Development of eight polymorphic microsatellites for a Zn/Cd hyperaccumulator Sedum alfredii Hance (Crassulaceae)

Sedum alfredii is a Zn/Cd hyperaccumulator distributed in East Asia. A total of eight polymorphic microsatellite markers were developed. These loci were screened in 25 individuals from one heavy metal-tolerant population and one nontolerant population, respectively. The average allele number of these markers was 5.25 per locus, ranging from two to nine. Population-specific alleles were found at each locus. The observed and expected heterozygosities ranged from 0.000 to 0.640 and from 0.451 to 0.819. Significant deviation from Hardy-Weinberg equilibrium was detected at both the species and the population level. No significant linkage disequilibrium was detected at population level.     

Isolation and characterization of microsatellite loci from Lochmaea suturalis, the heather beetle (Coleoptera: Chrysomelidae), a pest in Europe and a biocontrol agent in New Zealand

The heather beetle Lochmaea suturalis which is native to northwest Europe has been released as a biocontrol agent for heather in New Zealand. We have isolated and optimized eight microsatellite loci from New Zealand beetles. These loci provide markers with high polymorphism ranging from four to 20 alleles per locus. Observed heterozygosity averaged 0.631 per locus. These results suggest the markers are useful for population studies that will contribute to assessment of L. suturalis as a biocontrol agent.     

Isolation and validation of eight microsatellite loci in a damselfly Ischnura senegalensis (Odonata: Coenagrionidae) by pyrosequencing a bead-enriched library

Eight microsatellite markers for the population genetics and evolutionary ecology of Ischnura senegalensis (Rambur 1842), which shows body color polymorphism in females, were developed using a streptavidin-bead enrichment library and pyrosequence by a next generation sequencer. The number of alleles per locus and effective number of alleles ranged from 3 to 11 and from 1.24 to 5.51, respectively. Observed and expected heterozygosities were 0.18–0.75 and 0.19–0.77, respectively. No linkage disequilibrium between loci was detected. One locus, IsenAC75, deviated significantly from the Hardy–Weinberg equilibrium, and the locus and additional two loci, IsenAC40 and IsenAC8, were suspected for the presence of null alleles. Altogether, these eight microsatellite loci are considered to be useful for population genetic analyses because of the high polymorphic status and independency.     

Isolation and evaluation of 18 microsatellite markers in Siniperca chuatsi (Basilewsky)

Eighteen novel microsatellite markers were isolated in the Chinese perch Siniperca chuatsi (Basilewsky) using the FIASCO method, from (AC/TG)(n) , (AG/TC)(n) , (AT/TA)(n) , (GATA/CTAT)(n) and (GATT/CTAA)(n) repeat genomic libraries. The number of alleles per locus ranged from two to eight in a sample of 30 individuals from a wild population. Observed heterozygosity was between 0.100 and 0.737. Seven loci showed significant deviation from Hardy-Weinberg equilibrium, null alleles were suggested at nine loci but no linkage disequilibrium between loci was detected. These loci could be useful in the population genetic study of S. chuatsi.     

Isolation and characterization of 21 microsatellite markers in the barn owl (Tyto alba)

We report 21 new polymorphic microsatellite markers in the European barn owl (Tyto alba). The polymorphism of the reported markers was evaluated in a population situated in western Switzerland and in another from Tenerife, Canary Islands. The number of alleles per locus varies between two and 31, and expected heterozygosity per population ranges from 0.16 to 0.95. All loci are in Hardy-Weinberg equilibrium and no linkage disequilibrium was detected. Two loci exhibit a null allele in the Tenerife population.     

Characterization of 15 polymorphic microsatellite markers in the freshwater snail Aplexa marmorata (Mollusca, Gastropoda)

We describe 15 new variable microsatellites in the freshwater snail Aplexa (Physa) marmorata, as well as conditions for multiplexing and simultaneous genotyping sets of loci. Two to 11 alleles were detected per locus over the five populations studied, and up to eight alleles per locus and population. The observed heterozygosity was extremely low, most probably as the consequence of high selfing rates. The genetic differentiation among populations was large. These markers will constitute efficient tools for investigating the population structure in fragmented habitats. Cross-species amplification in three Physa species (P. acuta, P. fontinalis and P. gyrina) was rather unsuccessful.     

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae

Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of which seven have been identified to putatively play a role in heavy-metal tolerance or hyperaccumulation. Single nucleotide and length polymorphisms were assessed at four cleaved amplified polymorphic sequences (CAPS) and 11 simple sequence repeat (microsatellite) loci, respectively. The utility of these loci for genetic studies in T. caerulescens was measured among seven natural populations (135 individuals). Fourteen loci rendered polymorphism, and the number of alleles per locus varied from 2 to 5 and 1 to 27 for CAPS and microsatellites, respectively. Up to 12 alleles per locus were detected in a population. The global observed heterozygosity per population varied between 0.01 and 0.31. Additionally, cross-species/genera amplification of loci was investigated on eight other Brassicaceae (five individuals per population). Overall, 70% of the cross-species/genera amplifications were successful, and among them, more than 40% provided intraspecific polymorphisms within a single population. This indicates that such markers may, as well, allow comparative population genetic or mapping studies between and within several Brassicaceae, particularly for genes involved in traits such as heavy-metal tolerance and/or hyperaccumulation.     

Development of eight microsatellite markers in the parsley frog (Pelodytes punctatus)

We characterized eight microsatellite loci to study spatial and temporal population structure of Pelodytes punctatus, a European anuran that has a peculiar breeding pattern among amphibians. The eight loci proved to be highly polymorphic with the number of alleles per locus ranging from two to 15 within two populations. Cross-amplification indicates that those markers may be also useful for closely related species from the same family.     

Isolation and characterization of microsatellites in the woody shrub, Banksia sphaerocarpa var. caesia (Proteaceae)

Microsatellite markers were developed for the Australian bird-pollinated woody shrub Banksia sphaerocarpa var. caesia to study gene flow among populations in a highly fragmented landscape. Eight loci were developed, and in a sample of 40 individuals from one population, the number of alleles per locus ranged from five to 21 and observed heterozygosities ranged from 0.385 to 0.914. All eight loci showed independent inheritance. Analysis of open-pollinated progeny arrays confirmed Mendelian inheritance at seven loci, while null alleles were suspected at the remaining locus.     

Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers

We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.     

Isolation and characterization of microsatellite markers in the newly discovered invasive fruit fly pest in Africa, Bactrocera invadens (Diptera: Tephritidae)

We describe the isolation and characterization of 11 polymorphic microsatellite loci from the recently discovered fruit fly pest, Bactrocera invadens. The polymorphism of these loci was tested in individual flies from two natural populations (Sri Lanka and Democratic Republic of Congo). Allele number per locus ranged from three to 15 and eight loci displayed a polymorphic information content greater than 0.5. These microsatellite loci provide useful markers for studies of population dynamics and invasion history of this pest species.     

Development and characterization of polymorphic microsatellite DNA markers for Sasa senanensis (Poaceae: Bambuseae)

Sasa senanensis is a dwarf bamboo species distributed on the floors of cool temperate forests in Japan and adjacent regions. We isolated eight polymorphic microsatellite loci from this species. The number of alleles ranged from two to eight and the observed heterozygosity per locus from 0.13 to 0.74. Seven of the eight loci were also polymorphic in Sasa nipponica. Most of these markers were successfully amplified in other dwarf bamboo species. These markers will be useful for investigating clonal structure and population genetics in some dwarf bamboo species.     

Nuclear microsatellite loci for Arabidopsis halleri (Brassicaceae), a model species to study plant adaptation to heavy metals

? Premise of the study: Arabidopsis halleri is a model species to study the adaptation of plants to soils contaminated by zinc, cadmium, and lead. To provide a neutral genetic background with which adaptive genetic markers could be compared, we developed highly polymorphic neutral microsatellite markers. ? Methods and Results: Using a microsatellite-enriched library method, we identified 120 microsatellite loci for quantitative trait locus (QTL) mapping analysis, of which eight primer pairs were developed in a single multiplex for population genetic studies. Analyses were performed on 508 individuals from 26 populations. All loci were polymorphic with six to 23 alleles per locus. Genetic diversity varied between 0.56 and 0.76. ? Conclusions: Our results demonstrated the value of these eight microsatellite markers to investigate neutral population genetic structure in A. halleri. To increase the resolution of population genetic analyses, we suggest adding them to the 11 markers previously developed independently.     

Novel polymorphic microsatellite DNA markers from Malaysian giant freshwater prawn, Macrobrachium rosenbergii

Seven single locus microsatellite markers were characterized in Malaysian giant freshwater prawn, Macrobrachium rosenbergii from an enriched genomic library Primer pairs were designed to flank the repeat sequences and the loci characterized for this species. The bands resulting from the PCR amplifications of these eight microsatellite loci were polymorphic with the number of alleles ranging from 8 to 26 alleles per locus, whereas the observed heterozygosity ranged from 0.0641 to 0.6564. These newly developed microsatellite markers should prove to be useful for population studies and in the management of genetic variations in broodstocks of freshwater prawn, M. rosenbergii.     

Microsatellite markers for mungbean developed from sequence database

A novel set of microsatellite markers for mungbean [Vigna radiata (L.) Wilczek] was developed from the public sequence database. Seventy-eight primers were designed and evaluated for polymorphism among 22 cultivated accessions. Eight polymorphic loci detected two to three alleles per locus with an average of 2.25. The observed heterozygosity varied from 0.00 to 0.18, while the expected heterozygosity ranged from 0.09 to 0.46. Among them, all eight loci showed significant departuring from Hardy-Weinberg equilibrium, while four pairs of loci displayed significant pairwise linkage disequilibrium values. All eight loci except DMB-SSR1 showed heterozygote deficiency.     

Eleven novel microsatellite markers for the Asian oyster Crassostrea ariakensis

Clones from four partial genomic libraries of the Asian oyster Crassostrea ariakensis were screened to reveal 64 microsatellite-containing sequences. Polymerase chain reaction primers were designed for 34 of these loci. Reactions were optimized for 11 primer pairs and markers were evaluated in eight family crosses and one wild population from northern China. Zero to three null alleles per locus were identified in family crosses, and two of the 11 loci showed allele frequency deviations from Hardy-Weinberg equilibrium in the wild population. These markers have proven useful for genetic studies of C. ariakensis.     

Microsatellite markers for Ceiba pentandra (Bombacaceae), an endangered tree species of the Amazon forest

From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan‐tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra.     

Characterization of microsatellite markers for Thoropa taophora (Anura, Cycloramphidae), a frog endemic to the Brazilian Atlantic Rain Forest

Here we characterize nine microsatellite loci for Thoropa taophora collected from a coastal and an island population in southeastern Brazil. The number of alleles per locus ranged from three to 11 for the coastal population and from two to eight for the island population. Observed heterozygosities ranged from 0.308 to 0.778 for the coastal population and from zero to 0.737 for the island population. One locus did not conform to Hardy-Weinberg expectations on the coast, while two were in disequilibrium on the island. These markers are currently being used to examine genetic differentiation and patterns of dispersal in T. taophora.     

Microsatellite markers for genetic studies in the weasel (Mustela nivalis)

This study reports the first set of microsatellite markers for the weasel (Mustela nivalis). We chose to isolate loci with tetranucleotide repeat motifs because they can be scored less ambiguously than the more commonly used dinucleotide loci. All 11 loci showed considerable variation within a population sample of 28 individuals from Portugal, with number of alleles ranging from four to nine per locus and observed and expected heterozygosities ranging from 0.21 to 0.86 and from 0.40 to 0.84, respectively. No linkage disequilibrium was detected between pairs of loci, and only one locus (Mn 1.30) deviated from Hardy–Weinberg equilibrium expectations in the analyzed population sample. Among the 11 loci, Mn 1.30 was the only one for which all known males were homozygous. Analysis of an additional population sample of 23 individuals (14 males and 9 females) from Denmark revealed that all males, but only four females, were homozygous for Mn 1.30, supporting the idea that the locus is X-linked. These novel polymorphic microsatellite markers should be useful in studies of population genetics and molecular ecology of the weasel.     

Characterization of novel microsatellite markers for Eschscholzia californica (Papaveraceae), an invasive species in central Chile

? Premise of the study: We isolated and characterized microsatellite markers for the California poppy, Eschscholzia californica, which is an invasive species in central Chile. ? Methods and Results: A total of eight polymorphic and six monomorphic loci were developed for the species. Between one and 12 alleles were observed per locus. Polymorphic loci showed heterozygosity ranging from 0 to 0.875 in a sample of 96 individuals obtained from four populations. Only one locus showed significant departures from Hardy-Weinberg equilibrium at all sites. ? Conclusions: The successful microsatellite amplification makes this set of primers an important tool for understanding the recent and future patterns of invasion and adaptation of E. californica into the new Chilean geographic area. The variation detected is currently being used in a more inclusive study that assesses population expansion in central Chile.