Characterisation of 14 blue crane <Emphasis Type="Italic">Grus paradisea</Emphasis> (Gruidae,AVES) microsatellite loci for use in detecting illegal trade

Forty-two unique microsatellite loci were isolated from an unenriched and a tetranucleotide-enriched blue crane (Grus paradisea) genomic library. Fourteen polymorphic loci were characterised in 20 unrelated wild blue crane individuals from the Karoo region, South Africa, and displayed 4–27 alleles with observed heterozygosities ranging between 0.50 and 0.95. All 14 loci were also polymorphic in the grey-crowned crane (Balearica regulorum) and the wattled crane (Grus carunculatus). These markers are aimed at assisting the identification of illegal trade in the blue crane but have wider population and conservation applications for most, if not all, crane species.     

梨小食心虫微卫星标记的扩增稳定性及多态性分析

【目的】筛选适合我国梨小食心虫Grapholita molesta种群遗传学研究的微卫星位点,并依据所筛选的微卫星位点进行梨小食心虫地理种群的遗传多样性分析。【方法】利用欧洲梨小食心虫和苹果蠹蛾Cydia pomonella种群中已报道的11个微卫星位点, 分析各位点在我国12个种群257头梨小食心虫样本中的扩增稳定性,再进行其多态性分析,筛选适合的位点,然后进行种群遗传多态性分析。【结果】在分析的11个微卫星位点中, 位点Gm01, Gm03, Gm04和Cyd15无法稳定扩增; 位点Gm05扩增成功率较低, 位点Gm07遗传多态性较低; 而位点Gm02, Gm06, Gm08, Gm09和Gm10等扩增效果稳定且遗传多态性丰富。这5个稳定扩增的微卫星位点平均等位基因数量（N_A）为7.417~12.500, 平均观察杂合度（H_o）为0.366~0.655, 平均期望杂合度（H_e）为0.642~0.846, 多态信息含量（PIC）为0.800~0.935。【结论】本研究成功筛选出位点Gm02, Gm06, Gm08, Gm09和Gm10等5个微卫星位点。基于这5个微卫星位点标记的结果显示, 山东和陕西不同梨小食心虫地理种群均具有丰富的遗传多样性。 这5个位点可以适用于我国梨小食心虫种群的进一步遗传分析研究。     

New polymorphic microsatellite loci developed and characterized from edible dormouse (Glis glis)

Eight new polymorphic microsatellite loci were isolated and characterized from the edible dormouse (Glis glis). All loci were polymorphic in the 70 individuals tested. The number of alleles per locus ranged from 2 to 6, with a mean of 4. Observed and expected heterozygosities ranged from 0.10 to 0.71 and 0.15 to 0.67, respectively. No evidence of linkage disequilibrium between loci has been found. These eight new loci, plus previously characterized markers, now make it possible to undertake more detailed population genetic studies of G. glis, which is relevant to the preservation of this species.     

New microsatellite loci isolated from the field cricket Gryllus bimaculatus characterized in two cricket species, Gryllus bimaculatus and Gryllus campestris

We have developed a new set of 27 polymorphic markers for each of two cricket species, Gryllus bimaculatus and Gryllus campestris. Initially, 14 published G. bimaculatus loci were tested in G. campestris; however, only five loci were polymorphic. Therefore, we isolated an additional 50 new microsatellite loci from G. bimaculatus and tested these in both species. In a minimum of 20 individuals, 27 of the new loci were polymorphic in G. bimaculatus and 25 in G. campestris.     

Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.     

Characterization of Mauritius parakeet (Psittacula eques) microsatellite loci and their cross-utility in other parrots (Psittacidae, Aves)

We characterized 21 polymorphic microsatellite loci in the endangered Mauritius parakeet (Psittacula eques). Loci were isolated from a Mauritius parakeet genomic library that had been enriched separately for eight different repeat motifs. Loci were characterized in up to 43 putatively unrelated Mauritius parakeets from a single population inhabiting the Black River Gorges National Park, Mauritius. Each locus displayed between three and nine alleles, with the observed heterozygosity ranging between 0.39 and 0.96. All loci were tested in 10 other parrot species. Despite testing few individuals, between seven and 21 loci were polymorphic in each of seven species tested.     

Isolation and characterization of microsatellite loci in Portunus pelagicus (Crustacea: Portunidae)

Seven dinucleotide and one tetranucleotide microsatellite loci were isolated and characterized, using routine protocols, from the blue swimmer crab, Portunus pelagicus. These loci will be useful for investigating the population structure of this broadly distributed and economically important portunid. In particular, all eight loci were polymorphic in P. pelagicus collected from throughout Australia. In addition, the genotype frequencies at each locus in each population sample were usually not significantly different from those expected under Hardy–Weinberg equilibrium conditions. Six of the eight loci also showed moderate to high levels of polymorphism in an undescribed species of Portunus from northern Australia.     

Characterization of six microsatellite loci in the Baltic blue mussel <Emphasis Type="Italic">Mytilus trossulus</Emphasis> and cross-species amplification in North Sea <Emphasis Type="Italic">Mytilus edulis</Emphasis>

The blue mussel Mytilus trossulus occurs in the Pacific and in the North Atlantic. We developed and characterized six microsatellite loci for Baltic M. trossulus. Seventeen microsatellite loci were screened, of which six were polymorphic. The number of alleles among 50 individuals ranged from 3 to 13 and the observed and expected heterozygosity were 0.09–0.46 and 0.34–0.86, respectively. The loci were also tested for cross amplification in M. edulis, in which four of the six microsatellite loci were successfully amplified.     

A genome-wide set of 106 microsatellite markers for the blue tit (Cyanistes caeruleus)

We have characterized a set of 106 microsatellite markers in 26-127 individual blue tits (Cyanistes caeruleus), and assigned their location on the zebra finch (Taeniopygia guttata) and on the chicken (Gallus gallus) genome on the basis of sequence homology. Thirty-one markers are newly designed from zebra finch EST (expressed sequence tags) sequences, 22 markers were developed by others from EST sequences using different methods and the remaining 53 loci were previously designed or modified passerine markers. The 106 microsatellite markers are distributed over 26 and 24 chromosomes in the zebra finch and in the chicken genome respectively and the number of alleles varies between 2 and 49. Eight loci deviate significantly from Hardy-Weinberg equilibrium and show a high frequency of null alleles, and three pairs of markers located in the same chromosome appear to be in linkage disequilibrium. With the exception of these few loci, the polymorphic microsatellite markers presented here provide a useful genome-wide resource for population and evolutionary genetic studies of the blue tit, in addition to their potential utility in other passerine birds.     

两种鹤科动物MHC-Ⅰ基因高变区的对比分析

主要组织相容性复合体（MHC）是脊椎动物基因组中高度多态的基因家族,其编码产物在脊椎动物免疫系统中起着重要作用。受湿地生境污染和破坏等因素的影响,全球现存鹤科（Gruidae）动物大都已处于受胁状态。为了解鹤科动物MHC-I基因序列信息,本研究设计通用引物对灰鹤（Grus grus）和肉垂鹤（Bugeranus carunculatus）MHC-I基因进行分离。结果从1只灰鹤和1只肉垂鹤血液基因组中分别分离到2条和3条长约1 500 bp的序列片段,这暗示鹤科动物至少存在两个MHC-I基因座位。分离到的核苷酸序列均可翻译成正常的氨基酸,表明它们具有一定的生物学功能。MHC-I抗原结合区的核苷酸和氨基酸变异率,灰鹤分别为5.0%和9.6%,肉垂鹤为9.1%和14.6%。两种鹤抗原肽结合位点的非同义替代率与同义替代率的比值分别为7.348 8和2.145 2,表明其受到强烈的正选择作用。贝叶斯系统发生树显示,鹤科动物MHC-I基因并未按物种聚类,暗示MHC-I基因跨物种多态性的存在。本研究获得的MHC-I基因通用引物及序列信息,可为今后濒危鹤科动物的保护遗传学研究奠定基础。     

Isolation and characterization of 14 polymorphic microsatellite markers for the blue and red shrimp, Aristeus antennatus (Crustacea, Decapoda)

Eighteen microsatellite loci were isolated and characterized from the blue and red shrimp, Aristeus antennatus Risso 1816, a commercially exploited marine crustacean widely distributed throughout the Mediterranean Sea and in the eastern Atlantic. Polymorphism was assessed in a population (n = 20) from the southwestern Sardinian seas; 14 loci resulted polymorphic and showed from three to 13 alleles. The observed heterozygosity ranged from 0.2 to 0.85. These microsatellites will be potentially useful for the study of A. antennatus population genetic structure.     

Characterization of microsatellite loci In The hihi Notiomystis cincta (Notiomystidae, Aves)

We have characterized 20 polymorphic microsatellite loci in the hihi Notiomystis cincta. Loci were identified by testing loci originally isolated in other avian species and by isolating new microsatellites from a hihi genomic library. These loci were characterized in unrelated hihi from a single population on Tiritiri Matangi Island (n = 98). Each locus displayed between two and 10 alleles, and observed heterozygosities ranged between 0.29 and 0.91. Nineteen of the 20 polymorphic loci could be assigned a chromosome location in the zebra finch, Taeniopygia guttata genome based on sequence homology.     

Isolation and characterization of microsatellite loci in the western long-fingered bat, Miniopterus magnater

We isolated and characterized 10 microsatellite loci in the western long-fingered bat, Miniopterus magnater. These loci were tested on 48 individuals from Anhui Province of China, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.6 (range from six to 27). Observed and expected heterozygosity values ranged from 0.364 to 0.957, and from 0.676 to 0.951, respectively. After Bonferroni correction, four loci deviated significantly from Hardy-Weinberg equilibrium. No pairs of loci were in linkage disequilibrium. These polymorphic markers will be used to examine population structure and genetic diversity in this species.     

Characterization,multiplex conditions,and cross‐species utility of tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi)

We have isolated and characterized 17 tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi), an anuran common in the central USA. Sixteen loci were organized into four multiplex amplification reactions. These loci were highly polymorphic when screened in 55 individuals from two distant populations, with 11–48 alleles per locus (average = 24.8). Observed and expected heterozygosities ranged from 0.18 to 0.97 and from 0.17 to 0.96, respectively. Nine loci were also polymorphic in Acris crepitans crepitans, with seven polymorphic in Acris gryllus. Five loci amplified in all three taxa. These loci will be useful for population‐ and species‐level investigations of this widespread group.     

Isolation and characterization of microsatellite loci in the long-fingered bat Miniopterus fuliginosus

We isolated and characterized 10 microsatellite loci in the long-fingered bat Miniopterus fuliginosus. These loci were tested on 48 individuals from Anhui Province of China, and all loci were highly polymorphic. The mean number of observed alleles per locus was 13.6 (range from six to 27). Observed and expected heterozygosity values ranged from 0.364 to 0.957, and from 0.676 to 0.951, respectively. After Bonferroni correction, four loci deviated significantly from Hardy-Weinberg equilibrium. No pairs of loci were in linkage disequilibrium. These polymorphic markers will be used to examine population structure and genetic diversity in this species.     

Development and characterization of 16 polymorphic microsatellite loci in the Tibet endemic fish Glyptosternum maculatum

Sixteen novel polymorphic microsatellite loci were developed and characterized in Glyptosternum maculatum, an endemic fish inhabiting the Yarlung Zangbo River valley, Tibet, China. These loci were developed after the enrichment of microsatellite-containing genomic DNA fragments with a subtractive hybridization protocol. The polymorphism of these loci was analysed with 36 individuals representing a geographical population. The number of alleles found at these loci ranged from 3 to 10. The observed heterozygosity and expected heterozygosity ranged from 0 to 1 and from 0.31 to 0.75, respectively. These microsatellite loci will certainly facilitate the determination of the genetic structure of G. maculatum and the conservation of its genetic resource.     

Isolation and characterization of polymorphic tetranucleotide microsatellite loci in the pelagic perciform fish Pomatomus saltatrix (Linnaeus, 1766) from South Africa

Eight polymorphic microsatellite loci, containing simple tetranucleotide repeats, were isolated de novo from a Pomatomus saltatrix partial genomic library using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol. These loci were further characterized in 100 individuals from two putative populations off the South African east coast. The loci are highly polymorphic with 18-37 alleles (on average 24 alleles/locus) and the observed heterozygosity in both populations was high (0.79). These loci will be used to assess population structuring in P. saltatrix along the southern African coast with consideration of implications for future management of this important linefish species.     

Cross‐amplification of 10 new isolated polymorphic microsatellite loci for red mullet (Mullus barbatus) in striped red mullet (Mullus surmuletus)

Ten polymorphic dinucleotide microsatellite loci were isolated and characterized for the red mullet (Mullus barbatus). Allele variability was tested on both the red mullet and its congener the striped red mullet (Mullus surmuletus). Characterization of 30 individuals of both species from the western Mediterranean showed moderate to high allelic diversity ranging from two to 26 alleles per locus (mean 10.9). Three loci showed departures from Hardy–Weinberg proportions. No evidence of significant association between genotypes at pairs of loci was observed. These polymorphic loci could be suitable for population genetic assessments of both species.     

PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci in the Mediterranean shore crab Carcinus aestuarii (Decapoda, Portunidae)

We characterized nine polymorphic microsatellites in the Mediterranean shore crab Carcinus aestuarii (Decapoda: Portunidae). Microsatellites were isolated from a partial genomic library enriched for multiple motifs. All loci were polymorphic, with number of alleles ranging from two to 16 and a mean observed heterozygosity of 0.75. Seven loci were in Hardy-Weinberg equilibrium, and two showed weak heterozygote deficiency. No linkage disequilibrium was found between loci. In addition, we tested Hardy-Weinberg and linkage equilibrium of three Carcinus maenas loci, already reported to cross-amplify in C. aestuarii. These molecular markers will be potentially useful to investigate genetic structure of this species.     

Microsatellite loci for the Siberian flying squirrel,Pteromys volans

We report the isolation and characterization of polymorphic microsatellite loci for the Siberian flying squirrel Pteromys volans. The seven most useful loci had between six and 11 alleles and expected heterozygosities ranging from 0.477 to 0.866. We also tested the utility of these loci in other squirrel species, northern flying squirrels (Glaucomys sabrinus and G. volans) and the common red squirrel (Sciurus vulgaris). Three of the Siberian flying squirrel loci were polymorphic in other squirrel species, suggesting a limited potential for cross‐species use.