Genetic diversity of protein markers in sheep population from Ukraine

Based on polymorphism of genes for antigen factors of six blood-group systems and four blood protein loci, genetic structure and the main variation parameters were studied in three sheep breeds and three sheep breed types constituting the basis of purebred sheep resources in Ukraine. Specific features of the distribution of genotypes and alleles of polymorphic loci were determined in each of the studied sheep groups depending on their origin and production type. The molecular-genetic markers used in the analysis of the genetic relationships between the sheep breeds and breed types were shown to objectively reflect their breeding history and evolution. Integrally, each of the studied gene pools had a specific profile of gene frequencies reflecting breeding specificity, breed history, and genetic differentiation of breeds.     

Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers

To determine the genetic diversity and phylogenetic relationships among Chinese sheep, 10 indigenous breeds and one introduced breed were genotyped for 19 microsatellite loci. The mean number of alleles per breed ranged from 5.44 (Guide Black Fur sheep) to 9.13 (Ujumqin sheep and Hulunbeier sheep), the expected heterozygosity varied from 0.623 (Guide Black Fur sheep) to 0.737 (Zhaotong sheep), and the allelic richness ranged from 5.169 (Guide Black Fur sheep) to 7.610 (Zhaotong sheep). The deviation from Hardy–Weinberg equilibrium (HWE) was statistically significant (P < 0.05) at three loci (SRCRSP5, OarAE129 and DYMS1) in most of the breeds. Chinese sheep breeds had maintained a high level of within-population genetic differentiation (95.23%), with the remainder explained by differentiation among populations (4.77%). The genetic differentiation pattern and genetic relationships among Chinese sheep breeds displayed a high consistency with the traditional classification. Both the Bayesian cluster and principal component analyses showed a reliable clustering pattern, which revealed three major clusters in Chinese indigenous sheep (Mongolian sheep, Kazakh sheep and Tibetan sheep), except Zhaotong and Guide Black Fur sheep. There were probably caused by different breeding history, geography isolation and different levels of inbreeding. This study will help to interpret the genetic characters of Chinese indigenous sheep and benefit to the future conservation programs.     

新疆8个绵羊品种遗传多样性和系统发生关系的微卫星分析

为分析新疆北疆地区主要绵羊品种的遗传多样性和系统发生关系,利用10个微卫星标记,采用PCR扩增,12％非变性聚丙烯酰胺凝胶电泳、Sanguinetti银染法显色,对新疆北疆地区8个品种、1个杂交一代绵羊群体遗传多样性进行了检测,统计了各群体的等位基因组成、平均有效等位基因数(E)和平均基因纯合率,利用等位基因频率计算出各群体的平均遗传杂合度(h)、多态信息含量(PIC)和群体间的遗传距离。利用分子进化遗传分析软件,采用邻结法构建系统发生树;同时根据等位基因频率,利用PHYLIP(3．6)分析软件,采用最大似然法构建系统发生树,应用白举检验估计系统树中结点的白引导值,并进行了系统发生分析。结果表明：10个微卫星位点在9个绵羊群体中的多态信息含量除BMI824、MAF65为低、中度多态外,其余8个微卫星均为高度多态,可作为有效的遗传标记用于各绵羊品种的遗传多样性和系统发生关系的分析;所有绵羊群体的平均PIC(0．5631)、h(0．5721)和E(2．9)均低于国外其他品种的绵羊,其基因多态性和遗传多样性相对贫乏;新疆本地土种阿勒泰羊、哈萨克羊和巴什拜羊与国外引进绵羊品种及混有外血的本地培育品种遗传距离较远,他们聚为不同的两类,各绵羊品种的分子系统发生关系与其来源、育成史、分化及地理分布基本一致。     

Unfolding of population structure in Baltic sheep breeds using microsatellite analysis

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management.     

RAPD Analysis of DNA Polymorphism in Turkish Sheep Breeds

The genetic diversity and phylogenetic relationships of 108 individual sheep from three Turkish sheep breeds (K?v?rc?k, Gökçeada, and Sak?z) were studied using RAPD analysis. Polymorphisms within and between populations were assayed using 15 random primers, and 82 loci were amplified ranging from 250 to 2,500 bp. The percentage of polymorphic loci was found to be 80.49, 78.05, and 73.17%, for K?v?rc?k, Gökçeada, and Sak?z sheep breeds, respectively. Total genetic diversity was 0.2265, and the average coefficient of genetic differentiation was 0.1181. Genetically, the Gökçeada breed was more closely related to the Sak?z breed than to the K?v?rc?k breed.     

Hemotypes in Spanish sheep breeds

The structure and the genetic diversity of the Churra, Lacha and Manchega sheep breeds have been analysed using hemotypes observed in eight loci. The three breeds are different in their hemotypes in terms both of quantity and quality. The proportions of unique hemotypes in Churra (60%), Lacha (61%) and Manchega (67%) revealed a high level of individual diversity within each breed. Racial genetic diversity follows the descending order of: Manchega-Lacha-Churra. The value of N:H (number of animals: total hemotypes) in the multi-racial population was 3.05.     

21个野生,培育及地方猪种免疫及生化遗传标记基因位点的遗传分化研究

分析了亚,欧,美,非２１个野生,培育及地方猪种４个免疫遗传标记基因位点（Ｅ,Ｆ,Ｇ,Ｌ系统）和３人生化遗传标记基因位点（Ｃｐ,Ａｍ和Ｔｆ）的遗传多态性,认为Ｅ＾ａｅｇ,Ｆ＾ａ,Ｔｆ＾ｃ基因在亚洲猪种与欧美猪种间存在显著差异,是亚洲猪种３个重要的遗传标记基因,根据Ｆ＾ａ基因频率在亚,欧,美,非猪种的变化规律分析了其基因流向特点,证明欧美猪的育种过程中利用了中国地方猪种的血缘,计算了所测猪种间的Ｎｅｉ     

Sheep major histocompatibility complex OLA: Gene frequencies in two french breeds with scrapie

Gene frequencies of 13 sheep lymphocyte factors (11 factors controlled by the sheep OLA complex including three closely linked loci, and two factors by two minor loci) were compared in 189 sheep of two breeds: a. infected with scrapie, b. healthy in a contaminated environment, and c., normal. In a and c, OLA gene frequencies were similar. In healthy sheep in a contaminated environment (b), some OLA gene frequencies were higher in one breed and lower in the other. In each breed, three antigens had their frequencies significantly modified; two of them were the same in the two breeds, but they showed an inverse variation. Thus, the relative risk of clinical scrapie decreased in one breed and increased in the other for the same OLA gene. These data indicate first, that OLA antigens are not directly involved in causing scrapie, and second, that the OLA complex is linked to at least one scrapie resistance/susceptibility locus. In practice, it should be possible to select more resistent sheep, using some OLA antigens but an investigation of the OLA genes and the resistance to scrapie in a given breed is necessary before the selection.     

Analysis of the genetic structure of Tuvinian short-fat-tailed sheep populations with the use of the ISSR-PCR method

The genetic structure of populations of the Tuvinian short-fat-tailed sheep was studied with the use of the ISSR-PCR (Inter Simple Sequence Repeats) method in 18 farms of Tyva. Data on the spectrum of ISSR fragments of DNA were obtained using the (AG)₉C primer. Analysis of intermicrosatellite polymorphism permitted us to determine genomic characteristics of the populations, their genealogical relations, and the parameters of genetic diversity within the populations and the breed as a whole. Three genetic notions were considered on the basis of the results of this analysis: gene pool profile, gene pool standard, and breed-specific pattern. The data obtained can be used to carry out population genetic monitoring, to develop a breeding strategy, and to conserve in situ the Tuvinian sheep breed and breeds of other domesticated species.     

DNA variants of the MHC show location-specific convergence between sheep, goat and cattle

Interspecific convergent evolution in sheep, goat and cattle was analysed with the help of orthologous microsatellite markers. Six of the loci are located in the major histocompatibility complex (MHC) region and three on different chromosomes. Samples from at least 60 animals per autochthonous breed of the three species were collected in central and southeast Anatolia (Turkey) as well as Baden-Württemberg (Germany). Allelic diversity, heterozygosity, population differentiation and genetic distances were calculated. The loci were polymorphic in all species and breeds. Apart from MSDRB, the loci linked to the MHC were similarly polymorphic as compared to the other loci. Allele numbers in the Turkish sheep and in the cattle breeds were higher than in the other breeds. The predominant occurrence of distinct allele lengths per locus differed depending on the species. For the three geographic locations, the genetic distances between species based on the MHC loci were significantly closer in comparison with distances based on quasi-neutral loci. This indicates convergent evolution of the MHC loci between sheep, goat and cattle caused by effects of location and demonstrates an approach for quantifying influences of adaptation on genetic variability.     

Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity

Background

Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds.

Methods

For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds’ genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach.

Results

Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds’ genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank.

Conclusions

A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.     

Genetic diversity and assessment of 23 microsatellite markers for parentage testing of Santa Inês hair sheep in Brazil

Santa Inês is the most common hair sheep breed in Brazil and probably has the highest genetic diversity among sheep breeds in this country. Successful breeding programs for Brazilian sheep breeds are not common for various reasons, including a lack of control of parentage in the flocks. We developed an allele frequency database for 23 STR loci for the Santa Inês breed based on 285 animals sampled from five populations distributed across the central-western and north-eastern regions of Brazil. The marker set included seven microsatellites used in the 2011 International Society for Animal Genetics sheep genotyping comparison tests and all eight microsatellites currently approved by the Brazilian Agricultural Ministry laboratory accreditation guidelines for sheep identification. The microsatellites had an average of 10 alleles and a mean expected heterozygosity of 0.745. Combined paternity exclusion probabilities when no parent or one parent was known were >99.99%. A small proportion (5.8%) of the existing genetic variation was found to be among the Santa Inês populations, possibly derived from genetic drift and selection. We found that the marker panel proposed by the Agricultural Ministry, although generally useful, should be enhanced by including more markers for improved exclusionary power in parentage testing. This database provides a useful tool for parentage testing of this major Brazilian breed, contributing to improved management and breeding of existing herds.     

Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds

Finnsheep, Romanov, Oxford Down and three local breeds from Finland or northwestern Russia were assessed at 15 microsatellite and 7 protein loci. A novel albumin allele was identified. Diversity patterns were mostly concordant between marker types, but discrepancies appeared for the local Viena and Vepsia sheep, both demonstrating frequent linkage disequilibria for both marker types and excess of homozygotes for microsatellites, and in the case of Vepsia also for proteins as signs of breed fragmentation. On the basis of microsatellite data, the neighbour-joining tree and two-dimensional map constructed from DA distances suggested that difference in longitude of breed origin would relate to breed relationship, whereas on the basis of protein data latitude would have this quality. These different impressions resulted because genetic distances involving Vepsia sheep were relatively low for protein variation compared with microsatellites. Microsatellite variation correlated positively with protein variation, but for the local Viena sheep protein variation was comparatively low. Populations had significant differences in allelic richness, but not in genetic diversity. Analysis implied that at least 30 polymorphic loci were needed to detect a difference in diversity between populations using a paired t-test, if the true mean diversity difference was 0.2. In the total sample, proteins demonstrated larger theta-values, but this was reversed for Finnsheep, for which model-based clustering of microsatellite genotypes revealed a structure associated with coat colour. Imported and rare sheep exhibited lowered allelic variability and increased frequency of pairwise disequilibria between unlinked markers. Our results emphasize that more loci are required for studying fragmented breeds.     

Genetic analysis of Greek sheep breeds using microsatellite markers for setting conservation priorities

Ten Greek sheep breeds were analysed at 28 microsatellite markers in order to estimate their genetic diversity and differentiation. This study aims to provide information on the genetic structure of the breeds analysed and the ancestral populations, and give indications and proposals for the conservation strategies. The breeds included were the local sheep breeds raised in different regions of Greece. In total, 310 animals were sampled. Non-biased average expected heterozygosity ranged from 0.68 ± 0.134 (Skopelos breed) to 0.76 ± 0.103 (Karagouniko breed) with an average of 0.74, while the average observed heterozygosity ranged from 0.626 ± 0.132 (Skopelos) to 0.74 ± 0.135 (Kefallenias). Estimates of inbreeding coefficient (Fis) were significant for all breeds studied, except for Kefallenias and Lesvos breeds (P < 0.05). The results of the phylogenetic relationships are in accordance with the geographical location of the breeds, the history of the origin of the breeds and the breeding practices. The phylogenetic tree showed three groupings according to the bootstrapping values. Correspondence analysis showed the isolation of the Skopelos breed and the grouping of Sfakia and Anogeiano breeds in a separate cluster.     

Genetic diversity of three Chinese native sheep breeds

The sheep (Ovis aries L.) has been an important farm animal species since its domestication. A wide array of indigenous sheep breeds with abundant phenotypic diversity exists for domestication and selection. Therefore, assessing the genetic diversity of a local sheep resource using a multi-molecular system is helpful for maintaining and conserving those breeds. This study aimed to investigate the genetic diversity of three native Chinese sheep breeds (Tibetan sheep, Sishui Fur sheep, and Small-tailed Han sheep) using 15 microsatellite markers and the second exon of the DRA gene. In regards to the microsatellites, on average, 19 alleles per loci were observed among all individuals. Across loci, the HO within the population was 0.652 ± 0.022 in Tibetan sheep, 0.603 ± 0.023 in Small-tailed Han sheep and 0.635 ± 0.022 in SFS, and for most populations, the H _E and H _O were inconsistent. In addition, affluent private alleles within the breed indicated that the breeds have different domestication histories or sites. In regards to the 2 exon of the DRA gene, three haplotypes were constructed by seven single-nucleotide polymorphisms (SNPs), which were identified in the second DRA exon and inferred the potential for phenotypic variety in these Chinese native sheep. In summary, the current study reveals the importance of implementing effective conservation strategies for these three native Chinese sheep.     

我国主要地方绵羊品种随机扩增多态DNA研究

对蒙古羊、湖羊、滩羊、小尾寒羊、乌珠穆沁羊、藏绵羊、阿勒泰羊7个地方绵羊品种和无角陶赛特羊、德国美利奴羊、萨福克羊3个引入品种基因组DNA进行了RAPD分析。结果表明：（1）RAPD可作为一种有效的标记用于绵羊品种之间遗传亲缘关系的分析。（2）在所使用的43种随机引物中,有35种引物扩增出多态谱带,多态频率为66.24%,说明RAPD技术用于研究绵羊核DNA的遗传变异具有较高的检出率和灵敏度。（3）总群体平均遗传多样性指数（HSP)为0.9139,说明绵羊群体具有较为丰富的遗传多样性。（4）我国地方绵羊品种间的分子聚类关系与其所处的地理位置、考古学结果,以及细胞遗传学研究结果基本,引入品种间的分子聚类关系也与其育成史基本一致。     

Genetic relationships among Spanish sheep using microsatellites

Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa–Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa–Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance.     

Population structure in Indian sheep ascertained using microsatellite information

This study attempts to provide a comprehensive insight into the prevailing genetic status of Indian sheep breeds using microsatellite markers. Seventeen Indian sheep breeds from 3 agroecological zones were analysed using a panel of 25 microsatellite markers. All of the sheep breeds investigated were genetically diverse, as evident from the high allele (>6) and gene (>0.6) diversity values. The gene diversity values for all breeds ranged from 0.621 to 0.780. The within-population heterozygote deficit (F(IS)) varied from -0.098 to 0.234, reflecting significant levels for 12 of the 17 breeds investigated. The average genetic differentiation between all breeds (F(ST)) was 11.1%, revealing moderate discrimination between the indigenous sheep breeds. The genetic distance and principal component analysis revealed a separation of sheep breeds based on geographical propinquity. The Bayesian clustering approach suggested poor breed differentiation in the north-western arid and semi-arid region when compared to the breeds from the eastern and southern peninsular regions. The observed results mirror the divergent management strategies in the different agroecological regions, lack of specific selection policies, and intermixing of breeds in close proximity. Immediate steps to curb the intermixing and erosion of breed purity for some of these breeds need to be implemented, for example, by introducing measures like making proven rams available and ensuring their frequent exchange between flocks. The data generated here provides valuable information about the genetic structure of the 17 Indian sheep breeds and this can be used for designating priorities for their conservation.     

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H_E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.     

Genetic structure of a wide-spectrum chicken gene pool

The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.