Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such a conservation plan? The present study uses a marker assisted methodology to address these questions. The methodology combines core set diversity measures with a stochastic method for the estimation of expected future diversity and breed marginal diversities. The latter is defined as the change in the total diversity of all breeds caused by a one unit decrease in extinction probability of a particular breed. The stochastic method was validated by means of simulations. A large field data set consisting of 44 North Eurasian cattle breeds was analysed using simplified determined extinction probabilities. The results show that the expected loss of diversity in this set within the next 20 to 50 years is between 1 and 3% of the actual diversity, provided that the extinction probabilities which were used are approximately valid. If this loss is to be reduced, it is sufficient to include those three to five breeds with the highest marginal diversity in a conservation scheme.     

Conservation priorities of genetic diversity in domesticated metapopulations: a study in taurine cattle breeds

We estimated neutral diversity of 21 European cattle breeds with 105 microsatellites. Nine of them resembled unselected Balkan Buša strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated cattle breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Buša, while the maximization of total variance preferred inbred breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Buša.     

中国绵羊起源、进化和遗传多样性研究进展

中国地方绵羊品种资源丰富,部分品种具有繁殖力高、毛皮品质好、多角、多乳头、大尾脂、抗逆性强等独特性状,这些遗传资源引起了学者们对其进行深入研究的兴趣,但目前仍然存在绵羊起源问题的争议,缺乏对我国绵羊的遗传多样性进行全面系统研究等问题。本文综述了绵羊起源、品种分化等方面的研究进展,并从父系、母系、常染色体分子标记等不同层面介绍了中国绵羊遗传多样性的研究概况,为中国绵羊遗传资源的保护和利用、绵羊新品种(系)的培育以及我国绵羊产业良性发展提供参考。     

Relative breed contributions to neutral genetic diversity of a comprehensive representation of Iberian native cattle

This study is aimed at establishing priorities for the optimal conservation of genetic diversity among a comprehensive group of 40 cattle breeds from the Iberian Peninsula. Different sets of breed contributions to diversity were obtained with several methods that differ in the relative weight attributed to the within- and between-breed components of the genetic variation. The contributions to the Weitzman diversity and the expected heterozygosity (He) account for between- and within-breed variation only, respectively. Contributions to the core set obtained for several kinship matrices, incorporate both sources of variation, as well as the combined contributions of Ollivier and Foulley and those of Caballero and Toro. In general, breeds that ranked high in the different core set applications also ranked high in the contribution to the global He, for example, Sayaguesa, Retinta, Monchina, Berrenda en Colorado or Marismeña. As expected, the Weitzman method prioritised breeds with low contributions to the He, like Mallorquina, Menorquina, Berrenda en Negro, Mostrenca, Vaca Palmera or Mirandesa, all showing highly negative contributions to He – that is, their removal would significantly increase the average He. Weighing the within- and between-breed components with the F_ST produced a balanced set of contributions in which all the breeds ranking high in both approaches show up. Unlike the other methods, the contributions to the diversity proposed by Caballero and Toro prioritised a good number of Portuguese breeds (Arouquesa, Barrosã, Mertolenga and Preta ranking highest), but this might be caused by a sample size effect. Only Sayaguesa ranked high in all the methods tested. Considerations with regard to the conservation scheme should be made before adopting any of these approaches: in situv. cryoconservation, selection and adaptation within the breeds v. crossbreeding or the creation of synthetic breeds. There is no general consensus with regard to balancing within- and between-breed diversity and the decision of which source to favour will depend on the particular scenario. In addition to the genetic information, other factors, such as geographical, historical, economic, cultural, etc., also need to be considered in the formulation of a conservation plan. All these aspects will ultimately influence the distribution of resources by the decision-makers.     

边际多样性方法及其在绵羊品种保护中的应用

本文介绍了边际多样性方法,并利用微卫星DNA遗传距离、灭绝概率等结果分析了中国北方11个绵羊品种的品种贡献率、边际多样性及保护潜力。结果表明,苏尼特羊(Sunite sheep)的边际多样性最高（－0.2008）,其次为滩羊(Tan sheep)(－0.1932)、兰州大尾羊(Lanzhou large tailed sheep)(－0.1843);岷县黑裘皮羊(Minxian black fur sheep)最低（－0.1268）。保护潜力最大的品种为兰州大尾羊（0.1419）,其次为同羊(Tong sheep)（0.1017）,最小的为小尾寒羊(Small tailed Han sheep)（0.0365）。根据边际多样性方法,作者认为确定需要保护的品种应该依据最大保护潜力而不是品种的濒危程度。11个绵羊品种的保护顺序依次是兰州大尾羊、同羊、汉中羊(Hanzhong sheep)、甘家羊(Ganjia sheep)、欧拉羊(Oula sheep)、岷县黑裘皮羊、乔科羊(Qiaoke sheep)、苏尼特羊、乌珠穆沁羊(Ujumqin sheep)和小尾寒羊。     

Distribution, endemism and threat status of freshwater fishes in the Western Ghats of India

Aim To study (1) the large-scale distribution patterns of freshwater fishes in the Western Ghats of India; (2) the endemism and uniqueness of the fishes in various zones; and (3) the threat status of fishes by categorizing them under low risk (LR), vulnerable (VU), endangered (EN) and critically endangered (CR). Location The Western Ghats of India. Methods The scientific literature describing the freshwater fishes of the Western Ghats was reviewed. Data describing the lists of the species were extracted and complied. The species accumulation curve was plotted using Michaelis–Menten-like equation. The Western Ghats was divided into six zones and similarity of the species was calculated using Jacquard's index. Results Literature to date records 288 species belonging to 12 orders, 41 families and 109 genera, of which 118 species are endemic and 51 are unique. However, the species accumulation curve shows that there might be 345 species in this region, indicating that 16% species have not been recorded to date. An analysis of the distribution pattern of fishes in the Western Ghats suggests that the southern region is more diverse than the northern and central regions. The southern region shows high endemism and high uniqueness while the northern region shows high endemism but less uniqueness. The similarity index between the zones indicates that as the distance between the zones increases similarity decreases. The status of 105 of 288 species was not known due to data deficiency but among the remaining 183 species, 58 species were categorized as LR, 41 as VU, 54 as EN, 24 as CR while the remaining six species were introduced. Conclusions The distribution patterns of fishes in the Western Ghats are discussed in accordance with the geography of Western Ghats, its climatic conditions and ‘Satpura Hypothesis’. The threat status of fishes found in Western Ghats suggests that at least 41% of fish fauna is threatened by either being VU, EN or CR. Implication of potent conservation measures is necessary to conserve the fish fauna of Western Ghats.     

Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds

The population structure and genetic diversity of 57 European and Middle Eastern marginal and cosmopolitan sheep breeds from 15 countries were analysed by typing 31 microsatellite markers. Mean unbiased expected heterozygosities ranged from 0.63 in British Exmoor Horn to 0.77 in Albanian Ruda. South-eastern European and Middle-Eastern sheep breeds were significantly more variable than northwestern and western European breeds. An overall heterozygote deficiency (f) across all loci was observed (P < 0.001), while genetic differentiation (theta) was 5.7%. Principal component analysis and Bayesian model-based clustering indicate a south-east to north-west cline, but also revealed distinct groups of Middle-Eastern fat-tailed sheep, south-eastern European sheep and north-western/western European sheep. Within the last group, two less-distinct clusters comprised the Merino-type and Alpine breeds respectively. The incomplete demarcations of most clusters probably reflects cross-breeding and/or upgrading.     

西双版纳苔藓植物多样性及其濒危状况

在世界范围内, 目前被描述的苔藓超过20,000种, 因而, 苔藓植物成为多样性仅次于被子植物的第二大高等植物类群。西双版纳是世界生物多样性保护的关键和热点地区, 然而, 关于该地区苔藓植物多样性的认识却非常有限。为此, 本文结合野外调查和文献收集的方法, 编制了西双版纳苔藓植物名录, 并对其多样性和受威胁状况进行了初步分析。本次调查共采集苔藓植物标本307份, 最终有效鉴定37科70属101种, 其中有5种新记录种。综合野外调查与文献资料, 西双版纳地区共有苔藓植物82科233属661种(含种下分类单元), 占云南省苔藓植物种数的34.7%, 占全国的20.5%。其中苔类30科54属200种、角苔类3科7属12种、藓类49科172属449种, 包括9个东亚特有属、1个中国特有属和26个中国特有种。不同区域尺度、不同时期的红色名录中对西双版纳地区苔藓植物受威胁状况评估结果不同。西双版纳地区苔藓植物物种多样性存在被低估的可能, 随着未来调查区域的扩大和深入, 可能会有更多的苔藓物种被发现。本研究为进一步深入研究该地区苔藓植物区系、保护及利用提供了基础数据。     

Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches

Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated ( r  = −0.963, P  <   0.0001), because of the genetic structure of the breed set.     

Mitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds

This survey represents the first characterization of mitochondrial DNA diversity within three breeds of Indian sheep (two strains of the Deccani breed, as well as the Bannur and Garole breeds) from different geographic regions and with divergent phenotypic characteristics. A 1061-bp fragment of the mitochondrial genome spanning the control region, a portion of the 12S rRNA gene and the complete phenyl tRNA gene, was sequenced from 73 animals and compared with the corresponding published sequence from European and Asian breeds and the European Mouflon (Ovis musimon). Analysis of all 156 sequences revealed 73 haplotypes, 52 of which belonged to the Indian breeds. The three Indian breeds had no haplotypes in common, but one Indian haplotype was shared with European and other Asian breeds. The highest nucleotide and haplotype diversity was observed in the Bannur breed (0.00355 and 0.981 respectively), while the minimum was in the Sangamneri strain of the Deccani breed (0.00167 and 0.882 respectively). All 52 Indian haplotypes belonged to mitochondrial lineage A. Therefore, these Indian sheep are distinct from other Asian and European breeds studied so far. The relationships among the haplotypes showed strong breed structure and almost no introgression among these Indian breeds, consistent with Indian sheep husbandry, which discourages genetic exchange between breeds. These results have implications for the conservation of India's ovine biodiversity and suggest a common origin for the breeds investigated.     

Population structure, genetic variation and morphological diversity in indigenous sheep of Ethiopia

We investigated genetic and morphological diversity and population structure of 14 traditional sheep populations originating from four ecological zones in Ethiopia (sub-alpine, wet highland, sub-humid lowland and arid lowland). All animals (n = 672) were genotyped for 17 microsatellite markers and scored for 12 morphological characters. The sheep were initially classified as fat-tailed (11 populations), thin-tailed (one population) and fat-rumped sheep (two populations). These classifications are thought to correspond to three consecutive introduction events of sheep from the Near-East into East Africa. For the 14 populations, allelic richness ranged from 5.87 to 7.51 and expected heterozygosity (H(E)) from 0.66 to 0.75. Genetic differentiations (F(ST) values) between all pairs of populations, except between sub-alpine populations, were significantly different from zero (P < 0.001). Cluster analysis of morphological characters and a dendrogram constructed from genetic distances were broadly consistent with the classification into fat-tailed, thin-tailed and fat-rumped sheep. Bayesian cluster analysis using microsatellite markers indicated that there has been further genetic differentiation after the initial introduction of sheep into Ethiopia. Investigation of factors associated with genetic variation showed that an isolation-by-distance model, independently of other factors, explained most of the observed genetic variation. We also obtained a strong indication of adaptive divergence in morphological characters, patterns of morphological variation being highly associated with ecology even when the effect of neutral genetic divergence (F(ST)) was parcelled out in partial Mantel tests. Using a combination of F(ST) values, Bayesian clustering analysis and morphological divergence, we propose a classification of Ethiopian sheep into six breed groups and nine breeds.     

Assessing the contribution of breeds to genetic diversity in conservation schemes

The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles), whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%.     

Genetic variability of six French meat sheep breeds in relation to their genetic management

Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH), Blanc du Massif Central (BMC), Charollais (CHA) and Limousin (LIM); the other two breeds are under conservation: the Roussin de La Hague (RLH) and Solognot (SOL). Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount). The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not) for the ewes born from 1996 to 2000 were equal to 35 (BCH), 144 (BMC), 112 (CHA), 69 (LIM), 40 (RLH) and 49 (SOL). Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH), +0.045 (CHA), +0.036 (LIM), +0.098 (RLH) and +0.062 (SOL). The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.     

Native breeds demonstrate high contributions to the molecular variation in northern European sheep

Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.     

Assessment of DNA fingerprinting for determining genetic diversity in sheep populations

Genomic DNA, prepared from 12 animals from four sheep flocks, was digested with either HaeIII or Hin fI and probed with three DNA fingerprinting probes. Mean DNA fingerprint band sharing and band frequency calculated for each flock were used to estimate genetic diversity. Each of the DNA fingerprinting systems showed the same trend in diversity within the sampled flocks, and greater diversity between the flocks than within the flocks. DNA fingerprinting therefore provides a useful measure of genetic diversity in sheep.     

Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites

Nuclear genetic diversity and differentiation of 341 sheep belonging to 12 sheep breeds from Croatia and Bosnia and Herzegovina were examined. The aim of the study was to provide the understanding of the genetic structure and variability of the analysed pramenka sheep populations, and to give indications for conservation strategies based on the population diversity and structure information. The genetic variation of the sheep populations, examined at the nuclear level using 27 microsatellite loci, revealed considerable levels of genetic diversity, similar to the diversity found in other European indigenous low-production sheep breeds. Population-specific alleles were detected at most loci and in breeds analysed. The observed heterozygosity ranged from 0.643 (in Lika pramenka) to 0.743 (in Vlasic pramenka), and the expected heterozygosity ranged from 0.646 (in Lika pramenka) to 0.756 (in Dalmatian pramenka). Significant inbreeding coefficients were found for half of the populations studied and ranged from 0.040 (Pag island sheep) to 0.091 (Kupres pramenka). Moderate genetic differentiation was found between the studied sheep populations. The total genetic variability observed between different populations was 5.29%, whereas 94.71% of the variation was found within populations. Cres island sheep, Lika pramenka and Istrian sheep were identified as the most distinct populations, which was confirmed by the factorial analysis of correspondence and supported through a bootstrapping adjustment to correct for the difference in the sample sizes. The population structure analysis distinguished 12 clusters for the 12 sheep breeds analysed. However, the cluster differentiation was low for Dalmatian, Vlasic, Stolac and Krk pramenka. This systematic study identified Lika pramenka and Rab island sheep as those with the lowest diversity, whereas Istrian sheep and Pag island sheep had the highest. Conservation actions are proposed for Istrian, Rab and Cres island sheep, Lika and Kupres pramenka because of high estimated coefficients of inbreeding.     

Duration of the breeding season and response to reproductive manipulation in five breeds of sheep under northern prairie conditions

The breeding season was 157, 154, <126, 210 and 217 days for Rambouillet, Columbia, Suffolk, Rambouillet x Finnish Landrace and Columbia x Finnish Landrace ewes respectively. Treatment of cyclic ewes with pregnant mare serum gonadotropin (PMSG) (500 IU), following a 12-day treatment with progestin-containing intravaginal sponges, did not affect fertility, but did decrease the time from sponge removal to estrus, (control 48.0 +/- 3.1 hr; PMSG 39.4 +/- 1.8 hr) to the preovulatory surge of LH (control 52.7 +/- 2.8 hr; PMSG 39.0 +/- 1.7 hr) and FSH (control 52.3 +/- 2.9 hr; PMSG 42.8 +/- 1.6 hr) and caused an elevation of serum LH levels prior to the preovulatory surge (control 1.25 +/- 0.18 ng/ml; PMSG 2.31 +/- 0.22 ng/ml). Exposure of the purebred ewes to 18 hours of daylight in January, decreasing by 30 minutes a week subsequently, counteracted the seasonal reduction in the number of ewes lambing following induced breeding under natural daylight in May. Prolificacy was greatest in crossbred ewes and their fertility was not affected by season. Gestation period was longer for fall-bred ewes and varied with breed.     

Analysis of diversity and genetic relationships between four Chinese indigenous pig breeds and one Australian commercial pig breed

The genetic diversities and relationships of four Chinese indigenous pig breeds and one Australian commercial pig breed have been evaluated using 27 microsatellites recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO). The allele frequencies, effective numbers of alleles and the polymorphic information content have been calculated. Nei's standard genetic distances have been used to construct a UPGMA dendrogram, which has been evaluated by the Bootstrap test. The utility of microsatellites for evaluating genetic diversity of pigs is discussed.     

Ability of dairy cows to be inseminated according to breed and genetic merit for production traits under contrasting pasture-based feeding systems

Strong genetic selection on production traits is considered to be responsible for the declined ability of dairy cows to ensure reproduction. The present study aimed to quantify the effect of genetic characteristics (breeds and genetic merit for production traits) and feeding systems (FS) on the ability of dairy cows to be inseminated. An experiment was conducted during 9 years on Normande and Holstein cows assigned to contrasted pasture-based FS. Diets were based on maize silage in winter and grazing plus concentrate in spring in the High FS; and on grass silage in winter and grazing with no concentrate during spring in the low FS. Within breed, cows were classified into two genetic groups with similar estimated breeding values (EBV) for milk solids: cows with high EBV for milk yield were included in a Milk-Group and those with high EBV for fat and protein contents were included in a Content-Group. Holstein produced more milk throughout lactation than Normande cows (+2294 kg in the High FS and +1280 kg in the Low FS, P<0.001) and lost more body condition to nadir (−1.00 point in the High FS and −0.80 kg in the Low FS, P<0.001). They also showed a poorer ability to be inseminated because of both a delayed commencement of luteal activity (CLA) and delayed first service (more days from start of the breeding season to first service, DAI1). Cows in the Milk-Group produced more milk than cows in the Content-Group, but milk solids production was similar. Cows in the Content-Group had earlier CLA than cows in the Milk-Group (P<0.01). Genetic group neither affected ovulation detection rate nor DAI1. Within breed and FS, cows with high genetic merit for milk yield had later CLA and DAI1. Cows in the High FS produced more milk and lost less condition to nadir than cows in the Low FS. FS did not affect dairy cows’ ability to be inseminated. However, cows with higher milk protein content, and presumably better energy balance, had earlier CLA (P<0.01) and DAI1 (P<0.10). In addition, higher milk yield was associated with poorer ovulation detection rate and oestrus intensity (P<0.05). The study showed that at similar EBV level for milk solids, selection for increased milk fat and protein content resulted in improved cyclicity and similar oestrous expression and submission rates compared with selection for increased milk yield.