Genetic diversity in Swiss cattle breeds

Introduction First attempts at establishing the genetic relationships among cattle populations relied on archeological evidence (Epstein 1971; Epstein and Mason 1984) and protein polymorphisms (Baker and Manwell 1980, 1991). Loftus et al. (1994) examined mitochondrial DNA to determine the divergence time between Bos taurus and Bos indicus. Today most studies on genetic diversity are based on microsatellite analysis (Litt and Luty 1989; Tautz 1989; Weber and May 1989). Microsatellites were used in, e.g. man (Bowcock et al. 1994), canids (Roy et al. 1994; Fredholm and Winter ø ; 1995) and sheep (Buchanan et al. 1994). Recent studies in cattle are also microsatellite based (e.g. Machugh et al. 1994; Ciampolini et al. 1995; Moazami -Goudarzi et al. 1997) and aim at facilitating the development of management programs for endangered breeds (FAO 1981). Our microsatellite-based investigation on the genetic diversity between and within Swiss cattle breeds included Original Swiss Brown, purebred Simmental, Holstein, Hérens and Evolènard. Previous studies in Swiss breeds made use of blood group systems (Reuse 1969), serum transferrin and hemoglobin (Krummen 1964), amylase (Buser 1970) and carboanhydrases (Kä ;stli et al. 1980). The Hérens breed is endemic to the canton of Wallis. The Evolènard, which are very few in numbers and restricted to a single valley in the canton of Wallis, are phenotypically very similar to the Hérens with the exception of the coat colour. In the Aosta valley (Italy) which borders the canton of Wallis these two breeds find their counterparts. The phenotype of the Aosta Chestnut fits the Hérens and the Aosta Black Pied fits the Evolènard. The Holstein breed replaced the Fribourg breed which was a colour variant of the purebred Simmental breed (Engeler et al. 1961) and is now extinct. The Original Swiss Brown and the purebred Simmental are endemic to Switzerland.     

Molecular genetic characterization of ovine β-lactoglobulin C allele and detection by PCR-RFLP

Introduction β-Lactoglobulin (LGB), the major whey protein in sheep, consists of 162 amino acids and forms stable dimers in milk. Apart from its ability to bind and transport small hydrophobic molecules in milk, e.g. retinol and small fatty acids, its biological function is still unclear (Godovac -Zimmermann et al. 1985; Mac Leod et al. 1996). A positive effect on the digestion of milk lipids has been suggested (Perez et al. 1992). In nonruminant species two different forms, LGB I and II, are found, but in the milk of cattle, sheep and goat only one LGB is expressed. An LGB-pseudogene, lacking an active promotor was characterized by Passey and Mackinlay (1995). The deduced amino acid sequence is closely related to LGB II found in cat and horse, while the expressed LGB corresponds to LGB I. The LGB-pseudogene was mapped close to the LGB genes in cattle, goat and sheep (Passey and Mackinlay 1995; Folch et al. 1996). Three allelic variants (A, B and C) of ovine LGB can be discriminated using different electrophoretic techniques. Variants A and B are present in all breeds and differ by a Tyr/His substitution in position 20 (Kolde and Braunitzer , 1983) corresponding to a single nucleotide substitution in the LGB gene (Ali et al. 1990). A molecular genetic test for the differentiation of the A and B alleles by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) (RsaI) was developed (Schlee et al. 1993). The C variant was described first in 1989 in German Merinoland sheep at a frequency of 0.175 and in Hungarian Merino crosses (Erhardt 1989). In Spanish Merinos the C allele was found at low frequencies (0.013), too (Recio et al. 1995). There is little information available concerning the correlations of different LGB genetic variants with milk yield, protein content, cheese-making ability and other economic traits in sheep (Bolla et al. 1988; Garzon and Martinez 1992; Recio et al. 1995), but significant effects of LGB genotypes on whey and the resulting total protein content (Ng -Kwai -Hang et al. 1990; van den Berg et al. 1992; Hill 1993) and milk fat content (Aleandri et al. 1990; Falaki et al. 1997) were found in cattle. As the Merino breeds are one of the most widespread breed groups in the world, the inclusion of the LGB*C allele in further investigation of correlations of LGB genotypes with quantitative or economic traits in sheep is highly desirable. In addition, the occurrence of rare variants might help to clarify breed relationships. Examination of the LGB*C primary structure revealed a single amino acid substitution (Arg/Gln) in position 148 compared to the most common A allele (Erhardt et al. 1989). The test described by Schlee et al. (1993) does not discriminate LGB*C from LGB*A and leads to misidentification in animals with LGB*C. According to Ali et al. (1990) and Harris et al. (1993) amino acids 117–150 are encoded in exon V of the gene. Therefore this region was examined in the present study. Parts of exon V to VI of the gene were PCR-amplified, cloned and sequenced. Based on the sequencing results a PCR-RFLP typing procedure for identification of LGB*C was developed.     

Genetic trends and breed overlap derived from multiple-breed genetic evaluations of beef cattle for growth traits.

Genetic evaluations for a multiple-breed population of beef cattle were used to estimate genetic trends for five breeds, and genetic differences and overlap among 14 breeds. Genetic evaluations studied were for direct contributions to birth weight, gain from birth to 200 and 365 d, and maternal contribution to gain from birth to 200 d. Almost all genetic trends were positive, but the magnitude of the trends varied among breeds. Trends were nonlinear between 1985 and 1995 for most breed and trait combinations. The rates of increase in genetic trends were generally higher for the lighter weight breeds, and lighter weight breeds had faster growth rate genetic trends at 1995 than the heavier breeds. Genetic trend estimates for yearling gain at 1995 were 2.46, 2.23, 1.73, 1.70, and 1.46 kg/yr for Angus, Hereford, Limousin, Charolais, and Simmental, respectively. Corresponding birth weight genetic trends were .130, .226, .049, .130, and .048 kg/yr. Mean genetic differences between breeds have been decreasing in magnitude due to these differences in genetic trends between heavier and lighter breeds. Genetic variation for the traits studied seemed to be greater within than between breeds for calves born and cows calving between 1993 and 1995. Genetic trends at 1995 suggest that ratios of within:between breed variation will increase and that across-breed genetic improvement initiatives for growth traits will become more important in the future.     

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.     

A method for deriving the genetic matrix needed for selection across combinations of breeds

A method is described for deriving the genetic matrix G needed for breeders to select across breeds for any breeding objective. The matrix comprises partitions among selection criteria ( G₁₁ ), between selection criteria and the breeding objective traits ( G₁₂ ), and among the breeding objective traits ( G₂₂ ). A weighting procedure is used to combine the G matrix of individual breeds with known breed differences. Between-breed variances are added to the diagonals of the matrix. Selection across many breeds can be quite different from that across a subset of the breeds. The particular breeds, and the numbers of each breed, that the breeder is prepared to consider in selection changes the genetic matrix and the selection index that should be used.     

Genetic diversity studies in farm animals – a survey

During the past decade a large number of genetic diversity studies in domestic livestock based on microsatellite loci was carried out all over the world. A survey among research groups reveals that in 50% of 87 projects more than eight breeds are investigated. Breeds are chosen mainly because of their long history of isolation, unique phenotypic qualities or an evolution within a unique environment. In half of the projects the average planned sample size per breed is higher than 50. Small ruminants are investigated in the majority of projects. The most preferred type of sample is blood and the most preferred markers are microsatellite loci. To combine results from different diversity studies, the adherence to recommendations, e.g. which loci to genotype or required sample sizes per breed, is necessary. The so called International Society for Animal Genetics (ISAG)/FAO recommendations, which were developed for that purpose, are well known, but the use of recommended microsatellite loci varies between species. The highest acceptance was found in pig, and the lowest in chicken.     

Evaluation of genetic diversity in Japanese Brown cattle population by pedigree analysis

The Japanese Brown is the second most common domestic beef breed in Japan. However, nowadays this breed is facing reduction in numbers because of pressure from a profitable domestic breed. This breed is uniformly characterized by its brown coat colour, but is comprised of two isolated sub‐breeds, Kumamoto and Kouchi, each possessing a different gene pool. Pedigree analyses were carried out for the two sub‐breeds using the pedigree records of animals born from 1970 to 2000. The effective population size has been found to be consistently reducing during the last three decades in both sub‐breeds. The current effective sizes were estimated to be 25.5 and 6.0 for the Kumamoto and Kouchi sub‐breeds, respectively. The estimate of the effective number of founders (N_ef) in the Kumamoto sub‐breed decreased from 152.1 to 74.4; that of non‐founders (N_enf), from 41.7 to 5.3; and that of founder genome equivalents (N_ge), from 32.7 to 4.9. The corresponding changes in the Kouchi sub‐breed were from 108.2 to 79.4, 16.2 to 4.1, and 14.1 to 3.9. Increasing differences between the two genetic diversity indices in the sub‐breeds indicate that the greater part of the reduction of genetic diversity can be attributed to genetic drift that accumulated in the non‐founder generations. A comparison with published estimates for several cattle breeds suggests the extremely limited genetic diversity of Japanese Brown. In addition to the avoidance of further reduction of genetic diversity, it will be important to counteract the process of breed decline by establishing a production system to efficiently utilize the unique characteristics of this breed and by developing links between the breed and products with market value.     

我国部分地方鸭种的亲缘关系及起源分析

为揭示我国部分地方鸭种的亲缘关系及其起源,选取12对荧光标记微卫星引物,对12个地方鸭种及2个野鸭品种进行遗传多样性检测。利用Microsatellite-Toolkit软件将数据结果导入FSTAT和Dispan软件计算标准遗传距离DS、DA遗传距离,并对12个地方鸭群体与2个野鸭品种之间的遗传距离进行方差分析,最后基于标准遗传距离DS与DA遗传距离对14个鸭品种通过构建UPGMA系统发生树进行聚类分析。结果表明:该12个地方鸭种与绿头野鸭、斑嘴鸭之间的DA遗传距离(配对试验均数差异t检验)差异极显著(P<0.01),基于DS与DA遗传距离构建的UPGMA系统发生树都将14个品种聚为3类,并且斑嘴鸭单独聚为一类;可初步判定这12个地方鸭种起源于绿头野鸭,而与斑嘴鸭的遗传距离相对较远。     

Breeds of dogs involved in fatal human attacks in the United States between 1979 and 1998

OBJECTIVE: To summarize breeds of dogs involved in fatal human attacks during a 20-year period and to assess policy implications. ANIMALS: Dogs for which breed was reported involved in attacks on humans between 1979 and 1998 that resulted in human dog bite-related fatalities (DBRF). PROCEDURE: Data for human DBRF identified previously for the period of 1979 through 1996 were combined with human DBRF newly identified for 1997 and 1998. Human DBRF were identified by searching news accounts and by use of The Humane Society of the United States' registry databank. RESULTS: During 1997 and 1998, at least 27 people died of dog bite attacks (18 in 1997 and 9 in 1998). At least 25 breeds of dogs have been involved in 238 human DBRF during the past 20 years. Pit bull-type dogs and Rottweilers were involved in more than half of these deaths. Of 227 reports with relevant data, 55 (24%) human deaths involved unrestrained dogs off their owners' property, 133 (58%) involved unrestrained dogs on their owners' property, 38 (17%) involved restrained dogs on their owners' property, and 1 (< 1%) involved a restrained dog off its owner's property. CONCLUSIONS: Although fatal attacks on humans appear to be a breed-specific problem (pit bull-type dogs and Rottweilers), other breeds may bite and cause fatalities at higher rates. Because of difficulties inherent in determining a dog's breed with certainty, enforcement of breed-specific ordinances raises constitutional and practical issues. Fatal attacks represent a small proportion of dog bite injuries to humans and, therefore, should not be the primary factor driving public policy concerning dangerous dogs. Many practical alternatives to breed-specific ordinances exist and hold promise for prevention of dog bites.     

Geographical isolation of native sheep breeds in the UK—Evidence of endemism as a risk factor to genetic resources

This study addresses the potential risk to the genetic resources of UK sheep breeds from endemism. Twelve native breeds are analysed that exist in significant numbers and continue to be commercially farmed livestock. The breeds were selected to represent regions of the British Isles: North of England hill breeds (Herdwick, Rough Fell, Lonk, Dalesbred), South of England breeds (Southdown, Romney, Devon Closewool, Exmoor Horn), Scottish breed (South Country Cheviot) and Welsh/Welsh border breeds (Welsh Hill Speckled Face, South Wales Mountain (Nelson), Clun Forest).For each breed, numerical data were collected in collaboration with breed society members and analysed in terms of population size and structure together with the extent of their geographical range. The number of flocks per breed proved to be highly variable, questioning the assumption that has been made that the number of breeding units can be disregarded in the calculations of endangerment. The data also indicated that an average flock size for a breed cannot be estimated to gain an insight of the population structure, since this parameter was found to vary considerably within and between breeds. The endemism was best illustrated in the breed maps which clearly highlighted the degree to which each breed was associated with a distinct geographical area. From the maps, ten of the twelve breeds analysed were concentrated, but the flocks of two breeds were visually more dispersed. In numerical terms, the ten breeds were found to have up to 95% of their breed numbers concentrated within a radius of 65 km from the mean centre of each breed.The study provides a valuable foundation for future research into genetic diversity within and between the sheep breeds analysed, a baseline of information to enable population trends to be examined and a robust evidence-base for policy decisions on Farm Animal Genetic Resources (FAnGR).     

云南高黎贡山猪微卫星DNA多态性分析

高黎贡山猪是云南省独特的小型猪种,其肌内脂肪的非饱和脂肪酸和营养必需脂肪酸的含量远高于其他猪种,具有发展优质保健猪肉的良好潜质。本研究选用世界粮农组织（FAO）和国际动物遗传学会（ISAG）联合推荐的20个微卫星位点对高黎贡山猪和杂种群体进行遗传学检测和分析。结果表明：20个微卫星座位在群体中均表现为多态,每位点等位基因数2—5个。群体平均多态信息含量高黎贡山猪为0．6829,杂种群体为0．5924,平均杂合度分别为0．7302和0．6465。     

4个微卫星标记分析6个鸭群体之间的遗传关系

利用4对微卫星引物（AJ272577、AJ272578、AJ272579和AJ272580）对6个鸭群体（绍鸭、番鸭、樱桃谷鸭、北京鸭（Z4、Z1）和奥白星鸭）300只鸭的等位基因频率、群体多态信息含量、有效等位基因数、杂合度和遗传距离进行了检测。结果表明：4个微卫星基因座在6个鸭群体中均存在多态性，可以用于鸭的遗传多样性评估；且基因座AJ272578变异最大，基因座AJ272579变异最小，从不同群体来看，北京鸭Z1的遗传变异最大，奥白星鸭的遗传变异最小。基于Nei氏标准遗传距离，采用UPGMA方法构建了系统发生树，将绍鸭和樱桃谷鸭归为一类，北京鸭Z1、奥白星鸭和北京鸭Z4归为一类，番鸭归为一类。鸭的微卫星基因分型技术为检测品种（群体）之间的遗传关系提供了一个有用的工具。     

Genetic relationship and diversity analysis of Indian water buffalo (Bubalus bubalis)

The water buffalo (Bubalus bubalis) is an important dairy animal on the Indian subcontinent and in Southeast Asian countries. The diversity and differentiation among 12 populations or breeds of buffalo were studied. Data were generated and analyzed from 527 animals belonging to 10 recognized breeds and 2 additional populations of Indian buffalo by using 22 microsatellite loci. Relationships among buffalo breeds and populations were estimated based on genetic distances. The Bayesian analysis grouped 12 populations into 8 distinctive clusters. Geographically close breeds clustered together, except for the Jaffarabadi and Murrah, which were not in geographic contiguity. The Mantel test revealed nonsignificant correlations between genetic and geographic distances. This supports the hypothesis that buffaloes have been domesticated at different places for specific purposes. The phylogenetic relationship based on microsatellite loci supported the breed classification based on body size. The Toda breed, which is considered to be endangered, had genotypes similar to those of the surrounding buffalo populations.     

Population genetic analysis of the Brahman cattle (Bos indicus) in Colombia with microsatellite markers

Summary The Brahman is one of the most popular breeds for meat production in the Neotropics. However, genetic studies of the breed in Latin American countries have only recently begun. In total, 178 animals of the Brahman breed from 20 Colombian provinces were genotyped at 11 microsatellite markers with the aim of studying the genetic diversity of this population and its genetic relationships with zebuine and taurine breeds. The outcomes of multivariate analyses, Bayesian inferences and inter‐individual genetic distances suggested that there is no genetic sub‐structure in the population, because of the high rate of animal migration among provinces. The population shows a high degree of heterozygosity and allelic diversity compared with other breeds, reflecting its multibreed origin. The study of the genetic relationships among the breeds reveals that the Brahman breed belongs to the zebuine group. However, it is the population nearest to taurine breeds with high frequencies of taurine alleles. Intensive artificial selection may have favoured the taurine alleles after the breed was formed. There has also been some degree of mixture with local taurine breeds while the Brahman breed has evolved in Colombia.     

Genebank development for the conservation of livestock genetic resources in the United States of America

The USDA established the National Animal Germplasm Program (NAGP) to conserve livestock genetic resources in 1999. The NAGP is primarily concerned with the development of cryopreserved germplasm and tissue samples from U.S. livestock species. To execute the program's mission, subcomponents dealing with genetic diversity, cryopreservation, and database development have been initiated. An early decision was made to develop collections on all U. S. livestock breeds. Since that decision, collections on 119 breeds have been initiated and ten of the collections have reached the collection goal. An example of selecting animals for the collection is given using Jersey cattle. The selection procedure utilizes the coefficient of genetic relationship as a basis to cluster candidates for the collection and as a method for assessing how complete a breed's collection may be. By using this approach it was determined that 86% of the clusters were presently represented in the collection. With this information collection efforts could be planned to fill in the missing gaps. Performance information from a sample of the in-situ population and the collection were compared. This analysis indicated that there were no significant differences between the means for the Core Collection and the in-situ population sample for milk production, milk protein and net merit index. A significant difference was found for milk fat. While the total collection effort is not complete, samples have been distributed from the repository to perform QTL and genetic distancing studies, creation of a research population, and to introduce genetic variation into a rare cattle breed. Progress has been made in starting breed collections however, significant efforts are needed to: acquire additional accessions for the collection, develop the information system, and quantify levels of genetic diversity within and among breeds.     

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.     

中国地方鸭品种资源的分子遗传多样性

通过筛选的28个多态性较好的微卫星标记，检测了我国24个地方鸭品种的遗传多样性。利用等位基因频率计算了各群体的遗传参数和群体间的遗传距离，采用邻接法构建了聚类图，并进行了系统发生分析。结果表明：28个微卫星座位在我国家鸭群体中的多态信息含量除APL23和APL79为中度多态外，其他座位均为高度多态座位，可以作为有效的遗传标记用于鸭种之间遗传多样性分析和系统发生关系的分析；我国所有家鸭群体平均杂合度（0．569）低于国内的家鸡和家鹅，其遗传多样性相对贫乏；聚类结果分析表明了各家鸭品种的分子系统发生关系与其育成史、分化及地理分布比较一致。     

采用微卫星DNA标记分析巢湖鸭异地小群保种效果

本研究利用筛选后的12对荧光标记微卫星引物分析巢湖鸭原产地(庐江)与国家水禽种质资源基因库(泰州)2个群体的保种效果。检测判定了160个个体的基因型,通过计算2个群体的优势等位基因频率(P)i、期望杂合度(He)、多态信息含量(PIC)、群体内近交系数(Fi)s分析了巢湖鸭群体内和群体间的遗传变异,采用配对试验均数差异t检验比较了基因库保种群体与原产地群体的遗传差异。结果表明:基因库保种群体与原产地群体间的Pi无显著性差异(Pi=0.480>0.05);He和PIC均略高于原产地群体,但差异均不显著(PHe=0.209、PPIC=0.118);Fis显著高于原产地群体(PFis=0.022<0.05)。结果说明,基因库较好地保存了该品种并在一定程度上丰富了品种的遗传多样性,初步表明对巢湖鸭采取异地小群保种的方法是可行的。     

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on F_ST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour‐joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects.