A multiplex panel of dinucleotide microsatellite markers for the water vole,Arvicola terrestris

We isolated and characterized nine polymorphic dinucleotide microsatellite loci in the fossorial vole Arvicola terrestris Scherman (Shaw). A multiplex panel comprising all nine loci was developed and its application to a set of 31 individuals allowed clear and easy characterization of allele sizes. The number of alleles range from three to 14 per locus with the observed heterozygosity ranging from 0.42 to 0.90. These markers will be useful for analysis of questions concerning population genetic structure and reproductive behaviour.     

Eleven polymorphic microsatellite markers for Oedaleus decorus (Orthoptera, Acrididae), an endangered grasshopper in Central Europe

We isolated and characterized 11 microsatellite loci in the grasshopper Oedaleus decorus (Orthoptera: Acrididae), an endangered species in Central Europe. Polymorphism was studied from two populations, one out of two populations known from Switzerland (n = 20 individuals) and one site from south of France (n = 20). The number of alleles and the expected heterozygosity ranged from five to 12 and from 0.559 to 0.898, respectively, in the Swiss population, and from 14 to 23 and from 0.895 to 0.974, respectively, in the French population. These microsatellite markers are suitable for further conservation genetic studies of O. decorus.     

Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)

The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5.0 (SE = 0.2) and the mean heterozygosity per marker was 0.61 (SE = 0.03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.     

Isolation of polymorphic microsatellite markers for the demersal fish Helicolenus dactylopterus (Dela Roche 1809)

Six microsatellite loci were identified for the demersal deep‐sea fish Helicolenus dactylopterus. All loci were highly polymorphic (5–21 alleles per locus). Observed heterozygosities were from 0.378 to 0.868, while the expected heterozygosities ranged from 0.529 to 0.925. Multiplex PCR reactions were optimized. Microsatellite markers were developed for analysis of genetic structure including identification of stocks and migration patterns. The resulting data will be used to help in the establishment of scientifically based fisheries management for this species. Departures from the expected Hardy–Weinberg equilibrium were observed in three loci, and are likely to be a consequence of population structuring across the Azorean islands.     

Isolation and characterization of the first polymorphic microsatellite markers for Schistosoma haematobium and their application in multiplex reactions of larval stages

The ability of microsatellite loci to reveal genetic diversity within the trematode Schistosoma haematobium is demonstrated for the first time. Nine novel polymorphic microsatellite markers were isolated and their viability assessed on 36 S. haematobium adult worm individuals from three geographical populations. Allelic diversity and gene diversity ranged from two to seven and from 0.29 to 0.76, respectively, suggesting high variability between individuals and between unrelated populations. Three primers also amplified Schistosoma mansoni and two Schistosoma japonicum. The results suggest these primers are useful for population genetic analyses of S. haematobium.     

Microsatellite markers for Bromus tectorum (cheatgrass)

Bromus tectorum (cheatgrass) is a flourishing invasive weed in the western United States. The objective of our study is to characterize its genetic diversity. We made a B. tectorum genomic library in lambda phage and screened approximately 4000 clones for poly CA and poly CT dinucleotide repeats. Of 38 sequences with dinucleotide repeats isolated from the library, we designed primer sets for 18 loci. A preliminary screen of 40 individuals from four populations indicated that seven loci were polymorphic. These loci will be valuable for elucidation of cheatgrass genetic diversity and population structure.     

Isolation of microsatellite markers in mungbean,Vigna radiata

A simple and rapid method for isolating microsatellite loci in mungbean, Vigna radiata, based on the 5′‐anchored polymerase chain reaction technique revealed 23 microsatellite loci and six cryptically simple sequence repeats. We report on the characterization of seven polymorphic microsatellite loci in V. radiata. The number of alleles per locus ranged from 2 to 5 while the observed heterozygosity ranged from 0 to 0.9048. These markers should prove useful as tools for detecting genetic variation in mungbean varieties for germplasm management and crossbreeding purposes.     

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.     

Isolation,characterization and multiplex genotyping of raccoon tetranucleotide microsatellite loci

We have isolated and characterized 12 polymorphic tetranucleotide microsatellite loci in the raccoon (Procyon lotor). Three multiplex panels comprising the 12 loci were developed and 80 individuals from southeastern and western Ontario were genotyped; allele sizes were assigned without difficulty. One locus isolated was identified as an X‐linked marker. The number of alleles per locus ranged from six to 25 with the average heterozygosity ranging from 0.674 to 0.925. These loci will be used to characterize raccoon population structure across North America, and the data used to further understand the spread of raccoon rabies.     

Isolation and characterization of polymorphic microsatellite markers for Alternaria alternata

Alternaria alternata is of major significance as a food and feed contaminant and is able to produce a range of mycotoxins that may elicit adverse effects in both animals and humans. We describe the isolation and characterization of five microsatellite markers for studying A. alternata. Marker polymorphism was screened in 64 isolates of A. alternata. The number of alleles per locus ranged from eight to 24, and allelic diversity ranged from 0.425 to 0.882. These markers will be useful in the study of relationships and population genetics amongst isolates of A. alternata.     

Isolation and characterization of swift fox tetranucleotide microsatellite loci

Primers have been developed for nine polymorphic tetranucleotide microsatellite loci isolated from the swift fox (Vulpes velox). These can be amplified in three multiplex reactions and all loci can be scored easily and without ambiguity. The number of alleles per locus ranged from three to 14 and the overall heterozygosities ranged from 0.54 to 1.00. All loci were in Hardy‐Weinberg equilibrium, but two loci were in linkage disequilibrium. These loci will be used to monitor endangered swift fox populations on the Canadian prairies.     

Identification of microsatellite markers in the red flour beetle,Tribolium castaneum

We isolated and characterized microsatellite markers for the red flour beetle Tribolium castaneum, an important model species for studies in various areas of evolutionary biology and ecology. A microsatellite‐enriched genomic library was constructed and screened with single stranded oligonucleotide probes [(CCT)₁₇, (AAT)₁₇ and (CAG)₁₇]. Forty‐five primer pairs were designed of which 19 pairs produced successful amplification. Polymorphism screening involved beetles from five beetle strains and revealed 15 polymorphic and four monomorphic markers. The development of polymorphic microsatellite markers will facilitate future ecological and genetic studies involving T. castaneum beetles.     

Development of microsatellite markers for noninvasive DNA samples of the eastern green lizard Lacerta viridis

We report the isolation and characterization of microsatellite markers for the eastern green lizard (Lacerta viridis) usable for noninvasive samples. Ten polymorphic loci were obtained by screening 3000 recombinant clones and tested on 39 noninvasive DNA samples of individuals from different locations of the Danube area, Germany. Allelic richness ranged from three to nine alleles, the observed heterozygosity from 0.33 to 0.80, and the expected heterozygosity from 0.36 to 0.85. Our 10 loci, along with another 12 loci previously described, deliver effective analytical tools to analyse the genetic variability and to assess the social structure of eastern green lizard populations.     

Development and multiplex PCR amplification of novel microsatellite markers in the White‐tailed Sea Eagle,Haliaeetus albicilla (Aves: Falconiformes,Accipitridae)

We report the development of 14 novel polymorphic microsatellite markers cloned from the White‐tailed Sea Eagle, Haliaeetus albicilla, a formerly threatened raptor that has received much conservation attention throughout Eurasia. We also present a protocol for multiplex polymerase chain reaction (PCR) amplification of the loci. Among 40 unrelated H. albicilla individuals from southern Sweden, the markers produced two to eight alleles per locus, and average observed and expected heterozygosities were 0.463 and 0.468, respectively. We further present five microsatellite markers that appeared monomorphic in H. albicilla, but which may be of interest for use in other raptor species.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers and analysis of their inheritance in the Australian reptile tick, Bothriocroton hydrosauri

Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile tick species is not understood. We describe the development of primers amplifying 10 microsatellite Bothriocroton hydrosauri loci, for the study of population structure and dispersal patterns of this tick. The numbers of alleles per locus ranged from two to seven in ticks from the study site, and the observed heterozygosity between 0.28 and 0.69. Pedigree analysis indicates that one locus is inherited in a non-Mendelian manner in three families, which was not explained by null allele presence.     

Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens)

In order to assess the applicability of bovine microsatellite markers for population genetic studies in Swiss yak, 131 bovine microsatellite markers were tested on a panel of 10 animals. Efficient amplification was observed for 124 markers (94.6%) with a total of 476 alleles, of which 117 markers (94.3%) were polymorphic. The number of alleles per locus among the polymorphic markers ranged from two to nine. Seven loci (ILSTS005, BMS424B, BMS1825, BMS672, BM1314, ETH123 and BM6017) failed to amplify yak genomic DNA. Two cattle Y-chromosome specific microsatellite markers (INRA126 and BM861) amplified genomic DNA from both male and female yaks. However, two additional markers on cattle Y-chromosome (INRA124 and INRA189) amplified DNA from only males. Of the polymorphic markers, 24 microsatellites proposed by CaDBase for within- and cross-species comparisons and two additional highly polymorphic markers (MHCII and TGLA73) were used to investigate the genetic variability and the population structure of a Swiss yak herd that included 51 additional animals. The polymorphic information content ranged from 0.355 to 0.752, while observed heterozygosity (HO) ranged from 0.348 to 0.823. Furthermore, a set of 13 markers, organized into three multiplex polymerase chain reactions, was evaluated for routine parentage testing. This set provided an exclusion probability in a family of four yaks (both parents and two offspring) of 0.995. These microsatellites serve as useful tools for genetic characterization of the yak, which continues to be an important domestic livestock species.     

Polymorphic microsatellite markers for the human oomycete pathogen Pythium insidiosum

We describe the development and characterization of microsatellite loci from the human oomycete pathogen Pythium insidiosum. Nine of 15 microsatellite loci were shown to be appropriate for population genetic study. All loci were polymorphic with observed heterozygosities ranging from 0.241 to 0.912 and from five to 18 alleles per locus among 65 individuals in Thailand. These markers are being used to ascertain multilocus genotypes for molecular epidemiological and population genetic analyses of this little known human pathogen.     

Polymorphic microsatellite markers for the lizard Psammodromus algirus (Squamata: Lacertidae)

Eight microsatellite loci are described for the lizard Psammodromus algirus, a species widely used as a model in behavioural and ecological studies. All loci were highly polymorphic (six alleles or more per locus) in a sample of 24 individuals from a single site near Navacerrada (central Spain). Observed heterozygosity ranged from 0.29 to 0.96. These markers will be used to study mating strategies and determinants of reproductive success in this species.     

Development and characterization of microsatellite markers for the fungus Ceratocystis fimbriata

Ceratocystis fimbriata is a serious fungal pathogen on a wide range of plants, but many cryptic species within C. fimbriata are apparently host‐specialized. Anchor polymerase chain reaction (PCR) and simple sequence repeat (SSR) enriched libraries were used to develop 16 microsatellite markers for C. fimbriata. All markers were polymorphic when tested against isolates from four host‐specialized lineages of the pathogen. These markers will be valuable for phylogenetic and population genetic studies, as well as for tracking accidental introductions of host‐specialized forms of the pathogen.     

Dinucleotide microsatellite markers from Anopheles funestus

A total of 39 dinucleotide microsatellite‐containing clones were sequenced from a principal African malaria vector, Anopheles funestus. Primers designed to amplify 20 loci were used to genotype A. funestus mosquitoes from Burkina Faso and Kenya. Of nine polymorphic loci that amplified reliably and could be scored unambiguously, the overall within‐sample gene diversity was similar between locales, 0.77 and 0.78, with an allelic richness per locus of five to 11. Both the high level of polymorphism and absence of significant heterozygote deficiency at any locus favour these markers for studies of population structure that are vital to controlling this medically important species.