Prediction of prion protein genotype and association of this genotype with lamb performance traits of Suffolk sheep.

The association of the prion protein (PrP) gene with susceptibility to scrapie has formed the basis of selection programs aimed at eradicating the disease from sheep populations. Animals are genotyped for the PrP gene and those with the less susceptible genotypes are selected. The objectives of this study were to determine the effectiveness of predicting PrP genotypes by using information from relatives and to investigate the association of the PrP genotype with lamb performance traits in Suffolk sheep. Data were obtained from a scrapie-affected flock maintained in Scotland. A total of 643 were animals genotyped at codon 171 of the PrP gene with 2 alleles, R and Q. The genotypes of these animals were used to predict the genotypes of 5,173 nongenotyped animals in the same flock using segregation analysis. The genotype of nongenotyped animals was predicted from the probabilities for each possible genotype; further, an overall index for each animal was calculated to reflect the accuracy of prediction. Association analyses of the PrP gene (using animals with both known and inferred genotypes) with BW at birth, at weaning (56 d), and at 150 d, and for backfat and muscle depths at 150 d of age were carried out. A linear mixed model with random direct and maternal additive genetic effects, maternal permanent and temporary environmental effects, and year of birth was tested, and the most appropriate model was used for each trait. The expected number of Q alleles carried (from 0 to 2) by each animal was calculated and used in the model as a linear and quadratic covariate to test for associations with possible additive and dominance PrP gene effects, respectively. Results showed that the genotypes of relatively few animals (235) were inferred with certainty (compared with the 5,173 nongenotyped animals). Approximately 25% of the 5,173 predicted genotypes were inferred with a genotype probability index of 50% and greater. There was no significant association of the PrP gene with any of the performance traits studied (there were no significant additive or dominance effects). Such was the case whether data on animals with known or with both known and predicted genotypes were considered. It can be concluded that selection for PrP-resistant alleles in Suffolk sheep is unlikely to affect performance directly.

Scrapie-resistant sheep show certain coat colour characteristics.

Susceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated with PrP genotype. The objective of this study was to investigate the relationship between PrP genotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting and PrP genotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log-linear model using maximum likelihood. Results showed a strong significant association of PrP genotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only on PrP genotype could result in change in morphological diversity and affect other associated traits such as fitness.

Association of the prion protein gene with individual tissue weights in Scottish Blackface sheep.

This study investigated associations of prion protein (PrP) genotype with body composition and weight traits of Scottish Blackface ewes. Body composition was predicted using computer tomography (CT) scans to estimate muscle, carcass fat, internal fat, and bone weights. The traits were measured at 4 key seasonal production points (pre-mating, pregnancy, midlactation, and weaning) over 4 production cycles (2 to 5 yr old). There were 2,413 records for each of the CT traits measured on 335 ewes, and 26,649 records for each of the body condition score and BW traits for 2,356 ewes. From 1999 to 2004, animals were genotyped to determine polymorphisms at codons 136, 154, and 171, which are associated with scrapie susceptibility. Four alleles were found in the population (ARR, AHQ, ARQ, and VRQ). The data were analyzed using a linear mixed random regression model assuming that the direct additive genetic effect was a 2nd order Legendre polynomial function of time. The PrP genotype was included in the model as a fixed effect along with other fixed factors with significant effects (P < 0.05). Five separate analyses were carried out for each trait, depending on the method of classifying the PrP genotype. In the first analysis, animals were categorized according to the genotype. Only the 5 most common genotypes (ARR/ARR, ARR/AHQ, ARR/ARQ, AHQ/ARQ, and ARQ/ARQ) were included. In the last 4 analyses, animals were categorized according to the number of each PrP allele carried. For CT traits and body condition score, results showed that the PrP genotype has no association with the overall mean of the traits (averaged over age). For BW, ewes without the ARQ allele were at least 0.5 kg heavier than ARQ homozygous and heterozygous ewes. On the other hand, there was a significant interaction between PrP genotype and age of the ewe (i.e., the effect of PrP genotype was not the same at different ages for 5 out of the 6 traits studied). In general, ARQ carrying ewes mobilized more fat reserves at times of nutrient deficiency, such as during lactation, and gained it back more quickly by the mating season (when nutrients became abundant) than non-ARQ carriers. Therefore, selecting against this allele would have consequences on BW and seasonal mobilization of body reserves. The number of VRQ alleles (the most scrapie susceptible allele) carried was not significantly associated with any of the traits.

Associations of polymorphisms of the ovine prion protein gene with growth, carcass, and computerized tomography traits in Scottish Blackface lambs.

The objective of this study was to investigate and estimate the associations of the ovine prion protein (PrP) genotypes with a wide range of performance traits in Scottish Blackface lambs. Performance records of up to 7,138 sheep of known PrP genotypes born from 1999 to 2004 in 2 experimental farms were utilized. Performance traits studied were BW at birth, marking (when the sheep were identified with permanent ear tags at an average age of 52 d), and weaning (average age of 107 d); slaughter traits (BW at slaughter, slaughter age, carcass weight, and carcass conformation); ultrasonic muscle and fat depths; and computerized tomography-predicted carcass composition and carcass yield at weaning. Different linear mixed models, including random, direct animal effect, and up to 3 maternal effects (genetic, permanent, and temporary environmental) were used for the different traits. The PrP genotype was included in the model as a fixed effect, along with other fixed factors with significant effects (P < 0.05). Five separate analyses were carried out for each trait, differing in the method of PrP genotypic classification. The first analysis was based on classifying the sheep into categories according to all 9 available PrP genotypes. In the other 4 analyses, sheep were categorized according to the number of each PrP allele carried. Results showed that there were no significant differences between PrP genotypes for any of the performance traits studied when all 9 genotypes were compared (first analysis). Similarly, performance of the lambs did not significantly differ between genotypes with different numbers of ARR copies. However, there were significant variations in a few traits with respect to the number of ARQ, AHQ, and VRQ alleles carried. Heterozygous lambs for the AHQ or the ARQ allele were significantly heavier at some ages than lambs of the other genotypes. Lambs carrying the VRQ allele required approximately 10 d longer finishing time (P = 0.01) and yielded carcasses approximately 0.5 kg heavier (P = 0.03) compared with noncarriers. The few significant associations found do not have a negative influence on performance when selecting against the most susceptible PrP allele (VRQ) or in favor of the most resistant one (ARR). Overall, there were no major associations of PrP genotypes with most lamb performance traits in Scottish Blackface sheep.

Analyses of lamb survival of Scottish Blackface sheep.

Scottish Blackface lamb viability records at birth, and postnatal survival from 1 day to 14 days, from 15 days to 120 days and from 121 days to 180 days were used to determine influential factors and to estimate variance components of lamb survival traits. The binary trait viability at birth was analysed using a linear model whereas the postnatal survival traits were analysed as continuous traits using a Weibull model. The data consisted of about 15 000 survival records of lambs born from 1996 to 2005 on two farms in Scotland. The models included fixed factors that had significant effects and random direct and maternal additive genetic effects and maternal litter effects for viability at birth, and sire and maternal litter effects for the postnatal survival traits. The possible effect of maternal behaviour measured around lambing on lamb survival was investigated in separate analyses. Male lambs were found to be at a higher risk of mortality than females during all periods considered. The effect of type of birth and age of dam was more important during the preweaning period than at later ages. The postnatal hazard rate was not significantly affected by the behaviour score of the dams. The genetic merit of dams had more influence on viability at birth than the genetic merit of lambs themselves. Estimates of heritability for postnatal survival traits were in the range of 0.18 to 0.33 and were significantly greater than zero. These results indicate that lamb survival can be improved through farm management practices and genetic selection. Both animal and maternal genetic effects should be considered in breeding programmes for improving viability at birth.

Genetic evaluation of dairy cattle with test-day models with autoregressive covariance structures and with a 305-d model.

This study compared genetic evaluations from 3 test-day (TD) models with different assumptions about the environmental covariance structure for TD records and genetic evaluations from 305-d lactation records for dairy cows. Estimates of genetic values of 12,071 first-lactation Holstein cows were obtained with the 3 TD models using 106,472 TD records. The compound symmetry (CS) model was a simple test-day repeatability animal model with compound symmetry covariance structure for TD environmental effects. The ARs and ARe models also used TD records but with a first-order autoregressive covariance structure among short-term environmental effects or residuals, respectively. Estimates of genetic values with the TD models were also compared with those from a model using 305-d lactation records. Animals were genetically evaluated for milk, fat, and protein yields, and somatic cell score (SCS). The largest average estimates of accuracy of predicted breeding values were obtained with the ARs model and the smallest were with the 305-d model. The 305-d model resulted in smaller estimates of correlations between average predicted breeding values of the parents and lactation records of their daughters for milk and protein yields and SCS than did the CS and ARe models. Predicted breeding values with the 3 TD models were highly correlated (0.98 to 1.00). Predicted breeding values with 305-d lactation records were moderately correlated with those with TD models (0.71 to 0.87 for sires and 0.80 to 0.87 for cows). More genetic improvement can be achieved by using TD models to select for animals for higher milk, fat, and protein yields, and lower SCS than by using models with 305-d lactation records.

Evaluation of autoregressive covariance structures for test-day records of Holstein cows: estimates of parameters.

The objective of this study was to compare test-day (TD) models with autoregressive covariance structures for the estimation of genetic and environmental components of variance for milk, fat and protein yields, and somatic cell score (SCS) in Holstein cows. Four models were compared: model I (CS model) was a simple TD repeatability animal model with compound symmetry covariance structure for environmental effects, model II (ARpe model) and model III (ARe model) had first-order autoregressive covariance structures for TD permanent or residual environmental effects, respectively, and model IV (305-d model) was a simple animal model using 305-d records. Data were 106,472 first-lactation TD records of 12,071 Holstein cows calving from 1996 through 2001. Likelihood ratio tests indicated that ARpe and ARe models fit the data significantly better than the CS model. The ARe model resulted in slightly smaller estimates of genetic variance and heritability than did the CS model. Estimates of residual variance were always smaller with the CS model than with the ARe model with the autoregressive covariance structure among TD residual effects. Estimates of heritability with different TD models were in the range of 0.06 to 0.11. The 305-d model resulted in estimates of heritability in the range of 0.11 to 0.36. The autoregressive covariance structure among TD residual effects may help to prevent bias in heritability estimates for milk, fat and protein yields, and SCS.

Genetic relationship between milk score and litter weight for Targhee, Columbia, Rambouillet, and Polypay sheep.

This study was conducted to evaluate the relationship between milk score (MS) and litter weight at 70 d (LW) for four sheep breeds in the United States. Milk score is a subjective measure of milk production used to assess milk production of range ewes when milk yield cannot be quantitatively determined. Variance components for MS and LW were estimated for each of Targhee, Columbia, Rambouillet, and Polypay breeds. Data collected from 1990 through 2000 at the U.S. Sheep Exp. Stn. in Dubois, ID, were analyzed with an animal model using REML. There were 13,900 records of MS and LW for 5,807 ewes. Records were grouped according to parity as first, second, and greater (mature), and all records (lifetime). Estimates of heritability for MS were in the range of 0.05 to 0.18 for first, 0.01 to 0.27 for second, 0.05 to 0.10 for mature, and 0.08 to 0.13 for all lifetime parity groups. Estimates of genetic correlation between MS at first and second parities ranged from 0.74 to 1.00. Similarly, mature MS was highly correlated genetically with MS at first (0.83 to 1.00) and at second (0.60 to 1.00) parities, suggesting that additive genetic value for milking ability at maturity could be evaluated as early as at first parity. Heritability estimates for LW ranged from 0.00 to 0.18 over all breeds and parity groupings. The genetic correlation between LW at first and second parity groups ranged from 0.43 to 1.00. Estimates of genetic correlation between LW at first or second parity with mature LW were mostly high and positive, except for Targhee (-0.10) and Polypay (0.14) at first parity. Litter weight for mature ewes could be improved by selection at first or second parity. Estimates of genetic correlation at first parity between MS and LW were high (1.00) for Rambouillet and Polypay, and near zero for Columbia and Targhee. At second parity, estimates of genetic correlation between MS and LW were positive and moderate for Rambouillet and Polypay but more variable for Columbia and Targhee. Estimates of genetic correlation between MS and LW were mostly positive and may be favorable with smaller estimates of standard errors using all lifetime records rather than first or second parity records. Although estimates are variable, the average of the estimates of the genetic correlation suggests that LW can be improved by selecting ewes for favorable MS.