Genetic diversity and historic introgression in German Angler and Red Dual Purpose cattle and possibilities to reverse introgression

Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints.     

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds.     

Genetic diversity of Swiss sheep breeds in the focus of conservation research

There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from −12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (−0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.     

The benefit of native uniqueness in a local red cattle breed from Northern Germany

During last decades, native uniqueness decreased in local livestock breeds due to the introgression of high‐yielding breeds. Recovery of native uniqueness became important because of conservation aspects regarding native genetic diversity and native traits. Thereby the expectation exists, that the relation between native uniqueness and genetic gain is contradictory. The aim of this study was to explore the influence of native uniqueness on performance traits and the total merit index in a local red cattle breed from Northern Germany. Data contained a pedigree file of 178,255 Red Dual‐Purpose cattle, 809 target genotypes and 3,581 reference genotypes from introgressed breeds. Native genetic contributions were tested for correlation with performance traits of milk yield, longevity, foundation, somatic cells, fertility and maternal calving and the total merit index. The study revealed that native uniqueness is favourably related to longevity (0.16), foundation (0.23), and somatic cells (0.08), and the total merit index (0.10). Selection on native uniqueness could probably lead to an increased longevity, udder health and genetic gain of the Red Dual‐Purpose cattle. Moreover, it was shown that the Red Dual‐Purpose cattle was not upgraded through introgression of high‐yielding breeds.     

Genetic conservation of five endangered Spanish donkey breeds

The genetic diversity of most livestock species is being reduced, and it is not possible to preserve all of these livestock breeds. In order to preserve as much of the genetic diversity as possible, we must first have a robust method of measuring genetic diversity among breeds. Three different methods of study that graphically represent relationships among breeds are presented; Weitzman's method, principal component analysis (PCA) and a neighbour‐joining tree with allele sharing. Diversity was evaluated on the basis of 15 microsatellite markers typed over a total of 513 DNA samples collected from five Spanish donkey breeds. Breed differentiation was confirmed by the clustering based on the genetic distances between individuals, which essentially grouped all individuals in discrete clusters. The genetic distance among breeds was used to measure the global diversity of the set in breeds considered, and to evaluate the marginal loss of diversity attached to each breed. The Catalana breed appeared to be the most ‘unique’ in the set considered. In addition to this, the usefulness of global evaluations of diversity using molecular markers to choose breeds is worthy of conservation.     

Genetic structure and diversity among sheep breeds in the United States: identification of the major gene pools

Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed; therefore, we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and minor breeds were included in the analysis and consisted of 666 animals from 222 producers located in 38 states. The level of within-breed genetic diversity was variable and not dependent upon status of a breed as a major or minor breed. Bayesian cluster analysis indicated the breeds were grouped more by physiological differences (meat vs. wool production) rather than geographic origin. Results suggest several actionable items to improve in situ and ex situ conservation. The results clearly identify breeds in need of increased in situ and ex situ management (e.g., Hog Island and Karakul) and allow several suggestions for in situ management of flocks. Conversely, several of the breeds appear genetically similar and therefore require less emphasis on collecting germplasm samples for the gene bank. Commercially important breeds (e.g., Rambouillet and Suffolk) were found to have substantial variation, which should enable breeders to proceed, unencumbered by genetic diversity concerns, with selection strategies that maximize profit.     

On the origin of the Slovenian Cika cattle

In 2002, it was discovered that several Cika cattle in the mountain areas of Slovenia had escaped the official policy of cross‐breeding. Here, we report a genetic characterization to assess their status as autochthonous breed. We compared genotypes for 14 microsatellite markers in 150 Cika cattle individuals with data from 16 Central European cattle breeds. We show that Cika cattle are genetically as diverse as other Eastern Alpine breeds, are more diverse than Austrian Simmental but less than the Balkan Busha cattle. STRUCTURE analysis showed Pinzgauer admixture in several individuals but also indicated a unique genetic identity for Cika. This analysis also allowed a selection of the most genetically pure Cika individuals as assessed by the panel of microsatellites. These original Cika cattle form an Eastern Alpine breed cluster together with Pinzgauer and Pustertaler cattle. Cika cattle should be considered as an authentic and valuable genetic resource, which offers clear opportunities for sustainable agriculture and landscape conservation in marginal and mountain areas.     

Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account

From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds.     

Mate selection strategies to exploit across- and within-breed dominance variation

In multi‐breed livestock populations, dominance variance is found both between and within breeds for many economically important traits. Mate selection strategies were developed to exploit both types of dominance variation simultaneously, with the aim of maximizing genetic merit of progeny. The extended super‐breed model, in which breeds are viewed as groups of related and inbred animals within a ‘super‐breed’, was used to predict individual additive and dominance effects for use in mate selection. Performance of mate selection was assessed under a range of relative values of additive and dominance variances for one generation of breeding. Mate selection on total progeny merit, including additive effects, individual dominance effects, and value of heterosis, was the optimal breeding strategy at all values of (co)variance components, with improvements in total progeny performance of up to 12.5 % over truncation selection followed by random mating when dominance variance was large relative to total genetic variance. Improvement in progeny merit from mate selection, relative to truncation selection, followed by random mating or truncation selection, followed by mate allocation, was particularly great (up to 53 %) when there was considerable heterosis. Improvements were small if dominance variance was small relative to total genetic variance, and heterosis was low. If the target population is large, full mate selection on total progeny merit is computationally demanding, and unlikely to be practical. Alternative, less computationally demanding strategies made nearly optimal selection and mating decisions at some parameter estimates. Integrating multi‐breed genetic evaluation, using a superbreed model, with mate selection provides a powerful framework for the design of breeding programmes which exploit available sources of genetic merit.     

药用价值地方鸡种动态保种的研究

通过资源调查摸清我国10个药用价值地方鸡种的保存现状,发现金阳丝毛鸡已经濒临灭绝.其他9个药用价值地方鸡种均处于正常保种状态.通过筛选的27个多态性较好的微卫星标记,检测了我国9个药用价值地方鸡种的遗传多样性.利用等位基因频率计算了各群体的遗传参数、构建了聚类图,并进行了系统发生分析.根据调查结果及遗传多样性检测数据,分析的9个药用价值地方鸡种保存状态,并提出保护建议.     

Genetic characterization of the Burlina cattle breed using microsatellites markers.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.     

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.     

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.     

The genetic diversity and structure of 18 sheep breeds exposed to isolation and selection

The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north‐western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of various phylogenetic parameters offer a reasonable explanation for underlying evolutionary forces working in the investigated island and mainland sheep breeds under variable natural and artificial selection. More than 60% of total genetic, diversity was allocated to virtually unselected Pramenka strains, and an additional 25% to native moderately selected Graue Gehoernte Heidschnucke and intensively selected Ostfriesische Milchschafe. Some economically very important breeds and strains did not contribute to a pool with maximal genetic diversity, while they play an important role in the cultural heritage of respective countries.     

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re‐established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO‐recommended microsatellites of these landraces and three phenotypically similar Nordic‐type landraces and compared these breeds with central European, Mediterranean and south‐west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south‐west Asian domestication site with a south‐east‐to‐north‐west cline that is clearly steeper than the Mediterranean east‐to‐west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land‐races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long‐horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.     

The concept of effective population size loses its meaning in the context of optimal management of diversity using molecular markers

Effective population size is a key parameter in conservation genetics. In the management of conservation programs using pedigree information, there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global pedigree-based coancestry between potential parents weighted by their contributions. When using molecular data, the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will replace the pedigree-based coancestry. However, in this situation, the concept of effective population size loses its meaning because with optimal molecular management, genetic diversity increases in early generations and therefore effective population size takes negative values. Furthermore, in the long term, the molecular effective population size does not attain an asymptotic value but it shows an unpredictable behaviour.     

Consequences for diversity when animals are prioritized for conservation of the whole genome or of one specific allele

When animals are selected for one specific allele, for example for inclusion in a gene bank, this may result in the loss of diversity in other parts of the genome. The aim of this study was to quantify the risk of losing diversity across the genome when targeting a single allele for conservation when storing animals in a gene bank. From a small Holstein population, genotyped for 54 001 SNP loci, animals were prioritized for a single allele while maximizing the genomewide diversity using optimal contribution selection. Selection for a single allele was done for five different target frequencies: (i) no restriction on a target frequency; (ii) target frequency = original frequency in population; (iii) target frequency = 0.50; (iv) target frequency of the major allele = 1 (fixation); and (v) target frequency of the major allele = 0 (elimination). To do this, optimal contribution selection was extended with an extra constraint on the allele frequency of the target SNP marker. Results showed that elimination or fixation of alleles can result in substantial losses in genetic diversity around the targeted locus and also across the rest of the genome, depending on the allele frequency and the target frequency. It was concluded that losses of genetic diversity around the target allele are the largest when the target frequency is very different from the current allele frequency.     

地方、培育、引入品种资源的保存与发展的研究进展

作者就20世纪 80年代以来我国多次畜禽资源调查的结果作了详细的介绍,报道了576个品种在近30年来的变迁情况。除了常见的马、驴、黄牛、水牛、大额牛、牦牛、绵羊、山羊、猪、鸡、鸭、鹅、特禽的品种以外,尚有7种,如骆驼、兔、梅花鹿、马鹿、水貂、貉、蜂等动物。其中地方品种426个,培育品种73个,引入品种77个。已有19个地方品种灭绝,37个受严重威胁。作者回顾了20世纪末开始应用遗传检测手段,包括个体、细胞、蛋白质和分子水平4个层次的研究进展。证明多层次综合研究才能反映品种的全貌。建议资源调查中要着重选育强度带来的影响,品种调查提纲必须周密,要以品种特征和外貌为主,与遗传分析相结合,才可能提出可行的保种和开发方案。作者论证了配子和胚胎超低温保存、DNA保存的前景,并指出与企业合作进行保种的动向,国家应长期重点加以支持。     

Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers

The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20–122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within‐breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds’ genetic distances, pair‐wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.     

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding,extensive loss of genetic diversity and lack of correlation between inbreeding and health

One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid‐20th century and comprise 5–10 generations and 1 000–50 000 individuals per pedigree over our study period of 1980–2010. We compared levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals during this period in the investigated dog breeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) based on statistics on the extent of veterinary care obtained from Sweden's four largest insurance companies for pets. We found extensive loss of genetic variation and moderate levels of recent inbreeding in all breeds examined, but no strong indication of a difference in these parameters between healthy versus unhealthy breeds over this period. Thus, recent breeding history with respect to rate of inbreeding does not appear to be a main cause of poor health in the investigated dog breeds in Sweden. We identified both strengths and weaknesses of the dog pedigree data important to consider in future work of monitoring and conserving genetic diversity of dog breeds.