PrP genotype frequencies in German breeding sheep and the potential to breed for resistance to scrapie

Genetic susceptibility to scrapie is associated with polymorphisms in three different codons of the ovine prion protein (PrP) gene (136, 154, 171). Studies of PrP genotypes linked to scrapie have revealed the resistance of homozygous PrPARR/PrPARR animals and the high risk of PrPVRQ/PrPVRQ and PrPvRQ/PrPARQ animals in scrapie-affected flocks. The selection of PrPARR/PrPARR genotypes may therefore provide a strategy for controlling clinical scrapie. The genotypes of 1361 German breeding sheep from 15 different breeds in northern Germany were determined. Apart from the wildtype allele PrPARQ, at least four mutually exclusive allelic variants were found. The greatest variability within the PrP gene was encountered in texel sheep, in which 14 PrP genotypes were found. In the important meat breeds, Suffolk, German whiteheaded mutton and German blackheaded mutton, the PrPARR allele was predominant, and in these breeds the breeding of scrapie-resistant pedigree flocks within four generations seems to be a feasible option. In the texel sheep, the German merino, the German milk and the German land sheep breeds, the frequency of the PrPARR allele was much lower, and in several breeds no homozygous rams were available for breeding purposes. In these breeds the breeding strategy would depend on the number of heterozygous rams available, but resistant pedigree flocks could be achieved within nine generations.     

Breeding for scrapie resistance in the Hungarian sheep population

The first results of the Hungarian sheep prion protein (PrP) genotyping programme are discussed in this paper. To obtain initial genotype frequency data 10 commercial (Hungarian Merino, German Mutton Merino, Merino Landschaf, German Blackheaded, Suffolk, Texel, Ile de France, Charollais, Lacaune, British Milksheep) and 4 indigenous (Gyimes Racka, Hortobágy Racka, Tsigaja, Cikta) breeds were sampled in 2003 and 2004, and the PrP genotypes were determined by microsequencing analysis with capillary electrophoresis. In all commercial breeds, a higher number of sheep were genotyped in 2005 (3648) and in 2006 (3834) within the breeding programme to increase scrapie resistance, and the estimated frequency data were compared to the initial figures to evaluate the efficiency of selection. The new developments arising from the identification of the so-called 'atypical' scrapie cases are also discussed.     

Genotyping strategies of selection candidates in livestock breeding programmes

Benefits of genomic selection (GS) in livestock breeding operations are well known particularly where traits are sex‐limited, hard to measure, have a low heritability and/or measured later in life. Sheep and beef breeders have a higher cost:benefit ratio for GS compared to dairy. Therefore, strategies for genotyping selection candidates should be explored to maximize the economic benefit of GS. The aim of the paper was to investigate, via simulation, the additional genetic gain achieved by selecting proportions of male selection candidates to be genotyped via truncation selection. A two‐trait selection index was used that contained an easy and early‐in‐life measurement (such as post‐weaning weight) as well as a hard‐to‐measure trait (such as intra‐muscular fat). We also evaluated the optimal proportion of female selection candidates to be genotyped in breeding programmes using natural mating and/or artificial insemination (NatAI), multiple ovulation and embryo transfer (MOET) or juvenile in vitro fertilization and embryo transfer (JIVET). The final aim of the project was to investigate the total dollars spent to increase the genetic merit by one genetic standard deviation (SD) using GS and/or reproductive technologies. For NatAI and MOET breeding programmes, females were selected to have progeny by 2 years of age, while 1‐month‐old females were required for JIVET. Genomic testing the top 20% of male selection candidates achieved 80% of the maximum benefit from GS when selection of male candidates prior to genomic testing had an accuracy of 0.36, while 54% needed to be tested to get the same benefit when the prior selection accuracy was 0.11. To achieve 80% of the maximum benefit in female, selection required 66%, 47% and 56% of female selection candidates to be genotyped in NatAI, MOET and JIVET breeding programmes, respectively. While JIVET and MOET breeding programmes achieved the highest annual genetic gain, genotyping male selection candidates provides the most economical way to increase rates of genetic gain facilitated by genomic testing.     

Evaluating different PrP genotype selection strategies for expected severity of scrapie outbreaks and genetic progress in performance in commercial sheep

Stochastic computer simulations were used for quantifying the effect of selecting on prion protein (PrP) genotype on the risk of major outbreaks of classical scrapie and the rate of genetic progress in performance in commercial sheep populations already undergoing selection on performance. The risk of a major outbreak on a flock was measured by the basic reproduction ratio (R₀). The effectiveness of different PrP selection strategies for reducing the population risk was assessed by the percentage of flocks with R₀ < 1. When compared with the scenario where there was no selection on PrP genotype, selection against the VRQ allele had a minimal impact on genetic progress for performance traits. However, this strategy was not sufficient to eliminate the population risk after 15 years of selection when the initial frequency of the ARR allele was relatively low. More extreme PrP selection strategies aimed at increasing the frequency of the ARR allele and decreasing the frequency of the VRQ allele led to decreases in the rate of genetic progress for performance but reduced the population risk to very low values. The reduction in genetic progress was only large when the initial ARR frequency was low and, in general, the risk of major epidemics was very small when the frequency of this allele reached 0.7.     

Genetic diversity loss due to selection for scrapie resistance in the rare Spanish Xalda sheep breed

The effect of selection for scrapie resistance on genetic variability in the rare Xalda sheep breed was studied. Pedigree information comprised 1851 animals (1444 alive) at the moment of sampling. A total of 304 reproductive (or selected for reproduction) Xalda individuals were sampled and genotyped for 14 microsatellites. Genetic variability was assessed using: gene diversity (1 − average kinship, GD), mean average relatedness (AR) and self-coancestry (c_i) at the genealogical level; and expected heterozygosity (H_e), molecular mean kinship (Mk), molecular self-coancestry (s_i) and rarefacted average number of alleles per locus (A) at the molecular level. Two breeding strategies were evaluated: a) use of only young rams with genotype ARR/ARR and young ewes with low to moderate risk (risk groups R1 to R3); b) breeding without selection for PrP genotypes. The major cause of losses of genetic variability in the Xalda breed is the drift that occurs when a new group of reproductive individuals is selected. The loss of genetic variability is small in females compared to the males, where it is considerable. However, losses at the molecular level for young females with respect to adult females were above 5%. Young male individuals also retained most of the genetic variability assessed in adult rams. Selection against susceptibility to scrapie produced additional losses of more than 2% for H_e and A when rYF individuals are considered. As regards males, the situation becomes critical because of the scant number of available ARR/ARR young rams. The consequences for the management of the Xalda breed are discussed.     

不同犊牛培育方法对育成母牦牛生长发育的影响

采用不同犊牛培育方法,分别考察对传统饲养条件和高效繁育技术条件下对后代公犊牛及育成母牛生长发育的影响。研究结果表明:与传统对照组相比,犊牛培育组犊牛成活率达到97.23%,犊牛培育组的成活率、初选合格率、复选合格率和定选合格率分别为91.67%、80.56%和77.78%,分别比传统对照组提高12.90%、13.79%、11.54%和27.26%,差异显著(P<0.05)。犊牛体高、体斜长、胸围、管围及体重显著提高,差异显著(P<0.05)。采用犊牛培育技术,后代犊牛及育成牛生长发育各项指标较对照组明显增加,有效提高牦牛种母牛培育合格率,从而为建立优良种母牛核心群提供一条切实有效的生产途径。     

不同犊牛培育方法对育成公牦牛生长发育的影响

采用不同犊牛培育方法,考察对传统饲养条件、高效繁育技术条件下对后代公犊牛及育成种公牛生长发育的影响。研究结果表明:与传统对照组相比,犊牛培育组犊牛成活率、初选合格率、复选合格率和定选合格率分别为100.00%、95.00%、87.50%和80.00%,比传统对照组分别提高17.65%、26.67%、40%和60%,差异显著(P<0.05);与培育对照组相比,犊牛培育组的犊牛成活率、初选合格率、复选合格率和定选合格率分别提高5.27%、11.77%、12.91%和18.52%,差异显著(P<0.05)。采用犊牛培育技术,后代犊牛及育成牛生长发育各项指标较对照组明显增加,有效提高牦牛种公牛培育合格率,从而为大量生产优质牦牛种公牛提供一条切实有效的生产方式。     

分子标记辅助选择及其在畜禽抗病育种中的应用

利用分子标记辅助选择是现代畜禽育种的策略之一,尤其是在畜禽抗病育种中,具有广阔的应用潜力.本文对分子标记辅助育种作了简要介绍,结合抗病育种综述了其在育种中的具体作用,并对其应用前景进行了展望.     

Trends in genotype frequency resulting from breeding for resistance to classical scrapie in Belgium (2006~2011)

In sheep, susceptibility to scrapie is mainly determined by codons 136, 154, and 171 of the PRNP gene. Five haplotypes are usually present (ARR, ARQ, ARH, AHQ, and VRQ). The ARR haplotype confers the greatest resistance to classical scrapie while VRQ renders animals most susceptible. In 2004, the European Union implemented a breeding program that promotes selection of the ARR haplotype while reducing the incidence of VRQ. From 2006 to 2011 in Belgium, frequency for the ARR/ARR genotypes increased from 38.3% to 63.8% (n = 6,437), the ARQ haplotype diminished from 21.1% to 12.9%, and the VRQ haplotype decreased from 2.0% to 1.7%. The status of codon 141, a determinant for atypical scrapie, was also evaluated. Out of 27 different breeds (n = 5,163), nine were abundant. The ARR/ARR frequency increased in eight of these nine major breeds. The selection program has had a major impact on the ARR haplotype frequency in Belgium. However, the occurrence of atypical scrapie represents a critical point for this program that warrants the continuous monitoring of scrapie. Additionally, genotype frequencies among the breeds varied greatly. Texel, a breed that is common in Belgium, can still be selected for due to its average ARR frequency.     

Merino sheep breed's genetic resistance to scrapie: genetic structure and comparison of five eradication strategies

Three thousand one hundred and ninety-three Merino-breeding males were genotyped for Scrapie-resistance gene. They showed a high frequency of ARQ allele while VRQ allele frequency, linked to the highest susceptibility, was close to 0. Alleles linked to Scrapie-susceptibility frequencies have been studied in different Merino flocks. Most of the variability is intraflock, not interflock. In addition, there is an excess of heterozygotes due to crossbreeding or Wahlund effect.

Five control and prevention strategies were studied: first genotyping males and females and eliminating VRQ carriers and ARQ/ARQ rams; second genotyping males and females and eliminating VRQ carriers; third genotyping males and eliminating VRQ carriers and ARQ/ARQ rams; fourth genotyping males and using only as breeders ARR/ARR, ARR/AHQ, AHQ/AHQ and ARQ/ARQ rams; fifth genotyping males and using only as breeders ARR/ARR, ARR/AHQ and AHQ/AHQ rams. They were simulated from allelic and genotypic frequencies to decide which animals had to be genotyped and which animals had to be eliminated due to their genotypes and risk levels. The third option, to genotype rams and to eliminate ARQ/ARQ and VRQ carriers, would be the best strategy to improve the resistance and would cause minimal cost and loss of animals.     

Genetic variability following selection for scrapie resistance in six autochthonous sheep breeds in the province of Bolzano (northern Italy)

Scrapie is an ovine transmissible spongiform encephalopathy, and its susceptibility is associated with polymorphisms in the prion protein gene (PRNP). Genetic selection is currently the most effective mean for eradication of the susceptible VRQ allele in favour of resistant ARR allele. Maintenance of genetic diversity should be one of the major objectives in breeding programmes, especially in endangered breeds, and genetic information are an excellent alternative to pedigree data where these information are missing. The aim of our study was to determine changes of genetic variability in six native sheep breeds from autonomous province of Bolzano, northern Italy, following simulation of scrapie selection scenarios. A total of 684 rams were investigated for PRNP polymorphisms and for 10 microsatellite loci to estimate genetic variability. Across all loci, a total of 163 alleles were detected with a mean of 10.4 alleles per locus. Average observed (Ho) and unbiased expected (uHe) heterozygosity overall loci were 0.74 and 0.78, respectively, showing a statistically significant deviation from Hardy–Weinberg equilibrium (HWE) in all breeds. This heterozygosity deficit was confirmed by a positive fixation index (Fis), determining a moderate inbreeding in each breed. Simulating a soft selection, where only rams having at least a VRQ allele should be excluded from reproduction, Ho, uHe and Fis values remained almost unchanged, indicating that genetic variability should not be affected by the removal of these individuals. With a mild selection scenario, considering only rams with at least one ARR allele, we observed a decrease in the mean alleles per breed (8.9) and the maintenance of heterozygosity deficiency, except for two breeds, where it was any longer significant. These results showed that selection strategies allowing use of heterozygous as well homozygous ARR rams might be the right compromise to improve resistance to scrapie and to do not dramatically affect genetic variability of these breeds.     

不同饲喂方法对种用母猪繁殖性能的影响

母猪膘情与其繁殖性能及仔猪出生成本存在密切关系,我们选用同批次、出生时间在±15d,对猪瘟、蓝耳病、伪狂犬、口蹄疫抗体检测为阴性(-)的健康后备猪30头,分为3组。在相同条件下,对3组母猪分别饲喂质量相同但重量不同的饲料来控制各组母猪的膘情,通过配种时间、母猪淘汰率、分娩情况等指标来比较各组的优劣。结果表明:后备母猪(空怀母猪)过肥过瘦都会造成很大的经济损失,过肥比过瘦更为严重。只有使后备母猪(空怀母猪)维持合理膘情(7～8成膘)才能提高母猪的繁殖性能,且每头仔猪生产成本较其他饲喂方法可降低约50元人民币。     

Quantifying diversity losses due to selection for scrapie resistance in three endangered Spanish sheep breeds using microsatellite information

The effect of selection for scrapie resistance on genetic variability in three endangered Spanish sheep breeds (Colmenareña, Mallorquina and Rubia de El Molar) was studied using two different criteria for quantifying contributions to genetic variability: (a) molecular coancestry or genetic identity; and (b) average number of alleles per locus or allelic richness. A total of 236 (81 Colmenareña, 76 Mallorquina and 79 Rubia de El Molar) individuals were genotyped for the PrP gene and for 22 microsatellite markers. The analyses assumed a selective policy aimed at the elimination of the VRQ allele and the reduction of the frequency of the ARQ/ARQ genotype. These goals are approached by rejecting for breeding those individuals with the highest susceptibility for scrapie (risk groups R4 and R5) in a genetic scenario with no previous selection programmes considering the PrP gene polymorphism carried out. When all the individuals classified into risk groups R4 and R5 were removed from the dataset, the total molecular coancestry slightly increased in the Colmenareña breed illustrating that the carriers of undesirable PrP genotypes are not essential to maintain its overall gene diversity. When the allelic richness was considered, the removal of the R4 and R5 individuals gave high losses in the Rubia de El Molar breed. The analyses carried out considering the sex of the individuals informed that most increases in genetic identity in the Colmenareña breed resulted from the removal of the R4 and R5 males while in the Mallorquina breed resulted from the removal of the undesirable females. Losses of diversity in the Rubia de El Molar breed were basically independent of the sex of the individuals due to the balanced contributions to diversity of both sexes. As a general recommendation, not all the individuals of undesirable risk groups should be rejected for reproduction at the same time to avoid irretrievable loses of genetic diversity but according to the sex of the individuals.     

Effects of a breeding scheme combined by genomic pre‐selection and progeny testing on annual genetic gain in a dairy cattle population

The effectiveness of the incorporation of genomic pre‐selection into dairy cattle progeny testing (GS‐PT) was compared with that of progeny testing (PT) where the fraction of dam to breed bull (DB) selected was 0.01. When the fraction of sires to breed bulls (SB) selected without being progeny tested to produce young bulls (YB) in the next generation was 0.2, the annual genetic gain from GS‐PT was 13% to 43% greater when h² = 0.3 and 16% to 53% greater when h² = 0.1 compared with that from PT. Given h² = 0.3, a selection accuracy of 0.8 for both YB and DB, and selected fractions of 0.117 for YB and 0.04 for DB, GS‐PT produced 40% to 43% greater annual genetic gain than PT. Given h² = 0.1, a selection accuracy of 0.6 for both YB and DB, and selected fractions of 0.117 for YB and 0.04 for DB, annual genetic gain from GS‐PT was 48% to 53% greater than that from PT. When h² = 0.3, progeny testing capacity had little effect on annual genetic gain from GS‐PT. However, when h² = 0.1, annual genetic gain from GS‐PT increased with increasing progeny testing capacity.     

Effect of selection for scrapie resistance on genetic diversity in a rare and locally adapted sheep breed: The case of Sambucana

In Italy, since 2005 a breeding plan to increase scrapie resistance has been adopted. The impact of this selection on genetic diversity was assessed on Sambucana, an autochtonous sheep breed reared in southern Piedmont, by analysing the evolution of allele frequencies at different levels: PRNP (prion protein) gene, microsatellite loci on OAR13 (where PRNR maps), and microsatellite loci on other chromosomes, not subjected to selection for scrapie resistance. A total of 147 young rams, 80 born in 2004 and 67 in 2008–2009 were analysed. Evidence of diversity loss was observed for PRNP gene as a consequence of the directional selection. Diversity was affected in the immediate vicinity of PRNP but the effect on more distant loci on the same chromosome was trivial. With regard to neutral markers, lack of heterozygosis with no changeover of allele frequencies was observed suggesting an increase of inbreeding. Mating policies would be sufficient to solve these problems. A selection scheme based on genotyping rams and eliminating carriers of both susceptible and high susceptible alleles is the best way to improve natural resistance to scrapie with low costs and minimal problems in the current conservation programmes targeting rare breeds.     

家兔选育性状典型相关分析

选择日本大耳白和新西兰两个品种家兔的生长、繁殖、以及体尺3组共17个性状，应用多元统计方法进行了典型相关分析，结果表明；日本大耳白兔的初生重、初生窝重、21日龄重、泌乳力、胸围等5个性状，新西兰兔的产活仔数、初生重、21日龄重、泌乳力、断奶窝重、母兔体重等6个性状为主要性状。     

The impact of the genotype on the prevalence of classical scrapie at population level

ABSTRACT: Total number and genotypes of animals in holdings selected for the genotype & cull option in the Compulsory Scrapie Flock Scheme (CSFS) in Great Britain were extracted from the National Scrapie Plan data warehouse. The association between various genotype-related measures and scrapie prevalence infection was tested using zero-inflated negative binomial models with the counts of positive cases as dependent variable, and country, number of flocks in the scheme, flock size, surveillance source and the following genotype-related measurements: the centered-log ratios (clr) oof the 15 genotypes, of the proportions of the 5 alleles at codons 136, 154 and 171, of the proportions of the 5 NSP types, and two flock-susceptibility risk indicators, as explanatory variables. A total of 319341 genotyped animals from 168 holdings were included in the analysis. An increased proportion of the ARR/ARR genotype corresponded to a decrease in the number of scrapie cases. ARR/AHQ, AHQ/VRQ, ARH/VRQ and ARQ/VRQ genotypes, NSP type V, ARH, ARQ, AHQ and VRQ alleles and the low and high-susceptibility risk indicators are all associated with an increase risk in the number of scrapie cases.Regardless the management practices; the increased susceptibility that the non-ARR alleles confer on an individual could be extrapolated at the population level. Increasing prevalence of ARR allele reduces the overall risk of scrapie at population level. At genotype level, the VRQ/VRQ genotype, present a very low frequency in the study population, seems to play a residual effect in the overall risk of scrapie in a flock.     

Monte Carlo simulation of surveillance strategies for scrapie in Norwegian sheep

Our aim was to compare the efficiency of different surveillance strategies for detecting scrapie-infected sheep flocks in the Norwegian population using simulation modelling.The dynamic Monte Carlo simulation model has the flock as the unit. The input parameters include properties of the sheep population (number of flocks, flock size, age distribution, reasons for culling, breeds, prion protein-allele distribution); properties of scrapie (genotype-dependent infection rate and incubation periods, and age- and genotype-dependent prevalence of scrapie); properties of the surveillance strategy (selection of sheep for examination, period in which infected sheep are detectable, and properties of the diagnostic tests). For simplification, the prion protein-alleles were grouped into three allele groups: VRQ, ARR, and ARQ' (ARQ' represents ARQ, ARH and AHQ).Through either abattoir surveillance or surveillance of fallen stock, 70% of the detected sheep (compared to 33% in the underlying population). The model output was sensitive to the susceptibility of infection for the genotype ARQ'/ARQ'. The effect was large for abattoir surveillance (increased susceptibility increased the efficiency of abattoir surveillance).