A study on associations between PrP genotypes and meat traits in French sheep breeds

Comparison of the data mining and machine learning algorithms for predicting the final body weight for Romane sheep breed

The current study aimed to predict final body weight (weight of fourth months of age to select the future reproducers) by using birth weight, birth type, sex, suckling weight, age at suckling weight, weaning weight, age at weaning weight, and age of final body weight for the Romane sheep breed. For this purpose, classification and regression tree (CART), multivariate adaptive regression splines (MARS), and support vector machine regression (SVR) algorithms were used for training (80%) and testing (20%) sets. Different data mining and machine learning algorithms were used to predict final body weight of 393 Romane sheep (238 female and 155 male animals) were used with different artificial intelligence algorithms. The best prediction model was obtained by CART model, both training and testing set. Constructed CART models indicated that sex, suckling weight, weaning weight, age of weaning weight, and age of final weight could be used as an indirect selection measure to get a superior sheep flock on the final body weight of Romane sheep. If genetically established, the Romane sheep whose sex is female, age of final weight is over 142 days, and weaning weight is over 28 kg could be chosen for affording genetic improvement in final body weight. In conclusion, the usage of CART procedure may be worthy of reflection for identifying breed standards and choosing superior sheep for meat yield in France.

Review: A review on classical and atypical scrapie in caprine: Prion protein gene polymorphisms and their role in the disease

Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goat. It has been known for ~250 years and is characterised by the accumulation of an abnormal isoform of a host-encoded prion protein that leads to progressive neurodegeneration and death. Scrapie is recognised in two forms, classical and atypical scrapie. The susceptibility to both types of scrapie is influenced by polymorphisms of the prion protein gene (PRNP). Sheep susceptibility or resistance to classical scrapie is strongly regulated by the polymorphisms at codons 136, 154 and 171 of the PRNP. The genetic role in atypical scrapie in sheep has been defined by polymorphisms at codons 141, 154 and 171, which are associated with different degrees of risk in the occurrence of the ovine disease. Progress has been achieved in the prevention of scrapie in sheep due to efficient genetic breeding programmes based on eradication and control of the disease. In Europe, the success of these programmes has been verified by applying eradication and genetic selection plans. In general terms, the ovine selection plans aim to eliminate and reduce the susceptible allele and to enrich the resistant allele ARR. During outbreaks all susceptible animals are slaughtered, only ARR/ARR resistant rams and sheep and semi-resistant females are preserved. In the occurrence of scrapie positive goats a complete cull of the flock (stamping out) is performed with great economic loss and severe risk of extinction for the endangered breeds. The ability to select scrapie-resistant animals allows to define new breeding strategies aimed to boost genetic progress while reducing costs during scrapie outbreaks. Allelic variants of PRNP can be protective for caprine scrapie, and the knowledge of their distribution in goats has become very important. Over the past few years, the integration of genetic information on goat populations could be used to make selection decisions, commonly referred to as genetic selection. The objective of this review was to summarise the main findings of polymorphisms of the caprine prion protein (PrP) gene and to discuss the possible application of goat breeding schemes integrating genetic selection, with their relative advantages and limitations.

Association between PrP genotypes and performance traits in a Welsh Mountain flock

The UK national scrapie plan (NSP) for sheep is based on selection for the resistant ARR/ARR genotype and elimination of susceptible types of the ovine prion protein (PrP) gene. The aim of this study was to estimate the possible association of the PrP genotype and performance traits by using data from the CAMDA Welsh Mountain flock. Four alleles (ARH, ARQ, ARR and VRQ) and 10 genotypes covering all five NSP risk groups were present in the CAMDA flock. Overall, the most common allele was ARR (35.2%), and VRQ was the least common (5.4%). The commonest genotypes were ARR/ARQ (23.7%) and ARR/AHQ (23.1%). The most resistant genotype, ARR/ARR, and the most susceptible genotype, VRQ/VRQ, were found in 10.2% and 0.3%, respectively, of the population tested. The associations of PrP genotypes with weight and ultrasonically scanned traits were investigated in three analyses, the first using genotypes, the second using risk categories and the third using number of alleles. These associations were evaluated by univariate analysis of each trait using an animal model with maternal effects where appropriate, and PrP was included as a fixed effect. Selection for scrapie resistance will not adversely affect progress in the traits considered and is consistent with improvements in muscle depth.

Analysis of prion protein genotypes in relation to reproduction traits in local and cosmopolitan German sheep breeds

Due to the genetic determination of susceptibility to scrapie and other forms of transmissible spongiform encephalopathy (TSE) in sheep breeding to the less susceptible prion protein (PrP) genotype ARR/ARR was advanced within EU. In 4961 ewes of nine German sheep breeds (Coburg Fox sheep, Gray Horned Heath sheep, Merinoland sheep, Rhoen sheep, German Blackheaded Mutton sheep, Shropshire, Suffolk, Texel and White East Friesian Milk sheep) representing local and cosmopolitan breeds the reproductive traits number of lambs born, dead (including abortion at the end of pregnancy, stillbirth and death during the first 56 days post natum), weaned and rearing rate at each lambing were recorded and in 1641 of these ewes the PrP genotype was determined. A linear model was used to evaluate associations between PrP genotype and reproduction traits including the effects of PrP genotype (four classes: ewes with two, one and no copy of the ARR allele and with unknown PrP genotype), breed, interaction of PrP genotype and breed, number of lambing, lambing season and stock. Significant associations were only observed between the PrP genotype and the number of dead lambs at each lambing in Shropshire and Merinoland sheep and the rearing rate at each lambing in Shropshire. These significant associations were mainly caused by differences between animals with unknown PrP genotype and animals of the other PrP classes. In conclusion, breeding for TSE resistant sheep will not lead to a reduction in economically important reproduction traits.

Lambs with scrapie susceptible genotypes have higher postnatal survival

Background

Prion protein (PrP) alleles associated with scrapie susceptibility persist in many sheep populations even with high frequencies despite centuries of selection against them. This suggests that scrapie susceptibility alleles have a pleiotropic effect or are associated with fitness or other traits that have been subject to selection.

Methodology/Principal Findings

We genotyped all lambs in two scrapie-free Scottish Blackface sheep flocks for polymorphisms at codons 136, 154 and 171 of the PrP gene. We tested potential associations of the PrP genotype with lamb viability at birth and postnatal survival using a complementary log-log link function and a Weibull proportional hazard model, respectively. Here we show there is an association between PrP genotype, as defined by polymorphisms at codons 154 ad 171, and postnatal lamb survival in the absence of scrapie. Sheep carrying the wild-type ARQ allele have higher postnatal survival rates than sheep carrying the more scrapie-resistant alleles (ARR or AHQ).

Conclusion

The PrP genotypes associated with higher susceptibility to scrapie are associated with improved postnatal survival in the absence of the disease. This association helps to explain the existence, and in many instances the high frequency, of the ARQ allele in sheep populations.

Testing the equivalence of different ovine PrP genotypes for estimated breeding values

In this study we applied equivalence testing methods to prove the absence of differences in genetic values of ewes with different PrP genotypes. In particular, the milk production genetic value equivalence of ARR ovine prion protein (PrP) genotypes was analysed. There is no scientific evidence implying that the performances and genetic values of different PrP genotypes will be different, but it is interesting to confirm that the performance of one genotype is indistinguishable from another before starting a genetic scrapie control programme. Genotyping was performed on 204 ewes from a Spanish population of Lacaune breed. Ewes were sampled from the lower and upper tails for the distribution of estimated breeding value (EBV) for standardized lactation. The conditional probability that the number of ARR alleles contained in the group of higher EBV was larger than that found in the group of lower EBV was found to be in the interval between the true value (1/2) and two different pre-specified bounds (0.1 and 0.2). The results evidence the equivalence of ARR PrP genotypes for milk production EBV, and lead to the conclusion that the average genetic values for milk production of Lacaune flocks considered will not be affected by the selection of ewe carriers of resistance scrapie alleles (p<0.05).

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.