Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (H_o) and expected (H_e) heterozygosity, individual coancestry coefficients (f and f_m), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (f_a), effective population size (N_e and N_e(m)) and founder genome equivalents (N_g and N_g(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (f_m, Mk and N_g(m)). However, H_o and H_e showed the highest values for C1 and the molecular heterozygote deficiency within population (F_IS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f_(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.     

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.     

Genetic variability in the endangered Asturcón pony assessed using genealogical and molecular information

The aim of this analysis is to assess the genetic diversity in the black-coated Asturcón pony population using genealogical and molecular methods in order to ascertain the possible impact of the inclusion of the bay Asturcón individuals on the breed's recovery programme. Pedigree information registered in the studbook of the black-coated Asturcón (including a total of 1080 individuals) was analysed. Additionally, 261 blood samples from the black-coated Asturcón individuals were obtained and genotyped for 15 microsatellites. Furthermore, 58 blood samples were obtained and genotyped from bay Asturcón individuals in order to place the results within the context of an unselected population with no known genealogies. The results indicated high losses of genetic representation of founders in the present population of black-coated Asturcón ponies. Roughly 60% and 30% of the founder stallion and dam lines, respectively, are lost in the present population. Average inbreeding was 4.7%. The equivalent number of founders and equivalent number of ancestors were 18.1 and 13. The most relevant founders and ancestors identified belonged to the three major studs involved in the recovery of the breed. However, the results highlight the dependence of the breed on the management of the government-run Cayón stud, which has increased its genetic contribution to the breed over time from 35.6% to 50.1%. At a molecular level, genetic variability assessed in the black-coated Asturcón was lower than that observed in the bay Asturcón. Expected heterozygosity, F_IS(m) and rarefacted average number of alleles per locus were 0.755 and 0.828, 4.1% and 1.3%, and 9.5 and 9.2, respectively, for the black-coated and bay Asturcón. The expected molecular coancestry in the black-coated Asturcón base population (Ef₀) took a value of 0.229, which was near to the molecular coancestry computed in the bay Asturcón (0.231). Implications of the reported results in the recovery programme of the Asturcón pony breed are discussed.     

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.     

Genetic diversity in Polish hounds estimated by pedigree analysis

Data from 247 litters of Polish hounds born at 105 kennels between 1960 and 2004 was analysed in order to evaluate the genetic variability of the breed. The breed originated from 19 founders and the founder genome equivalent ranged from 2.043 to 1.287 over the span of forty-four years of breeding. The high imbalance of founder contributions to the gene pool was noted, with the dominant contribution of four founders. The low number of the founders and the high disproportion of particular dogs in breeding use resulted in the increasing value of inbreeding coefficient which ranged from 0.0771 to 0.370. The poor gene pool seems to be strictly connected to the deteriorating health of the population which draws into question the future of the breed.     

Selection for scrapie resistance and simultaneous restriction of inbreeding in the rare sheep breed "Mergellander"

Scrapie is a fatal infectious neurodegenerative disease for which susceptibility is associated with polymorphisms in the ovine prion protein (PrP) gene. Scrapie-eradication programmes are based on eliminating the susceptible VRQ allele and/or breeding for the resistant ARR allele. In rare breeds or breeds with a low frequency of the ARR allele this can lead to unacceptably high inbreeding rates with associated increased risk of genetic defects and inbreeding depression. The conservation status of populations with inbreeding rates (DeltaF) above 1% is considered critical. In the Dutch rare sheep breed the Mergellander animals carrying ARR alleles are closely related to one another, and could reach 1.53% when only ARR/ARR animals are used as parents. Inbreeding rates can be reduced by selecting the set of parents according to their average co-ancestry. We minimised inbreeding rates by calculating the optimal contribution of each ram and selection of ewes. This resulted in inbreeding rates of -0.17% with exclusive use of homozygous ARR rams, and -0.38% if use of heterozygous rams was allowed as well. Thus sophisticated breeding programs can prevent unacceptably high inbreeding rates when breeding for scrapie resistance.     

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.     

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.     

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.     

Protective effect of the AT137RQ and ARQK176 PrP alleles against classical scrapie in Sarda breed sheep

The susceptibility of sheep to scrapie is under the control of the host’s prion protein (PrP) gene and is also influenced by the strain of the agent. PrP polymorphisms at codons 136 (A/V), 154 (R/H) and 171 (Q/R/H) are the main determinants of susceptibility/resistance of sheep to classical scrapie. They are combined in four main variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programmes have been undertaken on this basis in the European Union and the USA to increase the frequency of the resistant ARR allele in sheep populations. Herein, we report the results of a multi-flock study showing the protective effect of polymorphisms other than those at codons 136, 154 and 171 in Sarda breed sheep. All ARQ/ARQ affected sheep (n = 154) and 378 negative ARQ/ARQ controls from four scrapie outbreaks were submitted to sequencing of the PrP gene. The distribution of variations other than those at the standard three codons, between scrapie cases and negative controls, was statistically different in all flocks. In particular, the AT₁₃₇RQ and ARQK₁₇₆ alleles showed a clear protective effect. This is the first study demonstrating a protective influence of alleles other than ARR under field conditions. If further investigations in other sheep breeds and with other scrapie sources confirm these findings, the availability of various protective alleles in breeding programmes of sheep for scrapie resistance could be useful in breeds with a low frequency of the ARR allele and would allow maintaining a wider variability of the PrP gene.     

Genetic study on pelt quality traits in the Gotland sheep breed

Abstract

Genetic parameters were estimated for pelt quality traits of the Gotland sheep breed using data from the Swedish Sheep Recording Scheme and multiple-trait animal models. Data on detailed pelt quality traits were available for 51,455 lambs born from 1991 to 2003. For 4,771 lambs there also was information about a subjectively measured overall score for pelt quality. Sex of lamb, age of ewe, litter size, age of lamb, and interactions between these had significant effects on pelt quality. Heritabilities were moderately high (0.20 to 0.48) and genetic correlations between the traits were low to highly positive (?0.18 to 0.95). Breeding for an increased overall score will in the short term improve score for quality of hair, score for curl, and score for nuance of colour. Size of curl and score for thickness of fleece may also increase and this is not always advantageous as these are traits with optimum values.     

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.     

Genetic relationships between pelt quality, maternal ability, and lamb production in the Gotland sheep breed

The aim of the present investigation was to study the genetic relationships between pelt quality traits (shade of fleece, size of curl, score for fleece colour, score for curl, score for quality of hair, score for thickness of fleece, sum of pelt scores, and overall score) on one hand and maternal ability, live weight, and carcass traits on the other hand for the Gotland sheep breed. Data were received from the Swedish Sheep Recording Scheme and included observations on 4-month weight (4MW) and pelt quality for 51,402 lambs and on weight (CW), fatness (FAT), and fleshiness (FLESH) of the carcass for 12,440 lambs. The lambs were born during the period 1991–2003. When maternal genetic and permanent environmental effects were included in the model direct heritabilities for the pelt quality traits varied between 0.16 and 0.25. Maternal heritabilities (0.01 to 0.05) and common environmental variances as a fraction of the total phenotypic variances (0.07 to 0.10) were low. Maternal heritabilities were higher for 4MW (0.11) and CW (0.12) than for the pelt quality traits. Direct-maternal genetic correlations were both for the pelt quality traits and for 4MW and CW generally negative and low to medium high. Direct genetic correlations between pelt quality traits on one hand and 4MW, CW, FAT or FLESH on the other hand were low (− 0.16 to 0.12). Maternal genetic correlations between pelt quality traits and 4MW or CW were positive and high (0.38 to 0.96). It was concluded that breeding for increased growth and improved carcass quality would not influence pelt quality negatively or vice versa. If maternal genetic effects are considered for 4MW and CW in the breeding program for the Gotland sheep breed, selection for maternal effects on 4MW and CW will have positive effects both on lamb weight and pelt quality.     

中国野牦牛种质资源库体系的建立及利用

介绍构建野牦牛种质资源信息收集、整理及调查的方法;建立了野牦牛50头规模的可良性运作的遗传繁育基地，可年产2万支冷冻精液的动态保存库，以及0.1万～0.15万枚野牦牛冷冻胚胎动态保存库的条件与规模;创建了国内外相关野生动物保护组织、行业、协会等保护和利用野牦牛遗传资源的共享平台.     

Genetic diversity in an indigenous horse breed: implications for mating strategies and the control of future inbreeding

The Franches-Montagnes is an indigenous Swiss horse breed, with approximately 2500 foalings per year. The stud book is closed, and no introgression from other horse breeds was conducted since 1998. Since 2006, breeding values for 43 different traits (conformation, performance and coat colour) are estimated with a best linear unbiased prediction (BLUP) multiple trait animal model. In this study, we evaluated the genetic diversity for the breeding population, considering the years from 2003 to 2008. Only horses with at least one progeny during that time span were included. Results were obtained based on pedigree information as well as from molecular markers. A series of software packages were screened to combine best the best linear unbiased prediction (BLUP) methodology with optimal genetic contribution theory. We looked for stallions with highest breeding values and lowest average relationship to the dam population. Breeding with such stallions is expected to lead to a selection gain, while lowering the future increase in inbreeding within the breed.     

Genetic variability of the resistance for three types of enteropathy in the growing rabbit

This paper describes the genetic variability for the resistance to three digestive stresses in the growing rabbit: after inoculation of coccidia (trial “coccidia”), with a fibre deficient diet (trial “FD”), and after experimental reproduction of epizootic rabbit enteropathy (trial “ERE”). Genetic variability was analysed from a sample of 48 sires, which produced the experimental young rabbits. These animals were examined on D0, D4, D11, D18, D25 and D32 after weaning (at 30 days old). Three clinical symptoms were checked: bloated abdomen, diarrhoea and mucus. Mortality and clinical symptoms were used to assess an individual response to each digestive stress. Two binary indexes were defined to describe this rabbit individual response. The first one (“Alive”) dealt with mortality. The second (“Tolerant”) dealt with mortality and morbidity. “Alive”, and “tolerant” percentages were low for the “coccidia” trial (61% and 23% respectively), high for the “FD” trial (75% and 36% respectively) and intermediate for the “ERE” trial (66% and 37% respectively). The sire effect was significant for each index in the “coccidia” and the “FD” trials. The sire effect was significant for the “tolerant” index in the “ERE” trial. Correlations between sire rankings for the two indexes of one trial were often significant. Correlations between sire rankings for indexes of “coccidia” and “FD” trials were weakly significant. Our results demonstrate that there is a genetic variability for the resistance to three different enteropathies.     

Genetic control of the environmental variance for birth weight in seven generations of a divergent selection experiment in mice

Data from seven generations of a divergent selection experiment designed for environmental variability of birth weight were analysed to estimate genetic parameters and to explore signs of selection response. A total of 10 783 birth weight records from 638 females and 1127 litters in combination with 10 007 pedigree records were used. Each record of birth weight was assigned to the mother of the pup in a heteroscedastic model, and after seven generations of selection, evidence of success in the selection process was shown. A Bayesian analysis showed that success of the selection process started from the first generation for birth weight and from the second generation for its environmental variability. Genetic parameters were estimated across generations. However, only from the third generation onwards were the records useful to consider the results to be reliable. The results showed a consistent positive and low genetic correlation between the birth weight trait and its environmental variability, which could allow an independent selection process. This study has demonstrated that the genetic control of the birth weight environmental variability is possible in mice. Nevertheless, before the results are applied directly in farm animals, it would be worth confirming any other implications on other important traits, such as robustness, longevity and welfare.     

Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.     

Evaluation of different enzyme-linked immunosorbent assays for the diagnosis of brucellosis due to Brucella melitensis in sheep

Six serological assays for the diagnosis of ovine brucellosis, due to Brucella melitensis were evaluated. Reference serum samples from sheep of known B. melitensis infection status (n = 118) were assessed using the Rose Bengal test (RBT), complement fixation test (CFT) and four commercial enzyme-linked immunosorbent assays (ELISAs), including two indirect ELISAs (iELISAs), one competitive ELISA (cELISA) and one blocking ELISA (bELISA).The highest differential positive rates (DPR) were obtained with the cELISA and bELISA, while the lowest DPR was estimated using iELISAs. A latent class analysis was performed to estimate the accuracy of the CFT, RBT and bELISA using 1827 sera from sheep undergoing testing as part of a surveillance and control programme. Lower sensitivity and specificity were obtained for the three serological tests when the field samples were used. A higher DPR was achieved by the CFT, compared to bELISA and RBT. The results suggest that ELISAs, and particularly the bELISA, might be suitable for inclusion in the European Union legislation on intra-community trade for diagnosing B. melitensis infection in sheep, as it has a similar test performance compared to the RBT.     

Genetic selection for resistance to mycoplasmal pneumonia of swine (MPS) in the Landrace line influences the expression of soluble factors in blood after MPS vaccine sensitization

We recently developed a Landrace line that is resistant to mycoplasmal pneumonia of swine (MPS) infection by genetic selection for five generations, and we reported that the immunophenotype of this line is different from that of the non‐selected line in terms of changes in peripheral blood leukocyte population after MPS vaccination. This study followed up previous findings demonstrating changes in soluble factors in blood, namely, hormones, Mycoplasma hyopneumoniae‐specific immunoglobulin G (IgG), and cytokines. These two lines were injected with MPS vaccine on days ?7 and 0 after blood sampling on those days, and blood samples were collected on days ?14, ?7, 0, 2, 7 and 14. We found changes in the levels of many hormones and cytokines in both lines. However, we found that only growth hormone (GH) and interferon (IFN)‐γ levels were statistically different between these two lines. GH concentration was reduced (day 0) and IFN‐γ concentration was increased (day 14) in the MPS‐selected line compared with the non‐selected line, despite unchanged IFN‐γ messenger RNA expression in blood cells. Although detailed mechanisms underlying these phenotypes remain unsolved, these traits would be useful to improve MPS resistance in pig production and provide an insight into MPS infection.