DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes

A multi-locus DNA probe, R18.1, derived from a bovine genomic library, detected DNA fingerprints of highly polymorphic loci in hybridization to genomic DNA from poultry and sheep, and of moderate polymorphic loci in cattle and human DNA. The average numbers of detected bands in chickens and sheep were 27.8 and 21.4, and the average band sharing levels were 0.25 and 0.33, respectively. In hybridization to cattle and human DNA, the results were less polymorphic; nevertheless, individual identification is feasible using probe R18.1. The results obtained by R18.1 were compared to results obtained by Jeffreys minisatellite probe 33.6 and two microsatellite oligonucleotides, (GT)12 and (GTG)5. The total number of detected loci using probes R18.1 and 33.6 were estimated in chickens through family analysis of broilers and the maximal number of detectable loci was calculated.     

Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations

Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub-structure and genetic variability in free-ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (H(O)) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre-dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.     

Genetic diversity of heavy metal-tolerant populations in Silene paradoxa L. (Caryophyllaceae): a chloroplast microsatellite analysis

Eight populations of Silene paradoxa L. (Caryophyllaceae) growing in copper mine deposits, in serpentine outcrops or in uncontaminated soil in central Italy were studied. Genetic diversity was estimated using five polymorphic chloroplast microsatellite loci (cpSSR), identifying 27 different chloroplast haplotypes. The effective number of alleles, the haplotypic diversity and a stepwise mutational model-based parameter (DSH2) were computed. The effective number of alleles observed within populations from copper mine deposits was 20% that of the serpentine neighbouring populations, suggesting the occurrence of a founder effect. Moreover, 13 of the 27 different haplotypes scored were exclusive to only one population, indicating genetic isolation for all tolerant populations. Even the copper-tolerant populations appeared to have evolved independently. Finally, analysis of molecular variance (AMOVA) of the cpSSR markers gave statistical significance to the grouping of populations according to their geographical location. This study demonstrates that cpSSR markers could be a useful complementary tool to isoenzymes or random amplified polymorphic DNA markers for elucidating the pattern of genetic differentiation in heavy metal-tolerant populations.     

合浦珠母贝三个养殖群体微卫星遗传多样性

以广东徐闻金碧公司养殖场、广西北海营盘镇养殖场和南海水产研究所海南实验基地3个合浦珠母贝养殖群体为对象,利用8个微卫星位点M1、M2、M3、M4、M5、M6、M7、M8的引物进行了遗传多样性分析.结果表明:8个微卫星标记位点在3个养殖群体中共检测到58个等位基因,观测等位基因数为2～9个,平均有效等位基因数3.72～5.06,平均观察杂合度0.41～0.56,平均期望杂合度0.67～0.75,3个群体的平均多态信息含量PIC值为0.62～0.70,全部为高度多态(PIC≥0.5),表明这几个合浦珠母贝养殖群体目前仍具有较高的遗传多样性,遗传信息丰富,遗传变异大,可以作为良好的育种材料;在这3个养殖群体中,南海水产研究所海南实验基地的养殖群体的遗传多样性最高,广西北海营盘镇养殖群体遗传多样性最低,这一结果可以为今后选择育种、种质保护提供可资借鉴的资料.

Abstract：

By using eight mierosatellite loci (M1, M2, M3, M4, M5, M6, M7 and MS), the genetic diversity of three Pinctada fucata populations from the pearl farms in Xuwen of Guang-dong and Beihai of Guangxi, and from the experimental base of South China Sea Fisheries Re-search Institute in Hainan was studied. A total of fifty eight alleles of these eight microsatellite lo-ci were detected, among which, the observed allele number was 2-9, average effective allele number was 3.72-5.06, average observed population heterozygosity was 0. 41-0. 56, and aver-age observed expected heterozygosity was 0. 67-0. 75. All the three populations had a polymor-phie information content (PIC) of 0. 62-0.70, suggesting their high polymorphism (PIC > 0. 5). Among the three populations, the cultured population from the experimental base of South China Sea Fisheries Institute had the highest polymorphism, and that from Beihai of Guangxi had the lowest one. These results provided useful information for the selective breeding and germplast conservation of P. Fucata.     

Variation at a chloroplast minisatellite locus reveals the signature of habitat fragmentation and genetic bottlenecks in the rare orchid Anacamptis palustris (Orchidaceae)

Geoclimatic changes during the Oligocene and more recent anthropogenic influences have shaped the current distribution and population structure of Mediterranean plant species. Anacamptis palustris (Orchidaceae) is a typical member of coastal wetlands, which have become increasingly fragmented and isolated. As a consequence, this orchid has become rare in the recent past. Length variation at a chloroplast minisatellite locus was used to estimate genetic variation within and between the largest extant populations of A. palustris. Genetic diversity was positively correlated with population size. Estimation of observed and expected gene diversity and analyses of haplotype number and haplotype frequency distributions provided evidence for population bottlenecks in the history of small populations. Comparison with an earlier study suggests that nuclear allozyme diversity was most likely lost during the Oligocene and could not recover subsequently due to low mutation rates, whereas genetic variation was restored at the highly variable chloroplast minisatellite locus. Population bottlenecks indicated by cpDNA variation occurred most likely as a consequence of more recent anthropogenic changes. The comparison of molecular markers with different levels of polymorphism provided valuable insights into the processes shaping genetic diversity and population structure in this rare orchid.     

山羊群体遗传多样性的微卫星分析

为了保护和合理利用我国地方山羊品种遗传资源提供理论基础,本研究利用国际农粮组织和国际家畜研究所推荐的10对微卫星引物,结合荧光标记PCR,检测了中国9个地方山羊品种和1个引进山羊品种的遗传多样性。所研究的10个品种中7个呈现出高度多态,3个呈现出中度多态。并共检测到119个等位基因,有效等位基因数在1.4641~9.2911之间,座位平均杂合度在0.2618~0.7672之间,品种平均杂合度在0.5196~0.7024之间,其中SRCRSP23位点和河西绒山羊(HXR)平均杂合度最高。聚类关系(NJ和UPGMA)和主成分分析结果与其起源、育成历史及地理分布基本一致。     

鄱阳湖日本沼虾15个群体遗传多样性的微卫星分析

利用徽卫星分子标记研究鄱阳湖15个日本沼虾(Macrobrachium nipponense野生群体的遗传多样性.结果表明:10个微卫星位点呈高度多态性,共检测到129个多态性位点;每个群体中至少有5个位点显著偏离Hardy-Weinberg平衡,表现出杂合不足;15个日本沼虾群体均表现出较高的遗传多样性,其中大坝外群体和星池群体遗传多样性较高,万户和湖口群体相对较低.瓶颈效应和突变-漂移平衡分析表明,鄱阳湖日本沼虾群体近期没有经历过瓶颈效应,群体数量也没有下降.群体间F统计量及AMOVA分析显示,鄱阳湖日本沼虾群体存在极显著的遗传分化程度(FST=0.04709,P＜O.01).综上所述,鄱阳湖日本沼虾群体具有丰富的遗传多样性,可作为日本沼虾选育的基础群.     

Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris

Habitat alteration, fragmentation and destruction as a consequence of human impact are a global phenomenon. Here we document changes in genetic variation in the marsh orchid Anacamptis palustris as a consequence of such habitat changes. We examined historical specimens that were collected during the nineteenth and early twentieth centuries, prior to the most recent massive habitat changes affecting this species. Sequences of a hypervariable region in the plastid DNA, located in the tRNA^LEU intron, from herbarium vouchers were compared with those from a near-exhaustive survey of the extant A. palustris populations on the Italian peninsula. It was found that private haplotypes and alleles found in small, extant populations were once widespread and more common in historic populations and that alleles, once present in historic populations, have gone extinct. In addition, genetic differentiation among populations has increased over time and haplotype frequencies significantly differ among historic and extant populations. These results document that human induced habitat changes have reduced genetic diversity and increased the importance of random genetic drift in this species. It is concluded that the analysis of herbarium specimens may provide important insights into changes of genetic diversity over time and may be critical for correct inference of the evolutionary history of rare and endangered species.     

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by （δμ）^2 and DA distances, and the divergence times between populations were estimated by （δμ）^2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles （10）, whereas Bohai black and Buffalo had the smallest number of private alleles （2）. Chinese Holstein showed the highest genetic variability. Its observed number of alleles （Na）, mean effective number of alleles （MNA）, and mean heterozygosity （He） were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago （MYA）, however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600 MYA, respectively.     

Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers

The genetic structure of five types of Taihu pig (Erhualian, Middle Meishan, Small Meishan, Mizhu and Shawutou), Jiangquhai and Dongchuan pigs in China were investigated, by means of 27 microsatellite markers proposed by the Food and Agriculture Organisation, International Society for Animal Genetics (FAO-ISAG). The Hardy-Weinberg equilibrium test indicated that genetic drift had occurred in these populations, which may be caused by founder effects, intensive selection and close breeding. Genetic heterozygosity and the effective number of alleles per population were calculated, and showed that the genetic variability of the Jiangquhai pig was the largest, while the Small Meishan had the lowest. Genetic differentiation was within each population as shown by the fixation index (F(ST)=0.18). Both a neighbour-joining (NJ) tree constructed from Nei's standard genetic distance and principal component analysis based on allele frequencies can distinguish types of Taihu pig from the other two breeds. Among Taihu pig populations, Erhualian and Mizhu grouped into one branch, while Middle Meishan, Small Meishan and Shawutou clustered as another branch. By including previously published data on European pigs reported, we confirmed that Chinese indigenous pigs and European pigs have diverged into two distinct groups.     

基于微卫星标记的中国枣食芽象甲地理种群遗传多样性分析

【目的】枣食芽象甲Scythropus yasumatsui是我国北方枣树Zizyphus jujuba上的一种重要的灾害性害虫,在陕西、山西、河北、河南等枣树主产区普遍发生。本研究旨在揭示我国枣食芽象甲不同种群间的遗传分化和基因交流规律。【方法】利用枣食芽象甲转录组测序的SSR序列,使用荧光标记PCR及毛细管电泳分型方法,筛选出8个微卫星位点,对我国5个省份(山西、陕西、宁夏、河北和河南)10个地理种群共308头枣食芽象甲样本进行种群遗传多样性分析。【结果】8个SSR位点均存在无效等位基因且偏离哈迪 温伯格平衡。各位点的有效等位基因数(Ne)为2.113~8.016,多态信息含量(PIC)为0.561~0.908,期望杂合度(He)为0.476~0.865;种群间遗传分化系数(Fst)平均值为0.151;基因流(Nm)平均值为1.594。枣食芽象甲种群间遗传分化系数与地理距离之间显著正相关(r=0.596, P=0.0035),基于Nei’s遗传距离和Cavalli-Sforza & Edwards余弦遗传距离的系统进化树将10个地理种群均聚为3个相同的分支。【结论】结果说明,枣食芽象甲种群遗传多样性较高,不同地理种群间存在高度的遗传分化,且有一定的基因交流;地理隔离是影响枣食芽象甲地理种群遗传分化和基因交流的重要因素。     

草鱼野生群体遗传变异的微卫星分析

利用12个微卫星标记, 对来自长江水系(邗江、吴江、九江、石首、木洞和万州)、珠江水系(肇庆)和黑龙江水系(嫩江)的8个草鱼野生地理群体进行了遗传多样性及遗传结构等分析。遗传多样性分析显示, 12个微卫星位点均为高度多态位点(PIC=0.755~0.930), 8个草鱼野生群体显示出较高的遗传多样性水平(Ho=0.839~0.893), 其中长江水系的6个群体和肇庆群体的多样性水平高于嫩江群体。瓶颈效应分析显示, 嫩江、肇庆群体及2个长江上游群体(木洞、万州)近期出现了瓶颈效应, 群体数量发生下降。群体间遗传分化指数F^ST及AMOVA分析显示, 群体间出现极显著遗传分化(P<0.01), 整体分化水平较低(F^ST<0.05)。遗传距离分析结果显示, 长江水系的6个群体与肇庆群体遗传距离较近, 与嫩江群体较远; 基于此的UPGMA聚类树显示, 长江水系下游、中游和上游的群体依次聚类, 然后与肇庆群体聚类, 最后与嫩江群体聚类, 遗传距离与地理距离呈现出较强的正相关性。遗传结构分析显示, 所有样本被划分为5个理论群, 肇庆和嫩江群体中个体的遗传结构相对独立, 而长江上游、中游和下游群体中个体的遗传结构则存在一定程度的混杂。综上所述, 中国草鱼野生资源具有较高的遗传多样性, 地理群体间存在遗传分化, 具有进一步遗传改良的潜力; 但部分群体出现的瓶颈效应也需要引起重视。     

Genetic diversity in Swiss goat breeds based on microsatellite analysis

Genetic diversity in eight Swiss goat breeds was estimated using PCR amplification of 20 bovine microsatellites on 20-40 unrelated animals per breed. In addition, the Creole breed from the Caribbean and samples of Ibex and Bezoar goat were included. A total of 352 animals were tested. The bovine microsatellites chosen amplified well in goat. The average heterozygosity within population was higher in domestic goat (0.51-0.58) than in Ibex (0.17) and Bezoar goat (0.19). Twenty-seven per cent of the genetic diversity in the total population could be attributed to differences between the populations. However, with the exclusion of Ibex from the total population, this proportion dropped to 17%. Principal component analysis showed that all Swiss goat breeds are closely related, whereas the Creole breed, Ibex and Bezoar goat are clearly distinct from all eight Swiss breeds.     

Development of microsatellite markers and their utilization in genetic diversity analysis of cultivated and wild populations of the mud carp （ Cirrhina molitorella）

Microsatellite markers have been increasingly used in genetic studies on fishery species because of their high applicability in selective breeding programs.Here we reported the development of microsatellite markers and their utilization in mud carp(Cirrhina molitorella).An (CA)15 enriched library has been constructed for mud carp,using the magnetic beads enrichment procedure.Sequence analysis of 60randomly picked positive colonies indicate that 56 (93.3%) of the colonies contain microsatellites.Microsatellite polymorphism was as-sessed using 10 mud carp individuals,and 12 microsatellite loci turned out to be polymorphic.We utilized these loci to study the genetic diversity of a wild population (WM) and a cultured population (CM) of the mud carp.A total of 109 alleles were detected with an average of 9.08 alleles per locus.The mean value of the observed heterozygosity of WM and CM was 0.6361 and 0.6417,respectively,and sig-nificant decrease of genetic diversity in CM was not observed.The genetic distance between the two populations was 0.1546 and the value of Gsr was 0.0473.This showed that there existed a slight genetic differentiation between WM and CM.     

微卫星标记分析罗非鱼群体的遗传潜力

利用25个微卫星标记,对奥利亚罗非鱼2个群体["夏奥1号"(ZA)、广西群体(GA)]和尼罗罗非鱼4个群体[埃及品系(ZN)、88品系(XN)、广西群体(GN)、美国品系(MN)]进行检测。共检测到7 775个扩增片段,长度在100~400 bp;等位基因数3~8个不等,共计143个等位基因;平均每个基因座扩增得到5.72个等位基因。各群体平均观测杂合度(H o)在0.7253~0.8160之间,平均期望杂合度(He)在0.5146~0.6834之间,平均多态信息含量(PIC)在0.4212~0.6105之间,平均有效等位基因数(A e)在2.20~3.23之间。ZA与GA遗传相似系数最高(0.9130),ZA与ZN遗传相似系数最低(0.4352)。总的说来,4个尼罗罗非鱼群体的遗传潜力较高,2个奥利亚罗非鱼群体的遗传潜力适中。     

Genetic diversity in Dactylorhiza majalis subsp. majalis populations (Orchidaceae) of northern Poland

We analysed 16 populations of Dactylorhiza majalis subsp. majalis from northern Poland, simultaneously utilizing both morphological and molecular data. Genetic differentiation was examined using five microsatellite loci, and morphological variation was assessed for 23 characters. At the species level, our results showed a moderate level of genetic diversity (A = 6.00; A_e = 1.86; H_o = 0.387; F_IS = 0.139) which varied between the studied populations (A = 2.60–4.20; A_e = 1.68–2.39; H_o = 0.270–0.523; F_IS = ?0.064–0.355). A significant excess of homozygotes was detected in five population, while excess of heterozygotes was observed in four populations, but the latter values were statistically insignificant. Moderate, but clear between population genetic differentiation was found (F_ST = 0.101; p < 0.001). Considering pairwise‐F_ST and number of migrants among populations, we recognized three population groups (I, II, III), where the first could be further divided into two subgroups (Ia, Ib). These three groups differed with respect to gene flow values (N_m = 0.39–1.12). The highest number of migrants per generation was noticed among populations of subgroup Ia (8.58), indicative of a central panmictic population with free gene flow surrounded by peripatric local populations (Ib) with more limited gene flow. Geographic isolation, habitat fragmentation and limited seed dispersal are inferred to have caused limitations to gene flow among the three indicated population groups. There was a significant correlation between the morphological and genetic distance matrices. A weak but significant pattern of isolation by distance was also observed (r = 0.351; p < 0.05).     

Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis

Twelve Chinese indigenous goat populations were genotyped for twenty-six microsatellite markers recommended by the EU Sheep and Goat Biodiversity Project. A total of 452 goats were tested. Seventeen of the 26 microsatellite markers used in this analysis had four or more alleles. The mean expected heterozygosity and the mean observed heterozygosity for the population varied from 0.611 to 0.784 and 0.602 to 0.783 respectively. The mean F_ST (0.105) demonstrated that about 89.5% of the total genetic variation was due to the genetic differentiation within each population. A phylogenetic tree based on the Nei (1978) standard genetic distance displayed a remarkable degree of consistency with their different geographical origins and their presumed migration throughout China. The correspondence analysis did not only distinguish population groups, but also confirmed the above results, classifying the important populations contributing to diversity. Additionally, some specific alleles were shown to be important in the construction of the population structure. The study analyzed the recent origins of these populations and contributed to the knowledge and genetic characterization of Chinese indigenous goat populations. In addition, the seventeen microsatellites recommended by the EU Sheep and Goat Biodiversity Project proved to be useful for the biodiversity studies in goat breeds.     

The variation of 15 autosomal microsatellite DNA loci in five indigenous populations of South Siberia

The allele frequencies of 15 autosomal STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, D16S539, D2S1338, D8S1179, D21S11, D18S51, and D19S433) included into the AmpFlSTR SGM Plus and AmpFlSTR Profiler Plus kits (Applied Biosystems, United States) were determined for five indigenous populations of South Siberia: Buryats, Altaians, Tofalars, Sojots, and Khakassians (N = 261). No significant differences in allele frequencies were found between the populations. The combined power of discrimination of the STR loci was determined for every population.