Development of compound microsatellite markers in the harmful dinoflagellate Cochlodinium polykrikoides (Dinophyceae)

We isolated 15 polymorphic microsatellites from Cochlodinium polykrikoides. These loci provide a class of highly variable genetic markers, as the number of alleles ranged from two to 15, and the estimate of gene diversity was from 0.083 to 0.880 across the 15 microsatellites. We consider that these loci have a potential to reveal the genetic structure and gene flow among C. polykrikoides populations.     

Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae)

Outbreaks of paralytic shellfish poisoning caused by the toxic dinoflagellate Alexandrium minutum (Dinophyceae) are a worldwide concern from both the economic and human health points of view. For population genetic studies of A. minutum distribution and dispersal, highly polymorphic genetic markers are of great value. We isolated 12 polymorphic microsatellites from this cosmopolitan, toxic dinoflagellate species. These loci provide one class of highly variable genetic markers, as the number of alleles ranged from four to 12, and the estimate of gene diversity was from 0.560 to 0.862 across the 12 microsatellites; these loci have the potential to reveal genetic structure and gene flow among A. minutum populations.     

Development of compound microsatellite markers in the marine phytoplankton Alexandrium tamiyavanichii (Dinophyceae)

We isolated 24 polymorphic microsatellite markers from the toxic dinoflagellate A. tamiyavanichii. These loci provide a class of highly variable genetic markers, as the number of alleles ranged from 2 to 6, and the estimate of gene diversity was from 0.269 to 0.739 across the 24 microsatellites. We consider that these loci have a potentially to reveal the genetic structure and gene flow among A. tamiyavanichii populations.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers in the Japanese common squid Todarodes pacificus (Ommastrephidae)

Todarodes pacificus is an important species for commercial fisheries, but its reproductive biology has been little understood. We isolated 11 polymorphic microsatellite loci from this species. These loci provided highly polymorphic microsatellite markers with four to 26 alleles per locus. The observed and expected heterozygosities ranged from 0.150 to 1.000, and from 0.660 to 0.974, respectively. These markers will be useful for research about the mating systems and genetic diversity of T. pacificus.     

New microsatellite markers isolated from mungbean (Vigna radiata (L.) Wilczek)

In this study, we reported the isolation and analysis of new polymorphic microsatellites in mungbean (Vigna radiata (L.) Wilczek). Twelve out of 210 primer pairs screened in 30 mungbean accessions gave polymorphism. The polymorphic markers detected two to three alleles per locus with an average of 2.08. Observed heterozygosity varied from 0 to 0.133, while expected heterozygosity ranged from 0.095 to 0.498. Tests for Hardy-Weinberg equilibrium (HWE) and pairwise linkage disequilibrium of the polymorphic loci revealed that all loci except MB-SSR14 significantly departed from HWE and four pairwise combinations, viz. MB-SSR14 vs. MB-SSR42, MB-SSR42 vs. MB-SSR87, MB-SSR114 vs. MB-SSR121, and MB-SSR175 vs. MB-SSR231 significantly deviated from linkage disequilibrium. The markers are being used to study genetic diversity and genome mapping of mungbean.     

Development of microsatellite markers for the red tide‐forming harmful species Chattonella antiqua,C. marina,and C. ovata (Raphidophyceae)

We have developed 11 microsatellite markers that are specific to Chattonella antiqua, C. marina, and C. ovata, the red tide‐forming harmful phytoplanktons. The 11 loci were amplified in the three species. The number of alleles per locus ranged from 5 to 16. The three species shared most microsatellite regions, although the genetic differences in specific loci were detected among them. These markers of the Chattonella species will be beneficial for biogeographical, detailed taxonomic, studies.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers in Rhinanthus angustifolius and cross-species amplification

Fifteen polymorphic microsatellite loci were developed from an enriched genomic library of the annual plant Rhinanthus angustifolius and characterized using 36 individuals. These markers provided high polymorphism ranging from two to 15 alleles per locus. Four loci showed significant departure from Hardy-Weinberg equilibrium, probably because of the occurrence of null alleles. No significant linkage disequilibrium was detected between pairs of loci. Tests of cross-species transferability were performed on four congeners with a success rate of 100% in Rhinanthus minor, 93% in R. mediterraneus and R. glacialis, and 80% in R. alectorolophus. These microsatellite loci will be useful tools to study mating system, gene flow and hybridization in the genus Rhinanthus.     

Development of new microsatellite markers from a salt-marsh sedge Carex rugulosa by compound simple sequence repeat-polymerase chain reaction

We developed 12 polymorphic microsatellite markers from a salt-marsh sedge Carex rugulosa. The number of alleles per locus ranged from two to four, with an average of 2.75. The observed and expected heterozygosities ranged from 0.067 to 0.600 and from 0.128 to 0.620, respectively. These simple sequence repeat markers will allow the identification of genets and evaluation of the genetic diversity of C. rugulosa.     

Development and characterization of microsatellite markers for Arenaria grandiflora L. (Caryophyllaceae)

Genomic libraries of Arenaria grandiflora enriched for di- and trinucleotide repeats were used for the development of novel microsatellite markers. The subset of 13 polymorphic markers was characterized on 40 individuals of A. grandiflora originating from lowland locations in France. The loci amplified 3 to 10 alleles per locus and expected heterozygosities ranged from 0.46 to 0.83. The newly developed markers will be used for population genetic studies and for assessing genetic composition of a restoration experiment of lowland A. grandiflora populations that are protected in France.     

Development of microsatellite markers for the Manila clam Ruditapes philippinarum

We isolated nine polymorphic microsatellites from the Manila clam Ruditapes philippinarum. These loci provide one class of highly variable genetic marker as the number of alleles ranged from six to 22, and the observed and expected heterozygosity ranged from 0.136 to 0.909 and from 0.553 to 0.954, respectively. We consider that these loci are potentially useful for detailing the genetic structure and gene flow among R. philippinarum populations.     

Development of microsatellite markers in the marine phytoplankton Karenia mikimotoi (Dinophyceae)

The marine phytoplankton, Karenia mikimotoi, causes severe red tides which are associated with mass mortality of marine fish, and have expanded their distributions in the coastal waters of western Japan. To assess the dispersal mechanism, a population genetic study using highly polymorphic genetic markers is one of the crucial approaches. Here we developed 12 polymorphic microsatellite markers from K. mikimotoi. These loci provide a class of highly variable genetic markers, as the number of alleles ranged from 5 to 23, and the estimate of gene diversity was from 0.551 to 0.933 across the 12 microsatellites. We consider these loci potentially useful for detailing the genetic structure and gene flow among K. mikimotoi populations.     

Isolation and characterization of 11 microsatellite markers from Sagittaria latifolia (Alismataceae)

We developed 11 microsatellite loci for Sagittaria latifolia, an aquatic plant common to wetlands of North America. From an (AG)-enriched library, we identified 66 unique microsatellite sequences for which primers could be designed. Twenty-two loci reliably amplified a clear single band of expected size, and 11 loci were scoreable and polymorphic. For these 11 loci, we genotyped a monoecious and a dioecious population, yielding four to 14 alleles per locus. Three loci exhibited significant linkage disequilibrium leaving eight independent variable loci. Eight loci also amplified in four other Sagittaria species. These microsatellite loci will be useful to compare genetic structure among monoecious and dioecious populations of S. latifolia.     

Development and characterization of microsatellite markers in Populus euphratica (Populaceae)

In this study, we developed 12 microsatellite loci for Populus euphratica and checked their variability in 27 individuals. The number of alleles for 12 loci ranged from five to nine, the observed and expected heterozygosities ranged from 0.32 to 0.48 and from 0.53 to 0.67. Frequencies of null alleles of all loci are not significantly greater than zero. None of the loci showed significant deviation from Hardy-Weinberg equilibrium. No significant linkage disequilibrium was observed between pairs of studied loci. These markers are useful in studies of population genetic structure of P. euphratica.     

Isolation and characterization of microsatellite markers in an endemic Hawaiian planthopper (Nesosydne chambersi: Delphacidae)

We have isolated and characterized 17 microsatellite loci for the endemic Hawaiian planthopper Nesosydne chambersi (Delphacidae), a member of a large Hawaiian Nesosydne radiation. Thirty individuals from one population and 10 individuals from two populations across the species' range were tested to investigate polymorphism. The observed loci contained two to nine alleles per locus. Expected heterozygosity within this species ranged from 0.2 to 0.85. These markers will be used to assess intraspecific differentiation and population structure within N. chambersi.     

Isolation of compound microsatellite loci in the herbaceous perennial Cirsium purpuratum (Maxim.) Matsum

The herbaceous perennial Cirsium purpuratum is a pioneer on the southeast side of Mount Fuji in Japan. For genetic analysis of reproduction in this species, we developed polymorphic compound microsatellite markers using an adaptor-ligated library method and a simpler method called the intercompound microsatellite method. The latter method was an effective method for developing compound simple sequence repeat markers. In total, 11 polymorphic, codominant microsatellite markers were developed and characterized for this species. These polymorphic markers had three to 20 alleles per locus, a range of observed heterozygosity from 0.25 to 0.90, and were considered effective for genetic analysis.     

Development and characterization of microsatellite markers in Zanthoxylum ailanthoides (Rutaceae)

Nine microsatellite markers were developed for Zanthoxylum ailanthoides, a typical pioneer tree. Averaged over the nine loci, the number of alleles per locus was 5.1. The observed and expected heterozygosities ranged from 0.233 to 0.833 and from 0.314 to 0.823, with averages of 0.606 and 0.641, respectively. No loci showed significant departures from Hardy–Weinberg equilibrium or linkage equilibrium after Bonferroni correction (P > 0.05). These markers will be useful for parentage analyses and studies of population genetic structure in the species.     

Mapping microsatellite markers identified in porcine EST sequences

A sequence search of swine expressed sequence tags (EST) data in GenBank identified over 100 sequence files which contained a microsatellite repeat or simple sequence repeat (SSR). Most of these repeat motifs were dinucleotide (CA/GT) repeats; however, a number of tri-, tetra-, penta- and hexa-nucleotide repeats were also detected. An initial assessment of six dinucleotide and 14 higher-order repeat markers indicated that only dinucleotide markers yielded a sufficient number of informative markers (100% vs. 14% for dinucleotide and higher order repeats, respectively). Primers were designed for an additional 50 di- and one tri-nucleotide SSRs. Overall, 42 markers were polymorphic in the US Meat Animal Research Center (MARC) reference population, 17 markers were uninformative and 12 primer pairs failed to satisfactorily amplify genomic DNA. A comparison of di-nucleotide repeat vs. markers with repeat motifs of three to six bases demonstrated that 72% of dinucleotide markers were informative relative to only 7% of other repeat motifs. The difference was the result of a much higher percentage of monomorphic markers in the three to six base repeat motif markers than in the dinucleotide markers (64% vs. 14%). Either higher order repeat motifs are less polymorphic in the porcine genome or our selection criteria for repeat length of more than 17 contiguous bases was too low. The mapped microsatellite markers add to the porcine genetic map and provide valuable links between the porcine and human genome.     

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.     

Development and characterization of polymorphic microsatellite markers in Rhododendron simsii (Ericaceae)

A set of 14 polymorphic microsatellite markers has been developed and characterized using FIASCO (fast isolation by AFLP of sequences containing repeats) methods for the garden plant, Rhododendron simsii Planch. Forty‐one R. simsii individuals showing large morphological differences were used to identify these markers. The total number of alleles for each locus ranged from 2 to 6, with an average value of 3.643. The expected heterozygosities and observed heterozygosities ranged from 0.137 to 0.778 and 0.000 to 0.769, respectively. Eight loci exhibited significant deviations from Hardy‐Weinberg equilibrium. Among these microsatellites, seven could successfully be transferred to four related species (R. pulchrum, R. hybrida, R. alutaceum and R. molle (Blume) G. Don). These novel microsatellite markers could be further used for assessment of genetic diversity and population structure, phylogeographic analysis and marker‐assisted selection for R. simsii and other Rhododendron species.