Isolation and characterization of microsatellite loci from yellowtail Seriola quinqueradiata and cross‐species amplification within the genus Seriola

We developed five microsatellite primer pairs for the yellowtail Seriola quinqueradiata. The loci were highly polymorphic, with eight to 14 alleles per locus, and can be used to study kinship and/or population structure. Many of these primer pairs amplified polymorphic loci in cross‐species amplification tests for two other Seriola species (S. lalandi and S. dumerili).     

Identification of polymorphic microsatellite markers from RAPD product in turbot (Scophthalmus maximus) and a test of cross‐species amplification

Five polymorphic microsatellite loci have been isolated and characterized from random amplified polymorphic DNA product in turbot, Scophthalmus maximus. Twelve microsatellites were selected for designing microsatellite primers, of which five gave working primer pairs. They had between four and nine alleles. Observed and expected heterozygosities varied from 0.76 to 0.90 and from 0.63 to 0.83, respectively. Five additional fish species assessed for cross‐species amplification revealed between one and three positive amplifications and between zero and two polymorphic loci per species.     

Characterization of microsatellite loci in village indigobirds Vidua chalybeata and cross‐species amplification in estrildid and ploceid finches

We characterized 11 microsatellite primer pairs for the village indigobird Vidua chalybeata. The loci were highly polymorphic, with 7–13 alleles per locus. Gene diversity, estimated as expected heterozygosity, ranged from 0.52 to 0.86, and was generally matched by levels of observed heterozygosity (0.49–0.91). Many of these primer pairs amplified polymorphic loci in cross‐species amplification trials with a variety of estrildid and ploceid finches and a sparrow, Passer griseus. These primers will be valuable for genetic analyses of the brood parasitic indigobirds and whydahs (genus Vidua) as well as other Old World finches.     

Isolation and characterization of microsatellite loci in the great bustard,Otis tarda

With the aim to study population genetics of the endangered great bustard, Otis tarda, dinucleotide microsatellite loci were isolated using an adapted hybrid‐capture enrichment protocol. This work reports the characterization of a set of six polymorphic microsatellite markers within the great bustard (n = 52). Results from cross‐species amplifications in several other members of the family Otididae demonstrate that five primer pairs also successfully amplified homologous loci outside the species Otis tarda.     

Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family

We characterized 24 polymorphic tetranucleotide microsatellite loci for delta smelt (Hypomesus transpacificus) endemic to the San Francisco Bay Estuary, CA, USA. Screening of samples (n = 30) yielded two to 26 alleles per locus with observed levels of heterozygosity ranging from 0.17 to 1.0. Only one locus deviated from Hardy–Weinberg equilibrium, suggesting these individuals originate from a single panmictic population. Linkage disequilibrium was found in two pairs of loci after excluding the locus out of Hardy–Weinberg equilibrium. Twenty‐two primer pairs cross‐amplified in wakasagi smelt (Hypomesus nipponensis), and 15 primer pairs cross‐amplified in longfin smelt (Spirinchus thaleichthys).     

Isolation and characterization of Ligustrum micranthum (Oleaceae) microsatellite loci using paired‐end Illumina reads

Twenty‐six microsatellite loci were developed and characterized for Ligustrum micranthum, a species endemic to the Ogasawara Islands, Japan. The genetic structure of this species must be clarified in order to restore the island's ecosystem. A total of 8511 primer pairs were designed from de novo sequencing. Of the 48 primer pairs selected, amplification and polymorphisms were tested using one population each from the Chichijima and Hahajima Islands of the Ogasawara Islands. Twenty‐six microsatellite loci were successfully amplified and the number of alleles for these loci ranged from five to 31 per locus, and the mean expected heterozygosities were 0.858 and 0.849, respectively. No significant deviation from the Hardy–Weinberg equilibrium was observed in either population, and no significant linkage disequilibrium was detected between any locus pair. The microsatellite loci reported in this study can be used in future studies to evaluate the genetic structure and mating system of L. micranthum.     

Microsatellite markers for the palaeotropic pioneer tree genus Macaranga (Euphorbiaceae) and their cross‐species transferability

We developed primer sequences for five polymorphic microsatellite loci in the tropical ant‐plant genus Macaranga (Euphorbiaceae). Population genetic parameters were determined on the basis of 30 individuals from each of two Macaranga species in Borneo. Allele numbers per locus ranged from three to 13. Expected and observed heterozygosities ranged from 0.160 to 0.850 and from 0.130 to 0.700, respectively. Four of the five primer pairs cross‐amplify polymorphic PCR products in a wide range of Macaranga species.     

Isolation of microsatellite loci from spotted gum (Corymbia variegata), and cross‐species amplification in Corymbia and Eucalyptus

Corymbia variegata (spotted gum) is an important commercial hardwood timber species in Australia. Fourteen polymorphic microsatellite loci were isolated from C. variegata, with 3–5 alleles amplified in three individuals examined. Cross‐species amplification in Corymbia was successful for all primer pairs, while 10 loci (71%) were successfully transferred to at least one species in the closely related genus Eucalyptus.     

Isolation and characterization of microsatellite loci in the marine gastropod Nucella lapillus

Our paper deals the cloning and characterization of microsatellites from Nucella lapillus, and tests cross‐species amplification in a congener and in two species of the confamilial genus Thais. Fourteen of 31 microsatellite loci tested were polymorphic, with 4–9 (mean 5.93) alleles per locus. The observed heterozygosity per locus varied from 0.10 to 0.85 (mean 0.37) and expected heterozygosity from 0.48 to 0.85 (mean 0.65). Most primer pairs were successfully amplified in N. freycineti, although only one primer pair was successfully amplified in both species of Thais. The markers are potentially useful for other species of Nucella.     

Isolation and characterization of microsatellite loci from the orchid Serapias vomeracea (Orchidaceae) and cross‐priming to other Serapias species

In this paper we describe the isolation and characterization of six polymorphic microsatellite loci from the orchid Serapias vomeracea. This species is widely distributed in the Mediterranean region. Microsatellite loci were isolated from an enriched library and primer pairs were designed for 18 loci. Primer pairs for six loci amplified well and were tested on samples from southern Italy. Levels of genetic variability detected at these six loci are high, with numbers of alleles per locus ranging from 3 to 6, and observed heterozygosity (H_O) ranging from 0.35 to 0.86. All primer pairs tested amplified DNA from four other Serapias species, indicating that the primers are useful for population genetic studies throughout the genus.     

Isolation and characterization of microsatellite loci in the Pacific pleasure oyster,Crassostrea corteziensis,and their cross‐species amplification in four other oyster species

Microsatellite loci were isolated in Crassostrea corteziensis using (GT)_n, (CT)_n and (CTGT)_n‐enriched genomic libraries. Within each of 45 sequenced clones, an average of three microsatellite regions (156 total) were observed. Thirty‐three primers were designed, from which 11 microsatellite loci amplified. Ten of those were polymorphic, with a range of two to 30 alleles. Three loci were not in Hardy–Weinberg equilibrium, and linkage disequilibrium was found for six pairs of loci. These microsatellite loci will be further tested for segregation distortions and null alleles to establish a set for population genetic studies of the species in the Northwest coasts of Mexico, and for optimization of aquaculture development. Seven of the microsatellite loci cross‐amplified in Crassostrea palmula, a sympatric species, and will be useful in further genetic studies.     

Characterization and cross‐species amplification of microsatellite loci in a Cyprinodon species flock

In this study, two new microsatellite loci from a library of Cyprinodon beltrani from Laguna Chichancanab, Mexico, were characterized. Additionally, cross‐species amplification with primer pairs developed for other Cyprinodon species was performed. The 11 markers show moderate to high levels of polymorphism (two to 33 alleles) in six species of the Cyprinodon flock from Laguna Chichancanab and in their sister species Cyprinodon artifrons. These loci were characterized for population genetic study to detect gene flow between the different endemic pupfish species.     

Isolation and characterization of polymorphic microsatellite loci from an EST‐library of red sea bream (Chrysophrys major) and cross‐species amplification

Microsatellite markers have been developed from a complementary DNA (cDNA) library of red sea bream, Chrysophrys major. Twenty‐eight microsatellites were selected for designing microsatellite primers, of which 11 gave working primer pairs. Observed and expected heterozygosities varied from 0.33 to 1.00 and from 0.38 to 0.83, respectively. Five additional fish species assessed for cross‐species amplification revealed between one and six positive amplifications and between 0 and 6 polymorphic loci per species.     

Microsatellites from Clarias batrachus and their polymorphism in seven additional catfish species

We isolated 18 novel microsatellite loci from the walking catfish (Clarias batrachus), and examined their cross‐amplification in seven additional catfish species from three families. Sixteen of the 18 microsatellites were polymorphic in the source species (allele number: 2–10/locus and expected heterozygosity: 0.30–0.87). Moreover, nine of these 18 primer pairs cross‐amplified specific and polymorphic products from the genome of at least six of the seven other catfish species tested. However, the success rate of cross‐species amplification varied from locus to locus, indicating that cross‐species amplification of microsatellites is locus‐dependent.     

Cross‐species amplification of microsatellite loci in Aquilegia and Semiaquilegia (Ranunculaceae)

We developed 16 microsatellite loci from an F₂ hybrid between Aquilegia formosa and Aquilegia pubescens. In samples of 28 individuals, we found an average of 14 alleles per locus from each parental species. We tested these loci for cross‐amplification in 10 additional species of Aquilegia and found that all 16 loci amplified in other North American species and 12 consistently amplified in European or Asian species. Nine loci amplified in the sister species to Aquilegia, Semiaquilegia adoxoides. The success of cross‐species amplification suggests that these microsatellites should prove useful for studies in a broad range of Aquilegia species.     

Microsatellite markers for testing host plant‐related population differentiation in the moth genus Yponomeuta

Nine microsatellite primers were developed for Yponomeuta padellus (Lepidoptera: Yponomeutidae) and tested for their applicability in analysing genetic population structure. Eight of the nine loci were highly polymorphic with on average 11.4 alleles. Cross‐species amplification of the nine primer pairs was tested in five other moth species. Primer pairs amplified in Y. cagnagellus, Y. malinellus, Y. evonymellus, and Y. rorellus but not in Y. sedellus and Plutella xylostella.     

Isolation and characterization of microsatellite loci in Lesquerella fendleri (Brassicaceae) and cross‐species amplification

Fifteen novel microsatellite primer pairs are presented for Lesquerella fendleri, which were developed from seven dinucleotide, five trinucleotide and three tetranucleotide microsatellite DNA loci. These loci were characterized for 40 individuals from 24 localities throughout the species range. The number of alleles observed per locus ranged from three to 16, the observed heterozygosity ranged from 0.175 to 0.750, and the polymorphic information content ranged from 0.218 to 0.889. Cross‐species transferability tested on nine species of Lesquerella and one species of the related genus Physaria indicates that these primer pairs may be useful for population genetic studies of other species in Lesquerella and possibly other closely related genera.     

Development of polymorphic microsatellite from RAPD bands of black sea bream Acanthopagrus schlegeli

Eight pairs of simple sequence repeat markers were developed from random amplified polymorphic DNA product in black sea bream Acanthopagrus schlegeli. Twenty microsatellites were selected for designing microsatellite primers, of which eight gave working primer pairs. They had between three and seven alleles. Observed and expected heterozygosities varied from 0.65 to 0.90, and from 0.58 to 0.82, respectively. Eight additional fish species assessed for cross‐species amplification revealed between two and five positive amplifications and between zero and three polymorphic loci per species.     

Isolation and characterization of sequence‐tagged microsatellite sites markers in chickpea (Cicer arietinum L.)

In this study we report the isolation of microsatellite sequences and their conversion to sequence‐tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Thirteen putative recombinants isolated from a chickpea genomic library were sequenced, and used to design 10 STMS primer pairs. These were utilized to analyse the genetic polymorphism in 15 C. arietinum varieties and two wild varieties, C. echinospermum and C. reticulatum. All the primer pairs amplified polymorphic loci ranging from four to seven alleles per locus. The observed heterozygosity ranged from 0 to 0.6667. Most of the STMS markers also amplified corresponding loci in the wild relatives suggesting conservation of these markers in the genus. Hence, these polymorphic markers will be useful for the evaluation of genetic diversity and molecular mapping in chickpea.     

Characterization of microsatellite markers in the interspecific hybrid Phytophthora alni ssp. alni,and cross‐amplification with related taxa

Phytophthora alni ssp. alni is an interspecific hybrid oomycete causing a large‐scale decay of alders throughout Europe. In this study we developed a set of 10 microsatellite markers that shows promise for population studies and for studying hybridization events between the parental species of the hybrid. Moreover, the genotype and the ploidy of the different subspecies of P. alni might be inferred from the quantitative ratio of amplified genome‐specific alleles. Nine primer pairs cross amplified with the related species Phytophthora cambivora and Phytophthora fragariae and yielded distinct alleles.