纯种犬在15个STR基因座上的遗传多态性

目的:指导纯种犬的繁育及建立一套简便的犬个体识别和亲权鉴定方法。方法:通过设计引物进行PCR扩增及PAGE检测的方法,分析了88头纯种犬在15个STR基因座上的遗传学多态性。结果:15个STR基因座的累积非父排除率(CPE)和累积个体识别率(TDP)分别为0.999678和0.999999999997,而平均杂合度和平均多态信息含量分别为0.607和0.640。12个STR基因座(PEZ1、PEZ2、PEZ3、PEZ5、PEZ6、PEZ8、PEZ12、FHC2010、FHC2054、FHC2087UbF、HC2132、FHC2611)的多态信息含量(PIC)和杂合度(H)大于0.5,它们的TDP和CPE值分别为0.999999999963和0.999334,能有效用于犬的个体识别和亲权鉴定。结论:这15个STR基因座可以用于指导犬的繁育,其中12个STR基因座能有效用于犬的个体识别和亲权鉴定。     

Characteristics of 13 polymorphic microsatellite markers in the corn earworm,Helicoverpa zea (Lepidoptera: Noctuidae)

Thirteen polymorphic microsatellite loci suitable for population genetic studies of Helicoverpa zea were discovered by screening partial genomic libraries enriched for microsatellite sequences. Insects collected (N = 96) in Stoneville, Mississippi were used to characterize these markers. The observed and effective number of alleles per locus ranged from two to nine (average 4.46) and from 1.07 to 2.45 (average 1.81), respectively. Fisher exact tests detected significant deviations from Hardy–Weinberg equilibrium at three loci, probably due to inbreeding, null alleles, or Wahlund's effect. Significant genotypic disequilibrium was not detected between any pair of loci.     

Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners

Eight new microsatellite loci were characterized for Littorina saxatilis (Olivi, 1792) and tested for their cross-hybridization in congeners. All loci were polymorphic in Irish and Celtic Sea samples, with an average number of alleles per locus of 15 (range, 6–31). Observed and expected locus heterozygosities ranged from 26 to 85% and from 53 to 92%, respectively. Three loci showed excess homozygosity and significant departures from Hardy–Weinberg expectations in one sample, possibly due to null alleles, population structuring or inbreeding. No linkage disequilibrium was detected among loci within samples. A high degree of cross-hybridization was observed in closely related congeners and most loci were polymorphic. These markers will be useful for investigating population genetic diversity and connectivity in coastal populations, especially for marine reserve design.     

德宏水牛微卫星标记分析的群体遗传变异

德宏水牛是云南省地方水牛的优良品种之一,为了进一步阐明其群体遗传变异和遗传结构,筛选了分别位于水牛14条染色体上的15对微卫星引物,对德宏水牛81个个体进行了检测分析.共检测到62个等位基因,每个座位等位基因数目从2到6个不等,平均等位基因数为4.13,该水牛群体期望杂合度和多态信息含量分别为0.6520±0.1526和0.5863±0.1789,各座位的遗传分化系数在0～0.0919之间,平均值为0.0202.每个座位的基因流较大,平均12.1502.研究结果表明德宏水牛群体遗传多样性较丰富,亚群间的遗传分化程度低,基因流较大,且很少发生近交.     

Genetic diversity among horse populations with a special focus on the Franches-Montagnes breed

Genetic characterization helps to assure breed integrity and to assign individuals to defined populations. The objective of this study was to characterize genetic diversity in six horse breeds and to analyse the population structure of the Franches-Montagnes breed, especially with regard to the degree of introgression with Warmblood. A total of 402 alleles from 50 microsatellite loci were used. The average number of alleles per locus was significantly lower in Thoroughbreds and Arabians. Average heterozygosities between breeds ranged from 0.61 to 0.72. The overall average of the coefficient of gene differentiation because of breed differences was 0.100, with a range of 0.036-0.263. No significant correlation was found between this parameter and the number of alleles per locus. An increase in the number of homozygous loci with increasing inbreeding could not be shown for the Franches-Montagnes horses. The proportion of shared alleles, combined with the neighbour-joining method, defined clusters for Icelandic Horse, Comtois, Arabians and Franches-Montagnes. A more disparate clustering could be seen for European Warmbloods and Thoroughbreds, presumably from frequent grading-up of Warmbloods with Thoroughbreds. Grading-up effects were also observed when Bayesian and Monte Carlo resampling approaches were used for individual assignment to a given population. Individual breed assignments to defined reference populations will be very difficult when introgression has occurred. The Bayesian approach within the Franches-Montagnes breed differentiated individuals with varied proportions of Warmblood.     

秦川母牛群体遗传特性的微卫星标记研究

为了从DNA分子水平揭示秦川牛群体遗传多态性和群体遗传结构,寻找可用于秦川牛的微卫星标记,本研究选择了12个普通牛（Bos taurus）微卫星标记检测了90头秦川母牛各微卫星位点的遗传变异及多态性。结果表明,在秦川母牛群体中,12个微卫星位点共检测到了247个等位基因,各位点的等位基因数在13（INRA005）～33个（HEL13）之间,平均每个微卫星位点的等位基因数为21个;总有效等位基因数和平均每个位点平均有效等位基因数（Ne）分别分为142．6229和11．8852。各位点平均基因频率取样方差（V（pij））为2．6036×10^-4。12个微卫星位点平均观察杂合度（Ho）和平均期望杂合度（He）在0．7842（INRA005）～0．9775（BM315）和0．7952（BM315）～0．9446（HEL13）之间。12个位点平均多态信息含量（PIC）在0．7653（INRA005）～0．9420（HEL13）之间,平均为0．8965．12个微卫星位点均属于高度多态位点,这表明秦川母牛群体中所检测各微卫星位点具有丰富的遗传多态性,具备较大的选择潜力。12个微卫星位点的平均固定指数（F）为-0．0076,即各位点杂合子的缺陷度不高,即偏离Hardy—Weinberg平衡的程度不大。     

Length polymorphism and allele structure of trinucleotide microsatellites in natural accessions of Arabidopsis thaliana

 The objective of this work was to assess the degree of trinucleotide microsatellite length polymorphism in the selfing species Arabidopsis thaliana. PCR amplifications of 12 microsatellite loci among 49 natural populations revealed between one to eight length variants (alleles) for each locus. The average number of alleles per locus was four and the average genetic diversity index was 0.43. Divergence between length variants was investigated at the nucleotide level. Several observations emerge from the sequence data: (1) for most loci, length polymorphism results only from variations in the number of trinucleotide repeats; (2) for a few others, some variability was noted in the flanking sequences; (3) for compound and interrupted loci containing two arrays of trinucleotide repeats, length variations preferentially affect the longest one. Five of the Arabidopsis thaliana accessions were clearly composed of two sublines. In 2 other accessions, some heterozygous individual plants, probably resulting from recent outcrosses, were found. A phylogenetic tree constructed on the basis of trinucleotide microsatellite allelic diversity shows that genetic relationships among the accessions are not correlated with their geographic origin. Received: 4 November 1997 / Accepted: 3 March 1998     

Development of microsatellite loci in pinto abalone (Haliotis kamtschatkana)

Twelve novel di‐, tri‐ and tetranucleotide microsatellite loci to the pinto abalone (Haliotis kamtschatkana) are described. Over 400 individuals were analysed at each microsatellite locus. Observed heterozygosities ranged from 0.44 to 0.93, and numbers of alleles from 20 to 63. Six of the loci contained excesses in homozygosity indicative of inbreeding, nonrandom mating, population admixture, or null alleles.     

Development of twelve novel polymorphic microsatellite DNA markers for the Boeseman’s rainbowfish (Melanotaenia boesemani) and tests for their cross-utility in 21 rainbowfish species from West Papua (Indonesia)

We developed 12 microsatellite markers for the endangered Boeseman’s rainbowfish (Melanotaenia boesemani). Twenty-eight individuals from the type locality at Ayamaru Lake were examined, and all loci were polymorphic with a number of alleles per locus varying from 3 to 18. Average observed and expected heterozygosities were 0.681 and 0.678, respectively. Cross-species amplification was successfully obtained for 21 Melanotaenia species, with a number of alleles per locus ranging between 1 and 20. Average observed and expected heterozygosities varied between 0.105 and 0.708 and 0.118–0.755, respectively. Only 21 inbreeding coefficient (Fis) values presented a significant homozygote excess among the 264 locus-by-locus calculated values. Tests for genotyping errors revealed that four of these 21 significant Fis values could be explained by the presence of null alleles. These new microsatellite markers appear highly reliable for further conservation purposes or population genetic studies of the many rainbowfish endangered species.     

Microsatellite primers for the four Galápagos mockingbird species (Mimus parvulus, Mimus macdonaldi, Mimus melanotis and Mimus trifasciatus)

Nineteen di- and tetranucleotide and one trinucleotide microsatellite DNA markers were isolated from the Galápagos mockingbird (Mimus parvulus) and tested for cross-species amplification in the other three mockingbird species in the Galápagos. In addition, primers for two microsatellite loci previously developed for Mimus polyglottos were redesigned to obtain shorter amplification fragments. The number of alleles per locus and species ranged from 1 to 8, and expected heterozygosity varied from 0.0 to 0.809. These microsatellite markers will be useful to study levels of inbreeding in different island populations.     

Polymorphic microsatellite loci isolated from the Atlanto‐Mediterranean colonial ascidian Pycnoclavella sp. (Ascidiacea,Tunicata)

Eight microsatellite loci were characterized in the colonial ascidian Pycnoclavella sp. from an enriched library of genomic DNA. Most microsatellites were large and compound. Allelic variation was assessed in 30 individuals collected from Cerro Gordo (SW Mediterranean Sea). The number of alleles per locus ranged from one to nine, observed heterozygosity from 0.05 to 0.29 and expected heterozygosity from 0.15 to 0.39. No significant linkage disequilibrium between pairs of loci was detected, but five loci showed significant heterozygote deficiency that may be explained either by inbreeding, population substructure or the presence of null alleles.     

Eighteen novel polymorphic microsatellite loci developed from the Père David’s deer (<Emphasis Type="Italic">Elaphurus davidianus</Emphasis>)

Père David’s deer is a severely bottlenecked species but without showing inbreeding depression, making it essential to develop molecular markers to explore her genetic mechanism of population recovery. In this study, we isolated 18 novel polymorphic microsatellite loci from a dinucleotide-enriched library. This suit of markers presented 2–3 alleles for each locus and their observed and expected heterozygosities were 0.057–0.610 and 0.056–0.598, respectively. These new microsatellite loci had an average of 2.12 alleles and thus contributed to relatively low exclusion probabilities of parentage and paternity testing (0.768 and 0.921). However, when these loci were examined in combination with previous microsatellite markers, overall probabilities of parentage and paternity exclusion went up to 0.905 and 0.990, respectively, showing that these 26 microsatellite loci should be adopted together in future genetic analyses for this highly inbred species.     

Microsatellite analysis of genetic diversity in wild and farmed Emus (Dromaius novaehollandiae)

The emu (Dromaius novaehollandiae) occupies most regions of the Australian continent and in recent times has been farmed for meat, oil, and leather. Very little is known about the genetic structure of natural or farmed populations of these birds. We report a preliminary study of genetic variation in emus undertaken by typing birds from five farms and two natural populations at five polymorphic microsatellite loci. Genetic diversity was high for all populations and there was little evidence of inbreeding, with most populations conforming to Hardy-Weinberg equilibrium for most loci. Significant heterozygote deficiencies at one locus in a number of populations were detected and may indicate the presence of null alleles. Comparisons of allele frequencies showed little evidence of genetic differentiation either among farmed populations or between farmed and natural populations.     

Isolation and characterization of 15 polymorphic microsatellite markers for the fig-pollinating wasp,Blastophaga nipponica (Hymenoptera: Agaonidae)

We developed microsatellite markers for the fig-pollinating wasp Blastophaga nipponica Grandi using a dual-suppression-PCR technique. Twenty-one candidates of microsatellite loci were obtained, of which 15 yielded scorable patterns. The degree of polymorphism for the 15 loci was further characterized using summary statistics describing the genetic variation in 60 individuals from three natural populations in Japan. All 15 loci were polymorphic and yielded 2–27 alleles per locus. Overall observed heterozygosity (H _O) and expected heterozygosity (H _E) were 0.465 and 0.631, respectively. As expected, based on the inbreeding tendency of this species, the mean inbreeding coefficient (F _IS) was high (= 0.255). These markers will contribute to studies on the population structure of this species.     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Isolation and characterization of 23 microsatellite loci in the hen flea Ceratophyllus gallinae

Nineteen dinucleotide, two trinucleotide and two tetranucleotide microsatellite loci developed for the hen flea Ceratophyllus gallinae are presented. Twenty fleas were screened at each locus. Loci were polymorphic (three to nine alleles per locus). These markers will provide a system to study population segregation and diversity, gene flow, dispersal and inbreeding.     

Isolation and characterization of 16 microsatellite loci in the Great Tit Parus major

Six dinucleotide, three trinucleotide and seven tetranucleotide microsatellite loci developed for the great tit Parus major are presented. Thirty individual birds were screened at each locus. Loci were polymorphic (four to 19 alleles per locus). These markers provide a system to study paternity, genetic diversity in natural populations, gene flow, dispersal and inbreeding.     

Isolation and characterization of microsatellite markers in the solitary hunting wasp Ancistrocerus adiabatus (Vespidae: Eumeninae) and their cross utility in other species of Ancistrocerus

We have developed seven microsatellite primers for the solitary wasp Ancistrocerus adiabatus. The number of alleles per locus ranged from three to 14. The markers were developed to study population structure, inbreeding and sex determination of A. adiabatus. For each locus, we genotyped 30 female wasps collected from Southwest Michigan. The observed heterozygosity ranges from 0.067 to 0.933. We have also determined that primers for these microsatellite loci amplify in three other species in the genus: Ancistrocerus antilope, Ancistrocerus catskill, and Ancistrocerus campesterus.     

Allozyme variation of Cyclobalanopsis championii (Fagaceae), a narrowly distributed species in southern Taiwan

Allozyme genetic variability in five natural populations of Cyclobalanopsis championii (Fagaceae) in Taiwan was investigated using 12 loci from 9 enzyme systems. The average values of parameters describing within-population variation, expected heterozygosity (He = 0.151), the percentage of polymorphic loci per individual (P = 50%), the average number of alleles per locus (A = 1.7), effective number of alleles per locus (Ae = 1.25), and the average number of alleles per polymorphic loci (AP = 2.2) are comparable to those of other long-lived woody plants. The overall fixation index (Fis = 0.208) indicates a significant deficiency of heterozygotes at the population level. Allelic frequency deviation from Hardy-Weinberg equilibrium was found for different loci in different populations. An exact test for population differentiation using the Tools for Population Genetic Analyses program also indicates that allelic frequencies among populations are significantly different (P < .001). Among-population variation, Gst, accounted for 9.2% of the total heterozygosity. The population at Shouchia and the southernmost population Nanjenshan had higher inbreeding coefficients (0.177 and 0.153, respectively) than did the northern populations. Genetic drift is supported by the observations of the variance components of linkage disequilibrium and a large proportion of loci in Nanjenshan and Shouchia that show pairwise locus disequilibrium. We believe continuous genetic drift in the southern populations will increase genetic divergence among populations of C. championii in Taiwan. Significant correlation was found between elevation and expected heterozygosity. We therefore inferred that temperature is the most important ecological factor to influence the genetic diversity of C. championii.     

Allelic and population variation of microsatellite loci in aspen (Populus tremuloides)

To develop a robust basis for inferences about population genetics and evolution, this work assayed 192 aspens (Populus tremuloides) from 11 sites in Wisconsin, USA, for allelic and population variation at 16 microsatellite loci distributed across the Populus genome. Frequency distributions of fluorochrome-labeled alleles resolved by capillary electrophoresis were analyzed for relationships to repeat size and number. Population-level statistics were compared with those of other studies, especially in Populus. All loci were polymorphic, varying widely in the number of alleles per locus (mean = 8.25, range 2-20). Expected and observed heterozygosities were high (0.45 and 0.41, respectively), with little differentiation among populations (F(ST) = 0.006-0.045) and a moderate level of inbreeding (F(IS) = 0.09), intermediate among levels reported in studies based on isozymes. Contrary to several other reports, allele frequencies clustered tightly around the modal frequency, and the genetic diversity (measured as alleles per locus or as expected heterozygosity) was not related to either the repeat unit size or to the number of repeats.