Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models.

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC π , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.

Estimation of genomic breed composition of individual animals in composite beef cattle.

Three statistical models (an admixture model, linear regression, and ridge-regression BLUP) and two strategies for selecting SNP panels (uniformly spaced vs. maximum Euclidean distance of SNP allele frequencies between ancestral breeds) were compared for estimating genomic-estimated breed composition (GBC) in Brangus and Santa Gertrudis cattle, respectively. Animals were genotyped with a GeneSeek Genomic Profiler bovine low-density version 4 SNP chip. The estimated GBC was consistent among the uniformly spaced SNP panels, and values were similar between the three models. However, estimated GBC varied considerably between the three methods when using fewer than 10 000 SNPs that maximized the Euclidean distance of allele frequencies between the ancestral breeds. The admixture model performed most consistently across various SNP panel sizes. For the other two models, stabilized estimates were obtained with an SNP panel size of 20 000 SNPs or more. Based on the uniformly spaced 20K SNP panel, the estimated GBC was 69.8-70.5% Angus and 29.5-30.2% Brahman for Brangus, and 63.9-65.3% Shorthorn and 34.7-36.1% Brahman in Santa Gertrudis. The estimated GBC of ancestries for Santa Gertrudis roughly agreed with the pedigree-expected values. However, the estimated GBC in Brangus showed a considerably larger Angus composition than the pedigree-expected value (62.5%). The elevated Angus composition in the Brangus could be due to the mixture of some 1/2 Ultrablack animals (Brangus × Angus). Another reason could be the consequences of selection in Brangus cattle for phenotypes where the Angus breed has advantages.

A unified local objective function for optimally selecting SNPs on arrays for agricultural genomics applications.

Over the years, ad-hoc procedures were used for designing SNP arrays, but the procedures and strategies varied considerably case by case. Recently, a multiple-objective, local optimization (MOLO) algorithm was proposed to select SNPs for SNP arrays, which maximizes the adjusted SNP information (E score) under multiple constraints, e.g. on MAF, uniformness of SNP locations (U score), the inclusion of obligatory SNPs and the number and size of gaps. In the MOLO, each chromosome is split into equally spaced segments and local optima are selected as the SNPs having the highest adjusted E score within each segment, conditional on the presence of obligatory SNPs. The computation of the adjusted E score, however, is empirical, and it does not scale well between the uniformness of SNP locations and SNP informativeness. In addition, the MOLO objective function does not accommodate the selection of uniformly distributed SNPs. In the present study, we proposed a unified local function for optimally selecting SNPs, as an amendment to the MOLO algorithm. This new local function takes scalable weights between the uniformness and informativeness of SNPs, which allows the selection of SNPs under varied scenarios. The results showed that the weighting between the U and the E scores led to a higher imputation concordance rate than the U score or E score alone. The results from the evaluation of six commercial bovine SNP chips further confirmed this conclusion.

Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples.

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele 'dropout' (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome-wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.

Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes.

Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled. The present study showed that the pooling of animals with both original or imputed 40K SNP genotypes substantially increased genomic prediction accuracies on the ten traits. By supplementing imputed genotypes, the relative gains in genomic prediction accuracies on estimated breeding values (EBV) were from 12.60% to 31.27%, and the relative gain in genomic prediction accuracies on de-regressed EBV was slightly small (i.e. 0.87%-18.75%). The present study also compared the performance of five genomic prediction models and two cross-validation methods. The five genomic models predicted EBV and de-regressed EBV of the ten traits similarly well. Of the two cross-validation methods, leave-one-out cross-validation maximized the number of animals at the stage of training for genomic prediction. Genomic prediction accuracy (GPA) on the ten quantitative traits was validated in 1,106 newly genotyped Brangus animals based on the SNP effects estimated in the previous set of 3,797 Brangus animals, and they were slightly lower than GPA in the original data. The present study was the first to leverage currently available genotype and phenotype resources in order to harness genomic prediction in Brangus beef cattle.

Accuracy of Igenity genomically estimated breeding values for predicting Australian Angus BREEDPLAN traits.

Genomically estimated breeding values (GEBV) for Angus beef cattle are available from at least 2 commercial suppliers (Igenity [http://www.igenity.com] and Zoetis [http://www.zoetis.com]). The utility of these GEBV for improving genetic evaluation depends on their accuracies, which can be estimated by the genetic correlation with phenotypic target traits. Genomically estimated breeding values of 1,032 Angus bulls calculated from prediction equations (PE) derived by 2 different procedures in the U.S. Angus population were supplied by Igenity. Both procedures were based on Illuminia BovineSNP50 BeadChip genotypes. In procedure sg, GEBV were calculated from PE that used subsets of only 392 SNP, where these subsets were individually selected for each trait by BayesCπ. In procedure rg GEBV were calculated from PE derived in a ridge regression approach using all available SNP. Because the total set of 1,032 bulls with GEBV contained 732 individuals used in the Igenity training population, GEBV subsets were formed characterized by a decreasing average relationship between individuals in the subsets and individuals in the training population. Accuracies of GEBV were estimated as genetic correlations between GEBV and their phenotypic target traits modeling GEBV as trait observations in a bivariate REML approach, in which phenotypic observations were those recorded in the commercial Australian Angus seed stock sector. Using results from the GEBV subset excluding all training individuals as a reference, estimated accuracies were generally in agreement with those already published, with both types of GEBV (sg and rg) yielding similar results. Accuracies for growth traits ranged from 0.29 to 0.45, for reproductive traits from 0.11 to 0.53, and for carcass traits from 0.3 to 0.75. Accuracies generally decreased with an increasing genetic distance between the training and the validation population. However, for some carcass traits characterized by a low number of phenotypic records (weight, intramuscular fat, and eye muscle area), accuracies were observed to increase but had large SE. Therefore, Igenity GEBV can be useful to Australian Angus breeders, either for blending EBV or as the sole basis for selection decisions if no other information is available. However, for carcass traits, additional phenotypic data are required.

Reliability of molecular breeding values for Warner-Bratzler shear force and carcass traits of beef cattle - an independent validation study.

Interest in genetic improvement of carcass and tenderness traits of beef cattle using genome-based selection (GS) and marker-assisted management programs is increasing. The success of such a program depends on the presence of linkage disequilibrium between the observed markers and the underlying QTL as well as on the relationship between the discovery, validation, and target populations. For molecular breeding values (MBV) predicted for a target population using SNP markers, reliabilities of these MBV can be obtained from validation analyses conducted in an independent population distinct from the discovery set. The objective of this study was to test MBV predicted for carcass and tenderness traits of beef cattle in a Canadian-based validation population that is largely independent of a United States-based discovery set. The discovery data set comprised of genotypes and phenotypes from >2,900 multibreed beef cattle while the validation population consisted of 802 crossbred feeder heifers and steers. A bivariate animal model that fitted actual phenotype and MBV was used for validation analyses. The reliability of MBV was defined as square of the genetic correlation (R(2) g) that represents the proportion of the additive genetic variance explained by the SNP markers. Several scenarios involving different starting marker panels (384, 3K, 7K, and 50K) and different sets of SNP selected to compute MBV (50, 100, 200, 375, 400, 600, and 800) were investigated. Validation results showed that the most reliable MBV (R(2) g) were 0.34 for HCW, 0.36 for back fat thickness, 0.28 for rib eye area, 0.30 for marbling score, 0.25 for yield grade, and 0.38 for Warner-Bratzler shear force across the different scenarios explored. The results indicate that smaller SNP panels can be developed for use in genetic improvement of beef carcass and tenderness traits to exploit GS benefits.

Identification of single nucleotide polymorphisms in genes involved in digestive and metabolic processes associated with feed efficiency and performance traits in beef cattle.

Discovery of genetic mutations that have a significant association with economically important traits would benefit beef cattle breeders. Objectives were to identify with an in silico approach new SNP in 8 genes involved in digestive function and metabolic processes and to examine the associations between the identified SNP and feed efficiency and performance traits. The association between SNP and daily DMI, ADG, midpoint metabolic weight (MMWT), residual feed intake (RFI), and feed conversion ratio (FCR; the ratio of average daily DMI to ADG) was tested in discovery and validation populations using a univariate mixed-inheritance animal model fitted in ASReml. Substitution effect of the T allele of SNP rs41256901 in protease, serine, 2 (trypsin 2; PRSS2) was associated with FCR (-0.293 ± 0.08 kg DMI kg(-1) BW gain; P < 0.001) and RFI (-0.199 ± 0.08 kg; P < 0.01) and although not significant in the validation population, the phase of association remained. In the cholecystokinin B receptor (CCKBR) gene, genotypes in rs42670351 were associated with RFI (P < 0.05) whereas genotypes in rs42670352 were associated with RFI (P = 0.002) and DMI (P < 0.05). Substitution of the G allele in rs42670352 was associated with DMI (-0.236 ± 0.12 kg; P = 0.055) and RFI (-0.175 ± 0.09 kg; P = 0.05). Substitution of the G allele of SNP rs42670353 was associated with ADG (0.043 ± 0.02 kg/d; P < 0.01) and FCR (0.114 ± 0.05 kg BW gain kg(-1) DMI; P < 0.05). In the validation dataset, SNP rs42670352 in gene CCKBR was significant for RFI and DMI and had the same phase of associations; SNP rs42670353 was significantly associated with FCR with same phase of association and the C allele in SNP rs42670351 was validated as decreasing DMI, RFI, and FCR. Substituting the G allele of SNP rs42670352 in CCKBR2 was associated with decreasing DMI and RFI in the validation study. New SNP were reported in genes PRSS2 and CCKBR, being associated with feed efficiency and performance traits in beef cattle. The association between these SNP with fertility, carcass, and meat quality traits must still be tested.

Short communication: Interactions of milk, fat, and protein yield genotypes with herd feeding characteristics.

Data from 879 Holstein cows from 11 tie-stall herds in Pennsylvania were analyzed to determine the effects of nutritional management practices on the level of genetic expression for milk, fat, and protein yields. Environments were defined according to the amount of dry matter refusals at the end of 24h for the average cow (DMR), diet crude protein percentage (CP), and diet NE(L) concentration. Sire predicted transmitting ability (PTA) was available for all cows, whereas 775 cows were genotyped and received a molecular breeding value (MBV) for milk, fat, and protein yields. Milk, fat, and protein yields were regressed on sire PTA and cow MBV independently in addition to combined breeding values (CBV) of sire PTA and cow MBV. Four-trait animal models with fat-corrected milk yield in high and low environments plus either body weight or body condition score in high and low environments treated as separate traits were also evaluated. Regressions on sire PTA (0.31 for fat yield to 0.54 for milk yield) were significantly lower in the 5 herds that had the lowest average DMR than in the 6 herds with highest average DMR (0.82 for fat yield to 1.11 for protein yield). The regressions of milk and protein yield on CBV were also significantly lower in the 5 herds with low NE(L) concentration in the ration than in herds that had high NE(L) concentration. Genetic correlations from animal models showed that large cows were more affected by low DMR, CP, and NE(L) concentration than smaller cows. Efforts to minimize feed wastage must ensure that cows receive adequate nutrient intake to avoid suppression of genetic potential for yield, particularly for larger cows.

Comparative cost-effectiveness of ivermectin versus topical organophosphate in feedlot yearlings.

A replicated-pen field trial was performed under commercial feedlot conditions in western Canada to determine the cost-effectiveness of administering ivermectin to yearling beef cattle upon entry to the feedlot after the grazing season, and to establish the level of trichostrongylid gastrointestinal parasite infection in this population, as estimated by fecal egg counts. Six thousand eight hundred and eighty-three, mixed breed, yearling steers were randomly allocated upon arrival at the feedlot to one of 2 experimental groups as follows: Ivermectin, which received topical ivermectin (0.5%) at the rate of 1.0 mL/10 kg body weight; or Fenthion, which received topical fenthion (20%) at the rate of 12 mL/295 kg body weight. There were 15 pens in each experimental group. Final weight, weight gain, average daily gain, and dry matter intake to gain ratio were significantly (P < 0.05) improved in the Ivermectin group as compared with the Fenthion group. There were no significant (P > or = 0.05) differences in initial weight, days on feed, or daily dry matter intake between the experimental groups. The geometric mean fecal egg counts at the time of allocation were 14.7 eggs/5 g and 16.6 eggs/5 g for the Ivermectin and Fenthion groups, respectively (P > or = 0.05). There were no significant (P > or = 0.05) differences in morbidity or mortality between the experimental groups. In the economic analysis, the significant improvements in feedlot performance in the Ivermectin group resulted in a net economic advantage of $4.20 CDN per animal.

Effect of antiparasitic treatment in beef replacement heifers.

Two studies were conducted in western Canada to evaluate the impact of antiparasitic treatment on weight gain and reproductive performance in beef replacement heifers from weaning to first breeding. Treatment of heifers at weaning with ivermectin increased the rate of weight gain in comparison to treatment with fenthion. The feed efficiency of ivermectin-treated animals was also significantly better than those treated with fenthion. Increased weight was associated with an increased number of animals in estrus at the end of the feeding period for heifers receiving ivermectin. We concluded that treatment with ivermectin improved feed efficiency and weight gain in heifers from weaning to breeding. In turn, this weight gain appeared to be associated with an increased number of heifers in estrus.

Epidemiological study of parasite infection in a cow-calf beef herd in Quebec.

The patterns of gastrointestinal and pulmonary nematode infections in a previously untreated Aberdeen Angus cow-calf herd were observed between May 1988 and December 1990. The cow-calf herd and replacement heifers were on separate pastures. The relatively high mean faecal egg counts of cows and heifers at the time of turnout were mainly owing to the maturation of hypobiotic worms. The strongyle egg counts of calves began to rise soon after turnout onto pasture and reached peak levels at the end of the grazing season. The number of infective larvae on pasture was highest during September/October. Ostertagia, Cooperia and Nematodirus were the most prevalent genera found at necropsy and on pasture. Larvae of these nematodes were able to overwinter on pasture and Ostertagia larvae, additionally, were able to overwinter in the host as arrested early fourth stage larvae. The high egg output of cows at the time of turnout may serve as a source of infection for their calves and be responsible for the late-season rise in pasture larval counts.

Environment, respiratory disease, and performance of pigs in three Saskatchewan grower-finisher barns.

A microcomputer-based environmental monitoring system was used to monitor temperature, humidity, and ventilation rate continuously in three commercial grower-finisher swine barns in Saskatchewan. During the monitoring period, a group of pigs in each barn was examined for growth rate, amount of lung affected with pneumonia, and degree of atrophic rhinitis. In addition, the total bacterial colony forming particle count within the airspace of each barn was measured once each week.Significant differences existed among barns for daily maximum and minimum temperature, relative humidity, ventilation rate, and average bacterial colony forming particle counts. There was no difference among farms in the average percentage of lung affected with pneumonia, average snout atrophy score, or growth rate of the test animals.On one farm, there was a significant positive correlation between snout score and percentage of lung affected with pneumonia. On another farm, there was a significant negative correlation between percentage of lung affected with pneumonia and growth rate.

Comparative cost-effectiveness of ivermectin versus topical organophosphate in feedlot calves.

A study was conducted in a commercial feedlot in western Canada to evaluate the impact of treatment with ivermectin versus a topical organophosphate on growth rate and feed efficiency in calves entering a feedlot at an average 275 kg liveweight.A total of 9527 head of cattle was used. Variables measured included average daily gain, average days occupation, and feed conversion.Ivermectin treated animals gained an average 0.08 kg per day more than those treated with topical organophosphate. In addition, they required an average 0.23 kg less feed/kg gain. Based on an average 227 kg of gain, this would result in 11 fewer days occupation and 52.3 kg less feed for ivermectin treated animals. This equaled a net benefit of $7.04 per head over treatment costs for ivermectin treatment versus topical organophosphate.

Predictable and unpredictable shock stimulates gastric contractility and causes mucosal injury in rats.

The effects of tailshock on gastric contractility and lesions were investigated in rats exposed to 100 1-mA tailshocks while confined inside plastic tubes. A light preceded each shock in one group and was randomly presented with respect to shock in the other. Following the session, animals were given 3 hr of rest before being sacrificed. Contractility of the corpus of the stomach was measured by means of chronically implanted extraluminal force transducers. Contractility was measured in 10-min blocks and analyzed by computer. Lesions were quantified by inspection; quantitative histology was performed on corpus and antrum sections. Signaled (n = 13) and unsignaled (n = 17) shock stimulated high-amplitude gastric contractions in fasted rats, which continued for 2 hr after the shock session. Cumulative contractile activity (1.5-hr shock plus 2-hr rest) in shocked animals was twice that in restrained and unrestrained control animals (n = 19, p less than .05), and contractile activity had a 30%-40% greater average amplitude than after a meal. Compared with unrestrained controls, shocked rats had visibly more mucosal injury (2.2 +/- 0.5 mm2 vs. 0.1 +/- 0 mm2). Larger cumulative contractile activity was associated with a larger area of erosions (r = .36, p less than .05). Frequency and duration of contractions did not distinguish between shocked and unshocked groups. We conclude that in rats, signaled and unsignaled tailshock stimulates persistent, high-amplitude gastric contractions and is associated with injury of the mucosa of the stomach.

An evaluation of a combination of injectable anesthetic agents for use in pigs.

A combination of atropine sulfate, fentanyl/droperidol, ketamine hydrochloride and pentobarbital was examined for its effectiveness as an anesthesia protocol for swine weighing up to 50 kg. While the dose rate and route of administration of atropine sulfate, fentanyl/droperidol and ketamine hydrochloride was held constant, the dose rate and route of administration of pentobarbital was altered until a combination was determined which would reliably and safely produce a satisfactory level of anesthesia. Following treatment, animals were monitored and the time taken to produce an effect was recorded. The degree of anesthesia as measured by the corneal reflex and the cutaneous response to a needle prick or actual surgery and the time elapsed until signs of recovery were evident were also noted.We found a combination of atropine sulfate (0.05 mg/kg) intramuscularly and fentanyl/droperidol (1 mL/13.7 kg) intramuscularly followed by ketamine hydrochloride (11 mg/kg) intramuscularly approximately ten minutes later and 3% pentobarbital solution (9 mg/kg) intravenously two minutes after that, to be a safe and reliable method for producing surgical anesthesia of 45 minutes duration.