for OVEc, and 0.36 for AUSh. The genomic correlation for RFI between AUSc and AUSh was 0.47 and that between AUSc and OVEc was 0.94, but these estimates were associated with large standard errors (range: 0.18-0.28). The reliability of lifetime RFI (a component of FS) in the trivariate analysis (i.e., including OVEc) increased from 11% to 20% compared with the 2015 model and was greater, by 12%, than in a bivariate analysis in which the reference population included only AUSc and AUSh. By applying the prediction equation of the 2020 model, the average reliability of the FS EBV in 20,816 AUSb that were born between 2010 and 2020 improved from 33% to 43%. Previous selection strategies-that is, using the predecessor of the Balanced Performance Index (Australian Profit Ranking index) that did not include FS-have resulted in an unfavorable genetic trend in FS. However, this unfavorable trend has stabilized since 2015, when FS was included in the Balanced Performance Index, and is expected to move in a favorable direction with selection on Balanced Performance Index or the Health Weighted Index. Doubling the reference population, particularly by incorporating international data for feed efficiency, has improved the reliability of the FS EBV. This could lead to increased genetic gain for feed efficiency in the Australian industry.

Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations.

The reliability of genomic evaluations depends on the proportion of genetic variation explained by the DNA markers. In this study, we have estimated the proportion of variance in daughter trait deviations (DTDs) of dairy bulls explained by 45 993 genome wide single-nucleotide polymorphism (SNP) markers for 29 traits in Australian Holstein-Friesian dairy cattle. We compare these proportions to the proportion of variance in DTDs explained by the additive relationship matrix derived from the pedigree, as well as the sum of variance explained by both pedigree and marker information when these were fitted simultaneously. The proportion of genetic variance in DTDs relative to the total genetic variance (the total genetic variance explained by the genomic relationships and pedigree relationships when both were fitted simultaneously) varied from 32% for fertility to approximately 80% for milk yield traits. When fitting genomic and pedigree relationships simultaneously, the variance unexplained (i.e. the residual variance) in DTDs of the total variance for most traits was reduced compared to fitting either individually, suggesting that there is not complete overlap between the effects. The proportion of genetic variance accounted by the genomic relationships can be used to modify the blending equations used to calculate genomic estimated breeding value (GEBV) from direct genomic breeding value (DGV) and parent average. Our results, from a validation population of young dairy bulls with DTD, suggest that this modification can improve the reliability of GEBV by up to 5%.

Breeding for resistance to footrot--the use of hoof lesion scoring to quantify footrot in sheep.

So that genetic studies can be undertaken on footrot in sheep, it is necessary that a reliable and repeatable method to categorise the phenotype is available. This paper summarises the methods used and results obtained from 1600 hoof lesion scores of 100 mixed-age ewes independently scored twice by two trained operators. Using a 5-pont scale describing the severity of foot lesions, residual correlations were used to assess agreement between scorers and scoring occasions. Data were analysed using both zero-1 and continuous data methods. The average prevalence of any score >0 was 15%, and of scores >1 was 12%. The residual correlation between scorers for SUM_FR was 0.87 and between scoring occasions it was also 0.87, indicating high repeatability or agreement both within and between scorers. No significant differences were detected between scorers or between scoring occasions for any of the traits analysed, or different analytical methods used.

Changes in connectedness over time in alternative sheep sire referencing schemes.

A statistic to measure the level of connectedness achieved among flocks would help producers to assess the risk of comparing EBV of animals from different flocks. The objectives of this research were to evaluate the pattern of change over time in selected connectedness measures and to determine how effectively these measures quantify the level of risk due to potential bias in EBV comparisons across production units. Connectedness was evaluated using simulated sheep populations, with connections established using sire referencing schemes (SRS). Pedigree and performance data for a single trait with a within-flock heritability of 0.25 were simulated (50 replications) for 15 flocks with 40 to 140 ewes per flock. Genetic means for each flock were sampled from a normal distribution with mean 0 and SD equal to the trait's genetic SD. After 10 yr of random mating, flocks had opportunity to join a SRS and selection began for the simulated trait. Yearling rams were chosen as reference sires randomly from the top one-sixth of the population ranked on BLUP EBV. Every year, in each flock, 3 reference sires were mated to 10 ewes each. Six sire referencing scenarios (including no SRS) and 2 sources of nonreference sires were simulated. Connectedness was measured in 2 ways: (i) as the average prediction error correlation (r(ij)) of the flock genetic means (flock r(ij)) or the EBV for the current crop of ram lambs (lamb r(ij)) or (ii) as the average scaled prediction error variance of differences (PEVD) in flock genetic means (flock PEVD) or in lamb EBV in the current crop of ram lambs (lamb PEVD). Flock r(ij) increased linearly in all scenarios while SRS was underway and leveled off if the flocks discontinued SRS. Lamb r(ij) increased rapidly as soon as SRS began but decreased substantially if the flocks discontinued SRS. Behavior of flock PEVD and lamb PEVD measures were similar but in the opposite direction (i.e., PEVD decreased with increasing r(ij)). Within scenarios, both flock r(ij) and flock PEVD had a nonlinear relationship with bias in comparing animals across flocks. However, only flock r(ij) exhibited a consistent relationship across simulation scenarios. When flock r(ij) reached 0.05 and 0.10, approximately 20 and 10%, respectively, of the bias due to initial differences in flock genetic means remained. These levels of flock r(ij) are suggested as benchmark levels for minimizing the risk of comparing animal EBV among units.

Genetic and phenotypic aspects of foot lesion scores in sheep of different breeds and ages.

Footrot is a costly endemic disease of sheep. This study investigates the potential to decrease its prevalence through selective breeding for decreased lesion score. Pedigreed mule and Scottish Blackface (SBF) ewes were scored for lesions on each hoof on a 0 to 4 scale for up to 2 (SBF ewes) or 4 (mules) times over 2 years. One score was obtained for SBF lambs. An animal was deemed to have lesions (severe lesions) if at least one hoof had a score of at least 1 (2). The prevalence of lesions was 34% in lambs, 17% in SBF ewes and 51% in mules. The heritability of lesions (severe lesions) analysed as repeated measurements of the same trait in a threshold model was 0.19 (0.26) in SBF ewes and 0.12 (0.19) in mules. Estimates for the sum and maximum of scores as well as the number of feet affected were much lower, as were estimates for permanent animal effects (i.e. non-genetic effects associated with an animal). When successive scores on the same animal were analysed as correlated traits, heritability estimates for most traits tended to be higher, except for severe footrot in mules where estimates varied greatly over time. The phenotypic correlations between successive scores in SBF ewes were close to 0, genetic correlations were moderately positive (0.18 to 0.55). Correlations in mules were generally of a similar size, but some genetic correlations were higher (up to 0.92). There was a clear trend for heritabilities for lesions and severe lesions to increase with higher prevalence of lesions, even when analysed in a threshold model. Heritability estimates for traits that combine scores over several events in mules, identifying the more persistently affected animals, ranged from 0.12 to 0.23 with the highest estimates for the average number of feet that were (severely) affected in animals scored for a minimum at two events. The heritability of all lesion traits in lambs was estimated as 0. It is concluded that selection for lower lesions is possible in ewes but not lambs, and that a simple binary score at an animal level is at least as effective as a comprehensive score at hoof level. Given the low repeatability of lesion scores, repeated measures over time will improve effectiveness of selection. Selection across environments (flocks, seasons) with different prevalences of lesions scores will need to take account of variation in the heritability.

The effect of footrot on weight gain in sheep.

Footrot is a highly contagious bacterial disease of sheep affecting the interdigital skin and surrounding soft and hard horn of a hoof, often resulting in severe lameness. This study was aimed at estimating the effect of footrot on weight gain of affected animals, and characterising the variation between animals in terms of phenotypic, environmental and genetic components. A general approach was developed describing the relationship between the disease and weight gain, defining new traits such as the maximum weight loss as a result of disease and the time after infection that this occurs. In two trials, 1267 Merino sheep were artificially challenged with footrot when 10 months old and re-infected through exposure to footrot on pasture 33 weeks later. Their feet were scored for footrot and live weights were measured approximately every 3 weeks. From data on animals that were not affected by footrot throughout each trial, normal growth curves were calculated and applied to affected animals to predict their growth had they remained healthy, so that weight loss as a result of footrot could be predicted. Animals with average footrot severity in the two trials suffered weight losses of 0.5 to 2.5 kg live weight, but most animals regained lost live weight later in the trials as footrot healed following vaccination. The estimates of the heritabilities of weight loss, adjusted for the severity of footrot, were about 0.30 and 0.15 in the experimental and natural challenge groups, respectively. Animals with higher genotypic values for weights at the start of each trial appeared to cope better with infections, in terms of lower weight losses. The time of highest footrot score and the time of maximum weight loss after infection had only very small genetic components.

Industry benefits from recent genetic progress in sheep and beef populations.

An analytical model that evaluates the benefits from 10 years of genetic improvement over a 20-year time frame was specified. Estimates of recent genetic trends in recorded traits, industry statistics and published estimates of the economic values of trait changes were used to parameterise the model for the UK sheep and beef industries. Despite rates of genetic change in the relevant performance-recorded breeding populations being substantially less than theoretical predictions, the financial benefits of genetic change were substantial. Over 20 years, the benefits from 10 years of genetic progress at recently achieved rates in recorded hill sheep, sheep crossing sire and sheep terminal sire breeding programmes was estimated to be £5.3, £1.0 and £11.5 million, respectively. If dissemination of genetic material is such that these rates of change are also realised across the entire ram breeding industry, the combined benefits would be £110.8 million. For beef cattle, genetic evaluation systems have been operating within all the major breeds for some years with quite widespread use of performance recording, and so genetic trends within the beef breeds were used as predictors of industry genetic change. Benefits from 10 years of genetic progress at recent rates of change, considering a 20-year time frame, in terminal sire beef breeds are expected to be £4.9 million. Benefits from genetic progress for growth and carcass characters in dual-purpose beef breeds were £18.2 million after subtraction of costs associated with a deterioration in calving traits. These benefits may be further offset by unfavourable associated changes in maternal traits. Additional benefits from identification and use of the best animals available from the breeding sector for commercial matings through performance recording and genetic evaluation could not be quantified. When benefits of genetic improvement were expressed on an annual present value basis and compared with lagged annual investment costs to achieve it, the internal rate of return (IRR) on the combined investment in sheep and beef cattle was 32%. Despite a much higher rate of participation in performance recording, the present value of benefits and the IRR were lower for beef cattle than for sheep. The implications of these results for future national and industry investment in genetic improvement infrastructure were discussed.

Relationship between the expression of hepatic but not testicular 3beta-hydroxysteroid dehydrogenase with androstenone deposition in pig adipose tissue.

This study investigated the relationship between expression of hepatic and testicular 3beta-hydroxysteroid dehydrogenase (3beta-HSD) and accumulation of androstenone in adipose tissue because of its relation to boar taint. The experiments were performed on 13 Large White (50%) x Landrace (50%) and Meishan (25%) x Large White (25%) x Landrace (50%), pigs, which differed in the level of backfat androstenone. Our previous work showed that the major product of the hepatic androstenone metabolism is 3beta-androstenol. In this study, the formation of 3beta-androstenol was inhibited by the specific 3beta-HSD inhibitor trilostane. These results are the first direct confirmation that 3beta-HSD is the enzyme responsible for androstenone metabolism in the pig. The expression of the hepatic but not testicular 3beta-HSD protein showed a negative relationship with the level of backfat androstenone (r2 = 0.64; P < 0.001) and was accompanied by a reduced rate of the hepatic androstenone clearance. Low expression of 3beta-HSD protein in the liver of high androstenone pigs was also accompanied by a reduced level of 3beta-HSD mRNA (P < 0.001), which suggests a defective regulation of the hepatic 3beta-HSD expression at the level of transcription. In contrast, expression of the testicular 3beta-HSD protein did not differ between animals with high and low androstenone levels (P > 0.05) and was lower compared with the hepatic 3beta-HSD expression. Cloning and sequencing of the 3beta-HSD coding regions established that the hepatic and testicular 3beta-HSD cDNA have identical sequences, which were 98% similar to the human 3beta-HSD isoform I. It is suggested that expression of a single 3beta-HSD gene is regulated by different mechanisms in pig liver and testis. The liver-specific regulation of 3beta-HSD expression contributes to the low rate of hepatic androstenone metabolism and therefore can be considered as one of the factors regulating deposition of androstenone in pig adipose tissue and subsequent development of boar taint.

Breeding programmes for TSE resistance in British sheep. I. Assessing the impact on prion protein (PrP) genotype frequencies.

From April 2005, member states of the European Union were required to implement a compulsory breeding programme for resistance to transmissible spongiform encephalopathies (TSEs) in sheep as part of measures to eradicate TSEs from national flocks. In this paper, we assessed the impact of four different breeding strategies on prion protein (PrP) genotype frequencies using a mathematical model which describes in detail gene flow in the British sheep flock. These strategies ranged from the minimum requirements laid down in by EU legislation to compulsory implementation of the current National Scrapie Plan for Great Britain (NSP) ram genotyping scheme. All four strategies were predicted to substantially reduce the frequency of the VRQ allele, which is associated with the highest risk of scrapie, although schemes with more stringent requirements produced a larger reduction. However, there were marked differences in the impact of the strategies on the frequency of other PrP alleles. In particular, restrictions beyond those required by EU legislation were necessary to change the frequency of other PrP alleles substantially. Consequently, a breeding programme which aims to reduce the risk to human health by reducing the frequency of the ARQ allele (associated with the highest risk of BSE in sheep) must place restrictions on ARQ-bearing animals. Similarly, a programme which seeks to increase the frequency of the ARR allele (associated with the lowest risk of TSE) must favour ARR-bearing animals.

Effect of recombinant porcine somatotropin on body composition and meat quality in growing pigs; Interactions with genotype, sex and slaughter weight.

Body composition in 96 pigs and meat quality in 36 pigs treated with porcine somatotropin (rpST) were investigated. Animals included both barrows and gilts from Pietrain, F(1) (Dutch Yorkshire × Dutch Landrace) and Duroc and were slaughtered at either 100 or 140 kg live weight. Treatment consisted of either 14 mg rpST or placebo twice weekly and started at 60 kg. Treatment with rpST enhanced the proportion of lean parts (on average +2·8% at 100 kg and + 5·5% at 140 kg) and reduced the proportion of fatty parts (-10·1% and -12·9% respectively). The latter tended to be more apparent in fatter animals (Duroc -14·5% and -13·3%, barrows -12·0% and -13·7%). Most organs increased in weight, especially kidneys (+14·8% at 100 kg and +17·6% at 140 kg). Meat quality parameters appeared to be not significantly affected, though intramuscular fat percentage was slightly decreased. Administration of rpST led to less fat and more uniformity in carcasses and meat quality among genotypes and sexes. No serious adverse effects were detected.

Effect of recombinant porcine somatotropin on growth and carcass quality in growing pigs: interactions with genotype, gender and slaughter weight.

Effects of recombinant porcine somatotropin (rpST) on growth, lean tissue growth, feed intake, feed conversion, lean tissue feed conversion, backfat thickness and lean percentage were examined in 96 growing pigs. The experiment used barrows and gilts from the genotypes Duroc, F1 (Dutch Yorkshire x Dutch Landrace) and Pietrain. Half the pigs received 14 mg rpST i.m. twice each week starting at 60 kg; others received a placebo. Pigs had ad libitum access to a diet containing 2,162 kcal net energy and 182 g crude protein per kilogram and were slaughtered at either 100 or 140 kg live weight. From 60 to 100 and from 100 to 140 kg, live weight responses to rpST averaged as follows: daily gain, +4.5 and +19.9%; feed intake, -4.4 and +3.5%; feed conversion, -8.4 and -13.9%; backfat thickness, -13.8 and -22.8%; lean percentage, +4.4 and +8.7%; lean tissue growth rate, +8.6 and +35.8%; and lean tissue feed conversion, -13.1 and -24.9%. No gender x rpST interaction was detected. However, a genotype x treatment interaction was significant for backfat thickness at both slaughter weights, showing a higher response to rpST in Duroc than in Pietrain and F1. Growth performance was improved more by rpST in F1 and Pietrain than in Duroc, especially at higher weights, but carcass traits were improved more by rpST in Duroc. The response to rpST in lean tissue growth rate from 60 to 100 kg was highest in fatter animals (Duroc, barrows), whereas from 100 to 140 kg, response in lean tissue growth rate to rpST was highest in leaner animals (Pietrain, F1, gilts).