Failure to transmit scrapie infection by transferring preimplantation embryos from naturally infected donor sheep

The objective of the study was to examine whether or not the preimplantation embryo can act as a carrier of classic scrapie infection. The study was carried out on quarantined premises with sheep of highly susceptible scrapie genotypes. Uninfected embryos, collected from New Zealand–derived Suffolk ewes, were surgically transferred into recipient ewes that were also of New Zealand origin. Seventeen negative control lambs were born on the study premises from these embryo transfers. Thirty-nine experimental lambs were from embryos collected from naturally infected donor ewes. The experimental lambs were also born on the study premises after their surgical transfer into recipient ewes of New Zealand origin. These embryos had been collected from donor ewes in a scrapie-infected flock where the ewes were clinically sick with scrapie or developed clinical scrapie after embryo collection. All lambs were confirmed as scrapie susceptible of the ARQ/ARQ genotype. Twenty-eight experimental animals survived to the end point of the study at 5 yr of age with a mean survival of 1579 d. In the negative control group, 12 of 17 sheep survived to 5 yr of age with a mean survival of 1508 d. Postmortem examinations were carried out on all animals derived by embryo transfer, and in none was histologic or immunohistochemical evidence of scrapie found. In contrast, in the originating flock the majority of scrapie cases occurred in ARQ/ARQ genotyped animals where a 56% mortality from scrapie had been recorded in animals of this genotype. Thus, the study provides no evidence for transmission of scrapie and reinforces published evidence that vertical transmission of scrapie may be circumvented by embryo transfer procedures.     

Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny

Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny).     

Epidemiological Characteristics of Classical Scrapie Outbreaks in 30 Sheep Flocks in the United Kingdom

Background

Most previous analyses of scrapie outbreaks have focused on flocks run by research institutes, which may not reflect the field situation. Within this study, we attempt to rectify this deficit by describing the epidemiological characteristics of 30 sheep flocks naturally-infected with classical scrapie, and by exploring possible underlying causes of variation in the characteristics between flocks, including flock-level prion protein (PrP) genotype profile. In total, the study involved PrP genotype data for nearly 8600 animals and over 400 scrapie cases.

Methodology/Principal Findings

We found that most scrapie cases were restricted to just two PrP genotypes (ARQ/VRQ and VRQ/VRQ), though two flocks had markedly different affected genotypes, despite having similar underlying genotype profiles to other flocks of the same breed; we identified differences amongst flocks in the age of cases of certain PrP genotypes; we found that the age-at-onset of clinical signs depended on peak incidence and flock type; we found evidence that purchasing infected animals is an important means of introducing scrapie to a flock; we found some evidence that flock-level PrP genotype profile and flock size account for variation in outbreak characteristics; identified seasonality in cases associated with lambing time in certain flocks; and we identified one case that was homozygous for phenylalanine at codon 141, a polymorphism associated with a very high risk of atypical scrapie, and 28 cases that were heterozygous at this codon.

Conclusions/Significance

This paper presents the largest study to date on commercially-run sheep flocks naturally-infected with classical scrapie, involving 30 study flocks, more than 400 scrapie cases and over 8500 PrP genotypes. We show that some of the observed variation in epidemiological characteristics between farms is related to differences in their PrP genotype profile; although much remains unexplained and may instead be attributed to the stochastic nature of scrapie dynamics.     

Estimating myostatin gene effect on milk performance traits using estimated gene content for a large number of non-genotyped cows

The objective of this study was to estimate the myostatin (mh) gene's effect on milk, protein and fat yield in a large heterogeneous cow population, of which only a small portion was genotyped. For this purpose, a total of 13 992 889 test-day records derived from 799 778 cows were available. The mh gene effect was estimated via BLUP using a multi-lactation, multi-trait random regression test-day model with an additional fixed regression on mh gene content. As only 1416 animals, (of which 1183 cows had test-day records) were genotyped, more animals of additional breeds with assumed known genotype were added to estimate the genotype (gene content) of the remaining cows more reliably. This was carried out using the conventional pedigree information between genotyped animals and their non-genotyped relatives. Applying this rule, mean estimated gene content over all cows with test-day records was 0.104, showing that most cows were homozygous +/+. In contrast, when gene content estimation was only based on genotyped animals, mean estimated gene content over all cows with test-day records was with 1.349 overestimated. Therefore, the applied method for gene content estimation in large populations needs additional genotype assumptions about additional animals representing genetic diversity when the breed composition in the complete population is heterogeneous and only a few animals from predominantly one breed are genotyped. Concerning allele substitution effects for one copy of the 'mh' gene variant, significant decreases of -76.1 kg milk, -3.6 kg fat and -2.8 kg protein/lactation were obtained on average when gene content estimation was additionally based on animals with assumed known genotype. Based on this result, knowledge of the mh genotypes and their effects has the potential to improve milk performance traits in cattle.     

Quantitative estimation of genetic risk for atypical scrapie in French sheep and potential consequences of the current breeding programme for resistance to scrapie on the risk of atypical scrapie

Background

Since 2002, active surveillance programmes have detected numerous atypical scrapie (AS) and classical scrapie cases (CS) in French sheep with almost all the PrP genotypes. The aim of this study was 1) to quantify the genetic risk of AS in French sheep and to compare it with the risk of CS, 2) to quantify the risk of AS associated with the increase of the ARR allele frequency as a result of the current genetic breeding programme against CS.

Methods

We obtained genotypes at codons 136, 141, 154 and 171 of the PRNP gene for representative samples of 248 AS and 245 CS cases. We used a random sample of 3,317 scrapie negative animals genotyped at codons 136, 154 and 171 and we made inferences on the position 141 by multiple imputations, using external data. To estimate the risk associated with PrP genotypes, we fitted multivariate logistic regression models and we estimated the prevalence of AS for the different genotypes. Then, we used the risk of AS estimated for the ALRR-ALRR genotype to analyse the risk of detecting an AS case in a flock homogenous for this genotype.

Results

Genotypes most at risk for AS were those including an AFRQ or ALHQ allele while genotypes including a VLRQ allele were less commonly associated with AS. Compared to ALRQ-ALRQ, the ALRR-ALRR genotype was significantly at risk for AS and was very significantly protective for CS. The prevalence of AS among ALRR-ALRR animals was 0.6‰ and was not different from the prevalence in the general population.

Conclusion

In conclusion, further selection of ALRR-ALRR animals will not result in an overall increase of AS prevalence in the French sheep population although this genotype is clearly susceptible to AS. However the probability of detecting AS cases in flocks participating in genetic breeding programme against CS should be considered.     

Implications of Conflicting Associations of the Prion Protein (PrP) Gene with Scrapie Susceptibility and Fitness on the Persistence of Scrapie

Background

Existing mathematical models for scrapie dynamics in sheep populations assume that the PrP gene is only associated with scrapie susceptibility and with no other fitness related traits. This assumption contrasts recent findings of PrP gene associations with post-natal lamb survival in scrapie free Scottish Blackface populations. Lambs with scrapie resistant genotypes were found to have significantly lower survival rates than those with susceptible genotypes. The present study aimed to investigate how these conflicting PrP gene associations may affect the dynamic patterns of PrP haplotype frequencies and disease prevalence.

Methodology/Principal Findings

A deterministic mathematical model was developed to explore how the associations between PrP genotype and both scrapie susceptibility and postnatal lamb mortality affect the prevalence of scrapie and the associated change in PrP gene frequencies in a closed flock of sheep. The model incorporates empirical evidence on epidemiological and biological characteristics of scrapie and on mortality rates induced by causes other than scrapie. The model results indicate that unfavorable associations of the scrapie resistant PrP haplotypes with post-natal lamb mortality, if sufficiently strong, can increase scrapie prevalence during an epidemic, and result in scrapie persisting in the population. The range of model parameters, for which such effects were observed, is realistic but relatively narrow.

Conclusions/Significance

The results of the present model suggest that for most parameter combinations an unfavourable association between PrP genotype and post-natal lamb mortality does not greatly alter the dynamics of scrapie and, hence, would not have an adverse impact on a breeding programme. There were, however, a range of scenarios, narrow, but realistic, in which such an unfavourable association resulted in an increased prevalence and in the persistence of infection. Consequently, associations between PrP genotypes and fitness traits should be taken into account when designing future models and breeding programmes.     

Prion protein (PrP) gene polymorphism in Red Maasai and Black Head Persian sheep breeds in Tanzania: Consistent profile regardless of locations

The status of scrapie in Africa is largely unknown. The susceptibility to scrapie and its pathology is determined by amino acid polymorphisms at positions 136 (A/V), 154 (R/H) and 171 (Q/R/H) of the ovine PrP gene (PrP genotype) of the animals. Despite the widely studied PrP gene polymorphisms worldwide, limited data is available on PrP genotypes of sheep from the African continent. Previously, we have reported six PrP genotypes derived from four different alleles in Red Maasai and Black Herd Persian (BHP), the ARQ/ARQ genotype being more frequent in the Red Maasai than in the BHP sheep. The highly susceptible VRQ allele was not found in any of the sheep breeds; the ARR allele was absent in the Red Maasai or occurred at a low frequency in the BHP. The lack of the highly susceptible VRQ alleles among Tanzanian sheep examined, necessitated further examinations on genetic susceptibility in sheep of the same breeds, but originating from an entirely different part of Tanzania. Consistently, ARQ/ARQ genotype was observed in 88% of Red Maasai and 64% of BHP sheep, ARQ/AHQ genotype was present in 12% in Red Maasai and 36% in BHP. Neither the highly resistant (ARR/ARR), nor the highly susceptible (VRQ/VRQ) genotypes were found. The ARQ and AHQ were the only alleles observed. The ARQ allele constituted 94%, 82% and 67% in the Red Maasai, BHP and cross-bred sheep, respectively. The AHQ constituted 6%, 18% and 33%, respectively. Data reported here, provide additional information on genetic susceptibility of the Red Maasai, BHP and their crosses; they may be helpful in policy formulation for future prevention of scrapie.     

Is there a relationship between prion protein genotype and ovulation rate and litter size in sheep?

The identification of an association between polymorphisms of the prion protein (PrP) gene and susceptibility to scrapie has enabled the development of breeding programmes to increase natural resistance to scrapie. It is, however, imperative to identify if such selection would affect important reproduction and production traits. The objective of this study was to determine if there is a relationship between polymorphisms at codons 136, 154 and 171 of the PrP gene and ovulation rate or litter size in sheep. Data were collected from a mixed-aged flock of Belclare ewes, over a 9-year period. Ovulation rate was determined annually using laparoscopy by counting the number of corpora lutea at each of two consecutive oestrous cycles, one immediately before and one after mating (2418 records from 366 ewes). Litter size was recorded at parturition (875 records from 353 ewes). The five common PrP alleles were present in the population and 14 PrP genotypes were represented among the animals studied. There was no significant overall effect of PrP genotype on ovulation rate or litter size and pairwise comparisons among genotypes did not reveal any significant differences for either trait. These data suggest that breeding programmes based on selection for specific polymorphisms of the PrP gene will not influence ovulation rate or litter size, at least in the breed studied.     

Lack of Prion Accumulation in Lymphoid Tissues of PRNP ARQ/ARR Sheep Intracranially Inoculated with the Agent of Scrapie

Sheep scrapie is a transmissible spongiform encephalopathy that can be transmitted horizontally. The prion protein gene (PRNP) profoundly influences the susceptibility of sheep to the scrapie agent and the tissue levels and distribution of PrP^Sc in affected sheep. The purpose of this study was to compare the survival time and PrP^Sc tissue distribution in sheep with highly resistant and highly susceptible PRNP genotypes after intracranial inoculation of the agent of scrapie. Five sheep each of genotype VRQ/VRQ, VRQ/ARR or ARQ/ARR were inoculated. Sheep were euthanized when clinical signs of scrapie became severe. Clinical signs, microscopic lesions, and western blot profiles were uniform across genotypes and consistent with manifestations of classical scrapie. Mean survival time differences were associated with the 171 polymorphic site with VRQ/VRQ sheep surviving 18 months, whereas VRQ/ARR and ARQ/ARR sheep survived 60 and 56 months, respectively. Labeling of PrP^Sc by immunohistochemistry revealed similar accumulations in central nervous system tissues regardless of host genotype. Immunoreactivity for PrP^Sc in lymphoid tissue was consistently abundant in VRQ/VRQ, present but confined to tonsil or retropharyngeal lymph node in 4/5 VRQ/ARR, and totally absent in ARQ/ARR sheep. The results of this study demonstrate the susceptibility of sheep with the ARQ/ARR genotype to scrapie by the intracranial inoculation route with PrP^Sc accumulation in CNS tissues, but prolonged incubation times and lack of PrP^Sc in lymphoid tissue.     

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.     

Genomic evaluations with many more genotypes

Background

Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly.

Methods

Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth) of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared.

Results

Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4%) with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50,000 markers and 1.6% lower with 500,000 markers.

Conclusions

Methods to impute genotypes and compute genomic evaluations were affordable with many more markers. Reliabilities for individual animals can be modified to reflect success of imputation. Breeders can improve reliability at lower cost by combining marker densities to increase both the numbers of markers and animals included in genomic evaluation. Larger gains are expected from increasing the number of animals than the number of markers.     

The signature of scrapie: differences in the PrP genotype profile of scrapie-affected and scrapie-free UK sheep flocks.

The amino-acid sequence of the PrP protein plays an important role in determining whether sheep are susceptible to scrapie. Although the genetics of scrapie susceptibility are now well understood, there have been few studies of the PrP gene at the population level, especially in commercially farmed sheep. Here we describe the PrP genetic profiles of the breeding stock of four UK sheep flocks, comprising nearly 650 animals in total. Two flocks had been scrapie affected for about eight years and two were scrapie free. Scrapie-resistant PrP genotypes predominated in all flocks but highly susceptible genotypes were present in each case. The distribution of PrP genotypes was similar in the scrapie-affected and scrapie-free flocks. The former, however, showed a slight but significant skew towards more susceptible genotypes despite their previous losses of susceptible sheep. Surprisingly, this skew was apparent in younger, but not older, sheep. We suggest that these patterns may occur if sheep flocks destined to become scrapie affected are predisposed by a genetic profile skewed towards susceptibility. The age structure of the scrapie-affected flocks suggests that the number of losses attributable directly or indirectly to scrapie considerably exceeds that recognized by the farmers, and also that significant losses may occur even in sheep of a moderately susceptible genotype. Similar patterns were not detected in the scrapie-free flocks, indicating that these losses are associated with scrapie infection as well as genotype.     

The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD-LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD-LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD-LA was larger than when all animals had phenotypes. Missing gene contents were predicted with higher accuracy using multiple-marker iterative peeling than with using mixed model methodology, but the difference in accuracy of total EBV was negligible and mixed model methodology was computationally much faster than multiple iterative peeling. For large livestock populations it can be concluded that gene-assisted breeding value estimation can be practically best performed by regression on gene contents, using mixed model methodology to predict missing marker genotypes, combining phenotypic information of genotyped and ungenotyped animals in one evaluation. This technique would be, in principle, also feasible for genomic selection. It is expected that genomic selection for ungenotyped animals using predicted single nucleotide polymorphism gene contents might be beneficial especially for low heritable traits.     

Frequencies of PrP genotypes and their implication for breeding against scrapie susceptibility in nine Pakistani sheep breeds

Prion protein (PrP) gene of 308 sheep was genotyped to investigate polymorphisms at scrapie-associated codons 136, 154 and 171 to assess the resistance of nine different Pakistani sheep breeds to natural/typical scrapie. As a result six genotypes were established on the basis of polymorphic codons 154 and 171. The most scrapie-susceptible codon 136 (A/V) was monomorphic (A) in all breeds. Wild-type genotype ARQ/ARQ was detected with maximum prevalence ranging from 63.2% in crossbred Pak-karakul to 100% in native Buchi, Kachi and Thalli breeds. The most frequent of typical scrapie-associated genotypes was ARQ/ARR as indicated by five of nine breeds. The coding region of PrP gene of 49 animals from the total sampled was also sequenced to ascertain additional polymorphisms. Polymorphism was found in 13 animals of the six breeds in codons 101(Q/R), 112(M/T), 146(N/S) and 189(Q/L) and ten genotypes were established on the basis of these polymorphic codons. Only Hissardale possessed five of the ten genotypes. The most frequent genotype was M¹¹²ARQ/T¹¹²ARQ detected in Hissardale, Pak-karakul and Awassi, whereas genotypes ARQr²³¹/ARQr²³¹ and ARQR²³¹/ARQr²³¹ (established on the basis of silent polymorphism agg/cgg-R/R) were detected in all breeds. Some animals consisted of three polymorphisms at different PrP codons that are not common in European breeds. An infrequent double heterozygosity (c/c a/g g/t) for codon 171 resulting in a genotype R/H was also detected in three animals each one from Kajli, Hissardale and Pak-karakul. This study concludes that all native sheep breeds are poor in scrapie-resistant PrP genotypes and could contract scrapie if exposed to prions.     

No temporal trends in the prevalence of atypical scrapie in British sheep, 2002–2006

Background

So-called atypical scrapie was first identified in Great Britain (GB) in 2002 following the introduction of wide-scale scrapie surveillance. In particular, abattoir and fallen stock surveys have been carried out in GB since 2002, with a total of 147 atypical positives identified by the end of 2006. The results of these surveys provide data with which to assess temporal trends in the prevalence of atypical scrapie in sheep in Great Britain between 2002 and 2006.

Results

Using the results of abattoir and fallen stock surveys, the prevalence of atypical scrapie (percentage of samples positive) was estimated. The prevalence in the abattoir and fallen stock surveys, for all years combined, was 0.09% (95% confidence interval (CI): 0.08%–0.11%) and 0.07% (95% CI: 0.05%–0.11%), respectively. There were no significant temporal trends in either survey. Comparing the surveys' results, there were no significant differences in annual prevalence or the prevalence within PrP genotypes. For the abattoir survey, the PrP genotype with the highest prevalence was AHQ/AHQ, which was significantly higher than all other genotypes, except ARR/AHQ, AHQ/ARH and ARH/ARQ.

Conclusion

The estimated prevalence of atypical scrapie was similar in both the abattoir and fallen stock surveys. Our results indicate there was no significant temporal trend in prevalence, adding to evidence that this atypical form of scrapie may be a sporadic condition or, if it is infectious, that the force of infection is very low.

     

A Method of Screening for Genes of Major Effect

This paper describes a method for screening animal populations on an index of calculated probabilities of genotype status at an unknown single locus. Animals selected by such a method might then be candidates in test matings and genetic marker analyses for major gene detection. The method relies on phenotypic measures for a continuous trait plus identification of sire and dam. Some missing phenotypes and missing pedigree information are permitted. The method is an iterative two-step procedure, the first step estimates genotype probabilities and the second step estimates genotypic effects by regressing phenotypes on genotype probabilities, modeled as true genotype status plus error. Prior knowledge or choice of major locus-free heritability for the trait of interest is required, plus initial starting estimates of the effect on phenotype of carrying one and two copies of the unknown gene. Gene frequency can be estimated by this method, but it is demonstrated that the consequences of using an incorrect fixed prior for gene frequency are not particularly adverse where true frequency of the allele with major effect is low. Simulations involving deterministic sampling from the normal distribution lead to convergence for estimates of genotype effects at the true values, for a reasonable range of starting values, illustrating that estimation of major gene effects has a rational basis. In the absence of polygenic effects, stochastic simulations of 600 animals in five generations resulted in estimates of genotypic effects close to the true values. However, stochastic simulations involving generation and fitting of both major genotype and animal polygenic effects showed upward bias in estimates of major genotype effects. This can be partially overcome by not using information from relatives when calculating genotype probabilities-a result which suggests a route to a modified method which is unbiased and yet does use this information.     

Prion protein gene polymorphisms in four goat breeds of Pakistan

Four different goat breeds (Pak-Angora, Dera Din Panah, Naachi and Teddy) of Pakistan were selected to investigate polymorphism in the prion protein gene (PrP gene) responsible for scrapie disease resistance in goats. Initially, genotyping of 187 animals of these four breeds by restriction fragment length polymorphism (RFLP) was done to see the genotype for codon 136 and 154. All the animals were monomorphic with a genotype of AARR except one animal of Teddy breed having the genotype of AARH. Sequencing of PrP gene of twenty animals representing these four goat breeds revealed two genotypes PPSSSS and PPSSPS with haplotypes PSS and PSP of PrP gene at the codon numbers 42, 138, and 240. All four breeds showed both wild type monomorphic sequence and mutant polymorphic sequences of these codons. The mutants of 42 and 138 codons translate the same amino acids as with the wild type sequences, while the mutant of codon 240 is responsible for a different amino acid translation i.e., serine to proline. In short, this study provides preliminary information about alleles and genotypes of PrP gene in four goat breeds of Pakistan.     

Association between the prion protein genotype and animal performance traits in a large multibreed sheep population

Genetic susceptibility to scrapie, a fatal disease of sheep and goats, is modulated by polymorphisms in the prion protein (PrP). Neither the frequency of the PrP genotypes nor their association with animal performance has been investigated in a large multibreed Irish sheep population. Scrapie genotypes were available on 16 416 animals; the breeds represented included purebred Belclare (733), Charollais (333), Suffolk (739), Texel (1 857), Vendeen (191), and crossbreds (12 563). Performance data on lambing, lamb and ewe performance as well as health traits were available. The association between alternative approaches of describing the PrP genotype (i.e. 15 individually called PrP genotypes, five genotype classes representing susceptibility to scrapie, or number of ARR haplotypes) and animal performance were quantified using animal linear mixed models. All 15 of the possible scrapie genotypes were detected, although the frequency differed by breed. The frequency of the five PrP haplotypes in the entire population were 0.70 (ARR), 0.15 (ARQ), 0.11 (ARH), 0.02 (AHQ) and 0.01 (VRQ); the most susceptible haplotype (VRQ) was only detected in purebred Texels and crossbreds. No association was detected between the PrP genotype of either the animal or dam and any of the lambing traits (i.e. lambing difficulty score, perinatal mortality and birth weight). With the exception of ultrasound muscle depth, no association between the PrP genotype and any of the lamb performance traits (i.e. lamb BW and carcass) was observed. Lambs carrying the category four PrP genotype (i.e. ARR/VRQ) had 1.20 (SE = 0.45) mm, 1.38 (SE = 0.12) mm, 1.47 (S = 0.25) mm shallower ultrasound muscle depth relative to lambs of the less susceptible scrapie categories of 1, 2, 3, respectively (P < 0.05). Nonetheless, no association between PrP genotype and lamb carcass conformation, the ultimate end goal of producers, was detected. Ewe litter size, body condition score or lameness did not differ by PrP genotype of the ewe (P > 0.05). For ewe mature BW, ARH/VRQ ewes differed from most other ewe PrP genotypes and were, on average, 3.79 (SE = 1.66) kg heavier than ARR/ARR genotype ewes. Lamb dag score differed by dam PrP genotype (P < 0.05), although the differences were small. Results from this study show that scrapie is segregating within the Irish sheep population, but the PrP genotype was not associated with most traits investigated and, where associations were detected, the biological significance was minimal. This suggests minimal impact of selection on PrP genotype on performance, at least for the traits investigated in the present study.     

Robust transmission/disequilibrium test for incomplete family genotypes

Several solutions have been proposed to extend the transmission disequilibrium test (TDT) to include cases with missing parental genotype. However, completion of the missing parental genotype may bias the test if the underlying missing data mechanism is informative. Furthermore, all these solutions resolve the problem of missing parental genotype, while offspring with missing genotypes are typically ignored. We propose here an extension to the TDT, called robust TDT (rTDT), able to handle incomplete genotypes on both parents and children and that does not rest on any assumption about the missing data mechanism. rTDT returns minimum and maximum values of TDT that are consistent with all the possible completions of the missing data. We also show that, in some situations, rTDT can achieve both greater power and greater significance than the popular TDT analysis of incomplete data. rTDT is applied to a database of markers of susceptibility to Crohn's disease and it shows that only 2 of the 11 markers originally associated with the phenotype do not depend on assumptions about the missing data mechanism.     

Evaluation of longevity modeling censored records in Nellore

The aim of the present study was to evaluate the prediction ability of models that cope with longevity phenotypic expression as uncensored and censored in Nellore cattle. Longevity was defined as the difference between the dates of last weaned calf and cow birth. There were information of 77 353 females, being 61 097 cows with uncensored phenotypic information and 16 256 cows with censored records. These data were analyzed considering three different models: (1) Gaussian linear model (LM), in which only uncensored records were considered; and two models that consider both uncensored and censored records: (2) Censored Gaussian linear model (CLM); and (3) Weibull frailty hazard model (WM). For the model prediction ability comparisons, the data set was randomly divided into training and validation sets, containing 80% and 20% of the records, respectively. There were considered 10 repetitions applying the following restrictions: (a) at least three animals per contemporary group in the training set; and (b) sires with more than 10 progenies with uncensored records (352 sires) should have daughters in the training and validation sets. The variance components estimated using the whole data set in each model were used as true values in the prediction of breeding values of the animals in the training set. The WM model showed the best prediction ability, providing the lowest χ² average and the highest number of sets in which a model had the smallest value of χ² statistics. The CLM and LM models showed prediction abilities 2.6% and 3.7% less efficient than WM, respectively. In addition, the accuracies of sire breeding values for LM and CLM were lower than those obtained for WM. The percentages of bulls in common, considering only 10% of sires with the highest breeding values, were around 75% and 54%, respectively, between LM–CLM and LM–WM models, considering all sires, and 75% between LM–CLM and LM–WM, when only sires with more than 10 progenies with uncensored records were taken into account. These results are indicative of reranking of animals in terms of genetic merit between LM, CLM and WM. The model in which censored records of longevity were excluded from the analysis showed the lowest prediction ability. The WM provides the best predictive performance, therefore this model would be recommended to perform genetic evaluation of longevity in this population.