Molecular characterization of breeds and its use in conservation

The conservation of farm animal resources is important for coping with future breeding needs and for facilitating the sustainable use of marginal areas. The increasing availability of molecular markers for most farm animal species and the development of techniques to analyse molecular variation is widening our capacity to characterise the genetic variation of breeds. In this paper we review the most popular molecular markers used in conservation and animal breeding studies, the different measures of genetic diversity that they provide, and their application for managing within-breed genetic diversity and for setting between-breed conservation priorities. We also address the relationship between genomic and marker heterozygosity, the relationship between molecular and quantitative measures of genetic diversity, and the characterization of breeds based on non-neutral markers.     

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.     

群内遗传多样性在畜禽保种中的应用

畜禽遗传资源的保存对应对未来的育种需要和畜牧业的可持续利用是非常重要的。分子标记广泛应用于大多数畜禽品种及分子变异分析技术的发展,促进了分析品种遗传变异的能力。作者对用于度量畜禽遗传资源的群内遗传多样性评价方法及其在确定种内遗传多样性,以及保种方案中的应用进行了综述。     

畜禽遗传资源的经济价值评估

畜禽遗传资源的生物多样性的减少正在成为动物保护和品种改良研究中最受关注的问题。为了提高动物保护和育种方案的决策制定能力,各国的学者提出了许多相关的经济价值评估方法。本文从经济学角度分析了畜禽遗传资源的经济价值及其范畴,对其相关的评估方法进行了回顾。其中包括线性规划与农场模拟模型、估计研究和发展价值的动态模型以及估计育种性状需求的计量经济学模型等内容。农场规划和模拟模型已经发展得很完善,但它们需要大量的数据信息。目前最可取的方法是假设价值评估方法,当目标为获取品种的非市场经济价值时尤其如此。     

保护中国各地动物品种资源多样性

中国各地动物品种资源多样性,既是人类赖以生存与经济可持续发展的物质基础; 又是中国各族人民长期积累的宝贵财富,也是“生物经济”时代遗传工程与产业化科技创新的战略性资源。据笔者对中国中西部地区陕、川、鄂、甘、青、重庆等8省市82县(市)的特种养殖业现状实地调查研究表明:目前中国西部地区经济动物养殖种类,合计共有6动物门、17纲、 57目、106科、411种,其中药用动物资源达79科、218种。从特种养殖这一视角反映了中国动物品种资源的多样性。如何保护、开发、利用这些宝贵遗传资源,对我国综合国力的提高具有极其重要意义,为此笔者提出若干措施与建议,以促进我国动物资源保护和经济的可持续发展。     

Present status of the conservation of livestock genetic resources in Brazil

Brazil has various species of domestic animals, which developed from breeds brought by the Portuguese settlers soon after the discovery of the country. After being submitted to a long process of natural selection, these breeds present characteristics adapted to specific Brazilian environmental conditions, and are known as “criollo”, “local” or naturalized breeds. From the beginning of the 20th century, some exotic breeds, selected in temperate regions, have begun to be imported, and, although more productive, they do not have adaptive traits, such as resistance to disease and parasites found in the naturalized breeds. Even so, they gradually replaced the native breeds, to such an extent that the latter are in danger of extinction. To avoid further loss of this important genetic material, in 1983 the National Research Center for Genetic Resources and Biotechnology (Cenargen) of the Brazilian Agricultural Research Corporation (Embrapa) decided to include conservation of animal genetic resources among its priorities. The conservation activities have been conducted under the Brazilian Genetic Resources Network — Renargen, and is carried out by various research centres of Embrapa, universities and State research institutions, as well as by private farmers, with a single coordinator at national level, Cenargen. The in situ conservation of cattle, horses, buffaloes, donkeys, goats, sheep and pigs is being carried out by Conservation Nuclei, located in the animal's original habitat. Ex situ conservation is centred at the Brazilian Animal Germplasm Bank (AGB), kept at Cenargen. This is responsible for the storage of semen and embryos of various breeds of domestic animals threatened with extinction. Presently the AGB has almost 60,000 doses of semen and more than 250 embryos, as well as over 7000 DNA samples. An important challenge for this program is to increase awareness within the different segments of society in terms of the importance of the conservation of animal genetic resources. The development and evolution of Renargen and its efforts to facilitate the conservation of genetic resources of livestock in Brazil are described in this paper.     

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.     

中国家养动物多样性概况

中国家养动物物种、品种和群体数量资源丰富,包括近缘野生种在内的家养动物物种有54个,品种1943个。它们在动物农业可持续发展中发挥重要作用。随着对家养动物认识的不断深入和人们需求的多样化,不断有新的资源被发现、引入、培育出来。与此同时,由于经济利益的驱动,许多具有优良特性的地方品种遗传资源,其数量不断下降,处于濒危、甚至灭绝的境地,这种趋势应引起足够重视。为保持动物农业的可持续发展,对家养动物多样性进行深入研究和有效保护是极为必要的。     

中国牛亚科家畜遗传多样性研究及其保护

中国是世界上牛品种资源最丰富的国家之一,但同时也面临着严重威胁。本文从遗传多样性的重要性、中国牛亚科家畜遗传多样性面临的严重威胁、遗传多样性研究进展及其保护现状等方面进行了综述。     

How developments in cryobiology, reproductive technologies and conservation genomics could shape gene banking strategies for (farm) animals

Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future use, for instance to recover a lost breed, to address new breeding goals, to support breeding schemes in small populations to minimize inbreeding, and for conservation genetics and genomics research. Developments in cryobiology and reproductive technology have generated several possibilities for preserving germplasm in farm animals. Furthermore, in some mammalian and bird species, gene banking of material is difficult or impossible, requiring development of new alternative methods or improvement of existing methods. Depending on the species, there are interesting possibilities or research developments in the use of epididymal spermatozoa, oocytes and embryos, ovarian and testicular tissue, primordial germ cells, and somatic cells for the conservation of genetic diversity in farm- and other animal species. Rapid developments in genomics research also provide new opportunities to optimize conservation and sampling strategies and to characterize genome-wide genetic variation. With regard to gene banks for farm animals, collaboration between European countries is being developed through a number of organizations, aimed at sharing knowledge and expertise between national programmes. It would be useful to explore further collaboration between countries, within the framework of a European gene banking strategy that should minimize costs of conservation and maximize opportunities for exploitation and sustainable use of genetic diversity.     

The status and need for characterization of Nordic animal genetic resources

ABSTRACT

The Nordic countries are committed to conserving farm animal genetic diversity. National reports on phenotypic and genetic characterization point towards a lack of characterization for many Nordic native breeds. Little to no knowledge on the traits of the animals and their derived products leads to potential remaining untapped. The objective of this study was to provide a quantitative assessment of phenotypic and genetic characterization of Nordic native breeds, through a literature search and obtaining census data. Six species and a total of 85 breeds were included. Studies were classified according to six different categories of characterization. Results showed that a large percentage of the breeds are not characterized at all. Moreover, most breeds have extremely low census sizes. A substantial effort to increase population sizes and document characteristics of Nordic native breeds, to promote conservation and sustainable use, is needed.     

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.     

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。     

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.     

Animal medical genetics: a perspective on the epidemiology and control of inherited disorders

This perspective considers genetic disorders of domestic animal populations, in particular their epidemiology and control. Inherited disorders of animals share the same basic molecular biology as those of human beings, but they differ in their epidemiology due largely to the breed structure of the various species, human control of breeding and a greater influence of the founder effect, particularly due to extensive use of a limited number of sires, and inbreeding. Control of genetic disorders in animals is also more practical through extensive screening for disease, or heterozygous animals within defined breed populations, followed by exclusion of affected or carrier animals from breeding. This is assisted by the fact that, within a breed, many inherited monogenic disorders are associated with a single mutation. However some of the more important disorders may be inherited in a non-Mendelian manner, being influenced by multiple genes as well as environmental factors. These aspects are discussed and contrasted with similar aspects in human medical genetics.     

Developing a typology for local cattle breed farmers in Europe

Recognizing cultural diversity among local breed farmers is crucial for the successful development and implementation of farm animal genetic resources FAnGr conservation policies and programmes. In this study based on survey data collected in the EUropean REgional CAttle breeds project from six European countries, a typology of local breed farmers was designed and profiles for each of the farmer types were developed to assist these policy needs. Three main farmer types were constructed: production‐oriented, product and service‐oriented and hobby‐oriented farmers. In addition, seven subtypes were characterized under the main types: sustainable producers, opportunists, multi‐users, brand makers, traditionalists, pragmatists and newcomers. These types have many similarities to the ‘productivist’, ‘multifunctional’ and ‘post‐productivist’ farmer types. The typology not only reveals the high level of diversity among local cattle breed farmers in Europe, which presents an opportunity for the in situ conservation of animal genetic resources, but also a challenge for policy to meet the differing requirements of the farmer types.     

子午岭黑山羊种质资源现状及保护措施探讨

子午岭黑山羊是皮绒肉兼用型地方优良品种,是畜牧业发展的重要遗传资源,可提供多元化产品,是提高当地经济发展的主要物质来源之一。由于各种因素导致该品种纯种数量减少、品种退化,亟需采取有效措施进行其遗传资源的保护和研究利用。本文阐述了该品种现状、存在的问题,最后提出了保种及开发利用的建议及保种措施,为子午岭黑山羊品种保护、研究利用提供了遵循,为稳固家畜品种资源库奠定了基础。     

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco‐zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F‐statistics revealed negligible genetic differentiation (F_ST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south‐north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.     

Analyses of genetic diversity in five Canadian dairy breeds using pedigree data

The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within‐breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised.     

There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study

Selection progress must be carefully balanced against the conservation of genetic variation in small populations of local breeds. Well-defined breeding programs?with specified selection traits are rare in local pig breeds. Given the small population size,?the focus is often on the management of genetic diversity. However, in local breeds, optimum contribution selection can be applied to control the rate of inbreeding and to avoid reduced performance in traits with high market value. The aim of this study was to assess the extent to which a breeding program aiming for improved product quality in a small local breed would be feasible. We used stochastic simulations to compare 25 scenarios. The scenarios differed in?size of population, selection intensity of boars, type of selection (random selection, truncation selection based on BLUP breeding values, or optimum contribution selection based on BLUP breeding values), and heritability of?the selection trait. It was assumed that the local breed is used in an extensive system for a high-meat-quality market.?The?simulations showed that in the smallest population (300 female reproducers), inbreeding increased by 0.8% when selection was performed at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P < 0.05), but at a considerably decreased rate of inbreeding (0.7 to 1.2 vs. 2.3 to 5.7%, P < 0.01). This confirmation of the potential utilization of OCS even in small populations is important in the context of sustainable management and the use of animal genetic resources.