Isolation and characterization of microsatellite markers for the endangered Monimopetalum chinense (Celastraceae)

We describe the isolation and characterization of 13 polymorphic microsatellite loci in the endangered Monimopetalum chinense (Celastraceae) using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol in this paper. The 13 loci were tested in 20 individuals from two populations. The number of alleles per locus varied from 2 to 8, with an average of 3.8. The expected and observed heterozygosities ranged from 0.05 to 0.87 and from 0.05 to 0.55, respectively. Two of the 13 loci were biased from Hardy–Weinberg equilibrium. No significant linkage disequilibrium was found among all loci. These polymorphic SSR markers will be useful in studying population genetics of M. chinense.     

Development and Characterization of 15 Polymorphic Micro satellite Markers for a Highly Adaptive and Wide-range Frog （Microhyla fissipes）

In order to analyze population genetic structure at multiple spatial scales, microsatellite loci were developed for the ornamented pygmy flog （Microhylafissipes）, and 15 polymorphic microsatellite loci were successfully screened from 105 individuals, of which 82 from four populations distributed in the Sichuan Basin and 23 from the Sangzhi population in western Hunan. Five loci were found to deviate significantly from Hardy-Weinberg equilibrium in one to three popu lations, probably due to small sample size or null alleles. The average number of alleles in all loci was 8.5, ranging from 4 to 13, and the observed and expected heterozygosity ranged from 0.26 to 0.90 and 0.63 to 0.90, respectively. The Sangzhi population and the remaining four populations can be clearly separated using Bayesian clustering methods, showing that the genetic structure of M. fissipes was probably affected by the topography, especially mountain barriers. These polymorphic microsatellite loci could be used for further study on the landscape genetics of this highly adaptive and widely distributed species.     

Ten polymorphic tetranucleotide microsatellite markers isolated from the Anolis roquet series of Caribbean lizards

The Anolis roquet series of Caribbean lizards provides natural replicates with which to examine the role of historical contingency and ecological determinism in shaping evolutionary patterns. Here, we describe 10 polymorphic tetranucleotide microsatellites to facilitate studies on population differentiation and gene flow. All loci successfully amplified in several species from this series. Genotyping 96 individuals from two A. roquet populations demonstrated the markers’ suitability as population genetic markers: genetic diversity was high (9–22 alleles per locus); there were no instances of linkage disequilibrium; and, with one exception, all genotypic frequencies conformed to Hardy–Weinberg equilibrium expectations.     

Characterization of expressed sequence tag‐derived microsatellites from the kuruma prawn,Marsupenaeus japonicus

The kuruma prawn, Marsupenaeus japonicus, is a commercially important benthic marine crustacean in East Asia. Understanding the species’ population structures will be very important for its proper stock assessment and management strategy. Herein, 13 polymorphic microsatellite loci originating from expressed sequence tag libraries of M. japonicus were isolated and characterized. Number of alleles per locus ranged from two to 15, observed and expected heterozygosities ranged from 0.250 to 0.906 and from 0.310 to 0.932, respectively. The adequate level of variability within the population renders these microsatellite loci ideal markers for population genetic analysis of M. japonicus.     

Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola

A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.     

Weak founder effect signal in a recent introduction of Caribbean Anolis

Species introductions provide a rare opportunity to study rapid evolutionary and genetic processes in natural systems, often under novel environmental pressures. Few empirical studies have been able to characterize genetic founder effects associated with demographic bottlenecks at the earliest stages of species introductions. This study utilizes prior mitochondrial DNA information which identifies the putative source population for a recently established ( c . 7 years between import and sampling) species introduction. We investigated the evidence for a founder effect in a highly successful introduction of a Puerto Rican Anolis species that has established itself on Dominica to the localized exclusion of the native, endemic anole. Five highly polymorphic microsatellite loci were used to explore the partitioning of genetic diversity within and between native source, native nonsource, and introduced populations of Anolis cristatellus . Group comparisons reveal significantly lower allelic richness and expected heterozygosity in introduced populations compared to native populations; however, tests for heterozygosity excess relative to allelic richness failed to provide consistent evidence for a founder effect within introduced populations. Significant levels of within-population genetic variation were present in both native and introduced populations. We suggest that aspects of the reproductive ecology of Anolis (high fecundity, sperm storage and multiple paternity) offer an important mechanism by which genetic variation may be maintained following demographic bottlenecks and founder events in some squamate taxa.     

微卫星DNA与生化标记分析对长爪沙鼠群体遗传分析的比较

目的比较生化标记和微卫星DNA标记方法对长爪沙鼠群体遗传分析的可靠性。方法应用27个生化位点和13个微卫星DNA位点,采用已建立的生化标记和微卫星DNA标记分析方法对国内2个长爪沙鼠群体进行遗传分析,计算并比较两种方法测得的各群体遗传参数。结果生化基因位点中有13个位点在整体中呈现遗传多态性,多态率为48.1%;微卫星位点中有11个位点在整体中表现出多态性,多态率均为84.6%。两种方法测得的平均有效等位基因数趋于一致,微卫星DNA的多态位点百分率和平均杂合度均明显高于生化标记方法。但生化标记和微卫星DNA检测对两个长爪沙鼠群体的遗传多样性差异反映一致,所反映的群体平衡状况也基本一致。结论生化标记分析和微卫星DNA方法均可较好地反映长爪沙鼠群体遗传结构。     

PERMANENT GENETIC RESOURCES: Polymorphic microsatellite loci and interspecific cross-amplification in the parasitoid wasps Megastigmus stigmatizans and Megastigmus dorsalis

We isolated and characterized 19 polymorphic microsatellite loci in the congeneric parasitoid wasps Megastigmus stigmatizans and Megastigmus dorsalis associated with cynipid oak galls. Loci isolated from species-specific libraries showed extensive cross-amplification, resulting in a total of 15 polymorphic loci for M. stigmatizans and 13 for M. dorsalis.     

Genetic analysis of fingerprints in Mérinos d''Arles X Booroola Merino crossbred sheep

The M13.13 minisatellite probe, consisting of a polymer of the M13 VNTR consensus sequence, cross-hybridized to ovine DNA and allowed detection of several polymorphic loci. Individual specific patterns were obtained in sheep using this probe. Pedigree analysis showed that individuals were heterozygous for most of the DNA fragments detected (88%). By studying the segregation of male's variable DNA fragments, a minimum of 10 loci were defined. The ovine DNA 'fingerprint' obtained with M13.13 is polymorphic enough to be used efficiently in animal identification, paternity testing, and possibly as a source of genetic markers for linkage analysis.     

Development of linkage map in F2 population of selected parents with respect to Macrophomina phaseolina resistance trait using screened polymorphic RAPD and developed SCAR markers of jute

Two molecular markers (RAPD and simple sequence repeat (SSR)) were applied on 12 Corchorus capsularis jute samples. Two of them were Macrophomina phaseolina-resistant and the remaining eight were M. phaseolina-susceptible accessions. Eleven SSR primer combinations out of 18 gave the polymorphic results between M. phaseolina-resistant and -susceptible accessions. Five pairs of sequence characterised amplified region (SCAR) primers designated as SCP-4, SCS-3, SCS-13, SCG-10 and SCU-10 were designed based on the polymorphic loci obtained between JRC-412 and CIM-036. Only SCU-10 and SCS-13 produced polymorphic markers corresponding to OPU-10 and OPS-13 amplified from ‘CIM-036’ and JRC-412, respectively. RAPD and SCAR markers were employed for construction of a linkage map using a set of 67 F2 population of a cross between JRC-412 and CIM-036 as a mapping population. Nine markers were assigned to two linkage groups (LGs) covering a total length of 628.4 cM with an average distance of 28 cM between markers.     

Characterization of novel microsatellite loci in rare minnow (<Emphasis Type="Italic">Gobiocypris rarus</Emphasis>) and amplification in closely related species in Gobioninae

Rare minnow (Gobiocypris rarus) is an endangered small fish endemic to upper reach of the Yangtze River. From a (GT)n enriched genomic library, 32 microsatellites were isolated and characterized. Nineteen of these loci were polymorphic in a test population with alleles ranging from 2–7, and observed and expected heterozygosities from zero to 0.8438, and 0.2679 to 0.8264, respectively. In the cross-species amplifications, 13 out of 19 polymorphic loci were found to be also polymorphic in at least one of the 7 closely related species of the subfamily Gobioninae. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the fine-scale population structure in rare minnow and its closely related species for the conservation purpose.     

Polymorphic dinucleotide microsatellites in tongue sole (Cynoglossus semilaevis)

The tongue sole, Cynoglossus semilaevis, is a rare marine flatfish distributed in Chinese coastal waters. From a (GT)_n‐enriched genomic library, 57 microsatellites were isolated and characterized. Seventeen of these loci were polymorphic in a test population with alleles ranging from three to 13, and observed and expected heterozygosities from 0.1613 to 1.0000 and from 0.2126 to 0.8983, respectively. Five loci deviated from the Hardy–Weinberg equilibrium in the sampled population, and linkage disequilibrium between two loci was significant after applying Bonferroni correction. Three additional fish species assessed for cross‐species amplification revealed that only one locus was also polymorphic in one species. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to evaluate the breeding strategy and investigate the fine‐scale population structure in C. semilaevis.     

Rapid isolation and characterization of polymorphic microsatellite loci in the mud crab, Scylla paramamosain (Portunidae)

Scylla paramamosain is a widespread and commercially important species of coastal marine crab. We identified 13 polymorphic microsatellite loci from a genome library constructed with 5'-anchored PCR method. Thirty-two S. paramamosain from the East China Sea were used to analyze the characteristics of these loci. The number of alleles per locus ranged from 3 to 8, with a mean of 5.923. Observed and expected heterozygosities ranged from 0.500 to 0.875 and from 0.500 to 0.859, respectively. Eleven of the 13 loci were highly polymorphic (polymorphic information content >0.5). All of the 13 novel loci were in Hardy-Weinberg equilibrium after Bonferroni's correction (P < 0.0038). There was no null allele, stuttering errors or evidence of allelic dropout in any of the loci analyzed by MICRO-CHECKER. According to pairwise tests, no significant linkage disequilibrium was found among the 13 loci (P < 0.0038, adjusted value). These novel developed microsatellites will be useful for studies of genetic variation, population structure, conservation genetics, and molecular-assisted selective breeding of S. paramamosain.     

Isolation and characterization of polymorphic microsatellite loci in Wuchang bream (Megalobrama amblycephala)

Wuchang bream (Megalobrama amblycephala) is an economically important fish in China. From a (GT)₁₃‐enriched genomic library, 20 microsatellites were developed. Nine of these 20 loci were polymorphic in a test population with allele numbers ranging from two to four, and the observed and expected heterozygosities ranging from 0.2609 to 0.7826 and from 0.3739 to 0.7546, respectively. In the cross‐species amplifications, six of these nine loci were also polymorphic in white amur bream (Parabramis pekinensis). These polymorphic microsatellite loci are potentially useful for population genetics of Wuchang bream and its closely related species.     

PERMANENT GENETIC RESOURCES: Isolation, characterization and multiplex genotyping of 11 autosomal and four sex-linked microsatellite loci in the reed bunting, Emberiza schoeniclus (Emberizidae, Aves)

Fifteen highly polymorphic microsatellite loci were characterized in the reed bunting, Emberiza schoeniclus. Eleven loci were autosomal and four linked to the Z chromosome. All loci were characterized and tested in 45 unrelated reed buntings from a Swiss population. Autosomal loci displayed seven to 17 and sex-linked loci displayed four to 13 alleles with heterozygosities ranging from 0.756 to 0.933 and from 0.478 to 0.957, respectively. These loci will be used in population genetic and mating system studies of reed buntings.     

Polymorphic microsatellite loci for the Puerto Rican crested anole (<Emphasis Type="Italic">Anolis cristatellus</Emphasis>) and their amplification in related Puerto Rican species

We isolate six highly polymorphic microsatellite loci for the Puerto Rican crested anole (Anolis cristatellus) from a genomic library enriched for CA repeats. The number of alleles per locus ranged from 14 to 19, with levels of observed heterozygosity ranging from 0.60 to 0.73. Most of these loci were successfully cross-amplified in other members of the cristatellus species group (A. evermanni, A. gundlachi, A. krugi, A. stratulus), but levels of polymorphism were lower.     

Isolation and characterization of 16 polymorphic microsatellite loci in the endemic Hawaiian damselfly Megalagrion xanthomelas (Odonata: Coenagrionidae)

Microsatellite loci have been isolated from two species of endemic Hawaiian damselflies, Megalagrion xanthomelas and M. eudytum, that are of conservation concern. Sixteen polymorphic loci were characterized in 32 M. xanthomelas from one population on Molokai and one on Hawaii Island. The total number of alleles per locus ranged from two to 16 and observed population heterozygosity ranged from 0.0 to 0.963. Eleven of these loci amplified successfully in M. eudytum as well. These loci will be used to further conservation efforts and infer genetic consequences of Pleistocene glaciations.     

Microsatellite markers for the common vole (<Emphasis Type="Italic">Microtus arvalis</Emphasis>) and their cross-species utility

Fragmentation of natural habitats of the common vole (Microtus arvalis) provides an excellent model system to study the consequences of restricted gene flow and small population sizes for isolated populations. Here we describe the isolation and characteristics of 10 autosomal and one X-linked microsatellite marker. These new markers were tested in 24 voles from a natural population in eastern Germany. Loci were highly polymorphic with numbers of alleles per locus ranging from three to 26 and expected heterozygosities from 0.51 to 0.97. All loci except for the X-linked locus Mar105 followed Hardy–Weinberg expectations. Cross-species amplifications revealed that most loci were polymorphic as well in M. agrestis, M. thomasi, and M. pennsylvanicus.     

Isolation and characterization of fourteen microsatellite loci for striped field mouse (<Emphasis Type="Italic">Apodemus agrarius</Emphasis>)

We describe the isolation and characterization of 14 microsatellite loci in the striped field mouse from genomic DNA-enriched libraries in this paper. The 14 new loci were tested in 24 individuals from four populations in Southwest China. These loci were highly polymorphic with numbers of alleles per locus ranging from 6 to 14 and expected heterozygosities from 0.789 to 0.925. All loci followed Hardy–Weinberg expectations except SFM4, SFM11 and SFM13 loci. No significant linkage association was found among all loci. The 14 novel polymorphic microsatellite loci will be useful in studying phylogeography and population genetics of the striped field mouse.