Genetic Diversity and Identity of Chinese Loquat Cultivars/Accessions (<Emphasis Type="Italic">Eriobotrya japonica</Emphasis>) Using Apple SSR Markers

Loquat (Eriobotrya japonica) is an underutilized fruit crop that originated in China and for which only a small number of molecular markers are available. This number can be increased by identifying apple SSRs that are transferable to loquat cultivars/accessions to provide new insight into the level of genetic diversity within loquat and synteny with apple. We evaluated 71 apple SSR markers distributed across 17 linkage groups, and identified 39 SSRs transferable to loquat. Testing 54 loquat accessions, from Japan, Spain, four provinces in China, and two wild species gave a total of 155 different alleles with a mean value of 3.38 per locus. The mean effective number of alleles was 2.21, and the mean observed heterozygosity was 0.47. These values indicate a high degree of genetic diversity in the set of Chinese loquat accessions analyzed. Unweighted pair-group method analysis based on simple matching coefficent clustered the accessions into two groups, cultivated and wild loquat. The cultivated loquat can be subdivided into three subgroups which generally reflect their geographic origin in China. The Spanish cultivars clustered with those of the Jiangsu and Zhejiang provinces. A core set of five SSR markers could distinguish most accessions.     

Isolation and characterization of 14 polymorphic microsatellite loci in the ringneck snake <Emphasis Type="Italic">Diadophis punctatus</Emphasis> (Colubridae: Dipsadinae)

We constructed a genomic library and developed 14 polymorphic loci to assess species boundaries between previously described mtDNA lineages and to examine the genetic variability between populations of the ringneck snake Diadophis punctatus species complex. Polymorphism was investigated for these markers in 34 individuals from populations in southeastern Louisiana and southern Florida. The number of alleles ranged from 5 to 29, expected heterozygosity ranged from 0.816 to 0.962 and observed heterozygosity ranged from 0.452 to 0.889. These new loci provide the tools necessary to examine species boundaries, population genetics within species and to determine the conservation status of imperiled populations.     

Polymorphic microsatellite DNA markers in Bactrocera cacuminata (Hering) (Diptera: Tephritidae)

Bactrocera cacuminata (Hering) is a nonpest member of the Bactrocera dorsalis complex offering a platform to check hypotheses extrapolated from the more studied pest species. Six polymorphic microsatellite loci were isolated from enriched genomic libraries constructed using a biotin/streptavidin capture protocol. Allele number varied between three and nine; the expected heterozygosity ranged between 0.29 and 0.81. No significant deviations from Hardy–Weinberg equilibrium or linkage disequilibrium were found. These microsatellite markers have potential to be used to examine population structure and mating systems in this tropical fruit fly.     

Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)

? Premise of the study: Microsatellite loci were developed for the endangered species Pityopsis ruthii and will permit genetic and conservation studies of the species. ? Methods and Results: A microsatellite-enriched library was used to develop 12 polymorphic microsatellite loci for P. ruthii. The loci amplified perfect and imperfect repeats with three to seven alleles per locus. Observed heterozygosity ranged from 0.05 to 0.80 and expected heterozygosity ranged from 0.23 to 0.75. ? Conclusions: These microsatellite loci provide a sufficient set of markers for further investigation of population genetics of P. ruthii.     

Characterization of novel microsatellite markers from the Yesso scallop Mizuhopecten yessoensis

Twelve polymorphic and informative microsatellite markers were isolated and characterized for the Yesso scallop, Mizuhopecten yessoensis. We characterized these loci by genotyping 48 individuals; the number of alleles ranged from two to eight, and the values of observed heterozygosity and expected heterozygosity varied from 0 to 0.8333 and from 0.2546 to 0.8231, respectively. No significant linkage disequilibrium between pairs of loci was found and three loci showed significant heterozygote deficiency from the Hardy–Weinberg equilibrium. These markers are potential for studies of the population structure, individual or hybrid identification of the species.     

Characterization of 31 EST-derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker)

We developed and characterized 31 microsatellite markers from expressed sequence tags of Pinctada martensii (Dunker). The number of alleles per locus ranged from 4 to 18 as determined in 44 individuals from a wild population. The expected heterozygosity ranged from 0.4121 to 0.9436, while the observed heterozygosity ranged from 0.4054 to 0.7273. Most of the loci are in Hardy-Weinberg equilibrium. These markers should be useful for population genetics studies, parentage and genome mapping in this species.     

Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel Perna viridis

We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species.     

Development of microsatellite markers in Byrsonima crassifolia (Malpighiaceae)

? Premise of the study: We developed and characterized microsatellite markers for Byrsonima crassifolia (Malpighiaceae), a widely distributed neotropical fruit tree. ? Methods and Results: Eight polymorphic and two monomorphic microsatellite loci were identified and screened in 60 samples from four geographically disparate populations (Bolivia, Brazil, Mexico, and Panama). Each locus exhibited between two and 11 alleles. Expected heterozygosity ranged from 0 to 0.839. All loci amplify in the congeners B. variabilis and B. basiloba, four amplify in B. bucidaefolia, and seven amplify in B. variabilis, although levels of polymorphism have not been assessed. ? Conclusions: These loci will provide novel tools for comparing genetic diversity present in cultivated and noncultivated populations of B. crassifolia throughout its range, and may prove valuable in related species.     

Development of EST-SSRs in scallop (Patinopecten yessoensis) from sequence database

Patinopecten yessoensis is a kind of cold water shellfish, and is an important economic species in China. In our study, we developed and evaluated simple sequence repeat (SSR) markers of P. yessoensis. Characteristics of 11 EST-SSR loci were investigated using 40 P. yessoensis individuals. The number of alleles per locus ranged from two to five. The observed heterozygosity ranged from 0.1026 to 0.9487, while the expected heterozygosity ranged from 0.1865 to 0.7433. All loci except P4 departed from Hardy–Weinberg equilibrium (P < 0.05) significantly. There was no LD observed between all pairs of EST-SSRs loci. These loci and markers will be useful for population genetics and systemic evolution of scallop.     

Fourteen microsatellite loci for the Chinese medicinal plant Epimedium sagittatum and cross-species application in other medicinal species

Epimedium sagittatum is a well-known medicinal plant as well as potential ground cover and ornamental plant. A total of 14 polymorphic microsatellite markers were developed for use in taxonomy, phylogenetics and conservation genetics. Markers were presented between two and eight alleles per locus. The observed heterozygosity (H(O) ) and expected heterozygosity (H(E) ) ranged from 0.03 to 0.81 and from 0.05 to 0.81, respectively. Cross-amplification among other four medicinal species revealed promising results in three to six polymorphic loci. These microsatellite loci contributed to the limited number of useful markers currently available for E. sagittatum.     

Polymorphic microsatellite DNA markers from the Oriental Fruit Fly Bactrocera dorsalis (Hendel)

Six polymorphic microsatellite loci are isolated from the Oriental fruit fly Bactrocera dorsalis (Hendel), an agricultural pest in Asia, including Taiwan. To assess their potential utility as high‐resolution genetic markers, polymerase chain reaction (PCR) primers, amplification conditions, and an automated fluorescence detection protocol were developed. In analyses of 71 individual flies from six different areas of Taiwan, allele numbers ranged from five to 25 were detected for each locus. The observed heterozygosity ranged between 0.268 and 0.737 among these loci. No linkage disequilibrium was found. These microsatellite markers have potential utility to population structure and gene flow studies of B. dorsalis (Hendel).     

Development and characteristics of microsatellite markers in Pinus merkusii

Pinus merkusii is an important industrial species that is distributed only in Southeast Asia. We isolated 10 microsatellite markers from this species using a dual‐suppression‐polymerase chain reaction technique. Of these markers, five loci were codominant and polymorphic. The number of alleles per locus ranged from three to six and the expected heterozygosity ranged from 0.389 to 0.728. These microsatellite markers will be available for analysis on population genetics and mating patterns.     

Isolation and characterization of fourteen polymorphic microsatellite markers in the viperine snake Natrix maura

Nineteen polymorphic microsatellite loci were identified and developed for Natrix maura. Polymorphism was assessed for 120 individuals sampled across four sampling sites from the French Pyrenees Mountains. The number of alleles per locus ranged from 3 to 15, and expected heterozygosity per locus ranged from 0.227 to 0.863. We tested for deviation from Hardy–Weinberg equilibrium and linkage disequilibrium and assessed the presence of null alleles for all loci, resulting in a selection of 14 high‐quality polymorphic markers. These markers will be extremely useful in identifying fine‐scale genetic structures and providing insight into conservation management plans of this species.     

Isolation and characterization of microsatellite loci in the highland papaya Vasconcellea × heilbornii V. Badillo (Caricaceae)

Nine polymorphic microsatellite loci were identified in the tropical plant Vasconcellea ×heilbornii and used to estimate allelic diversity in two populations of southern Ecuador. Allelic richness ranged from two to five alleles, observed heterozygosity ranged from 0.150 to 0.947 and expected heterozygosity ranged from 0.186 to 0.701. Most of these markers also amplified microsatellite loci in two other Vasconcellea species (Vasconcellea stipulata and Vasconcellea cundinamarcensis). Hence, these markers will be useful for population genetic analysis and the evaluation of genetic diversity and gene flow in these species.     

Polymorphic microsatellite DNA markers in the endangered land snail,Trichia caelata (Gastropoda,Stylommatophora)

Eight novel polymorphic microsatellite loci are presented for the endangered land snail Trichia caelata, a rare species endemic to the Northwestern Jura mountains, Switzerland. The number of alleles per locus ranged from six to 17. At seven loci, the expected heterozygosity differed significantly from observed heterozygosity. No evidence for linkage disequilibrium was detected between locus pairs. We are currently using these markers to investigate the genetic population structure of T. caelata in its restricted distribution area.     

A panel of polymorphic EST-derived microsatellite loci for the small yellow croaker (Larimichthys polyactis)

Small yellow croaker (Larimichthys polyactis) is an important economic species of marine fishery. We developed and evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Pseudosciaena crocea, Paralichthys olivaceus and Psetta maxima. Characteristics of nine EST–SSR loci were investigated using 46 L. polyactis individuals. The number of alleles per locus ranged from 2 to 6. The observed heterozygosity ranged from 0.0652 to 0.7391, while the expected heterozygosity ranged from 0.0638 to 0.7754. Seven loci departed from Hardy–Weinberg equilibrium (P < 0.01) significantly. These loci and markers will be useful for population genetics and systemic evolution among species of small yellow croaker.     

Development and characterization of microsatellites in Torreya jackii (Taxaceae), an endangered species in China

? Premise of the study: Polymorphic microsatellite loci were developed in Torreya jackii, an endangered species in China, to provide markers for further studies on the genetic diversity of this species. ? Methods and Results: Eight polymorphic loci and one monomorphic locus were developed and characterized in four T. jackii populations (Xianju, Songyang, Pujiang, and Tonglu) from Zhejiang Province, China. The number of alleles per locus ranged from one to eight across 80 T. jackii individuals. At the eight polymorphic loci, the observed heterozygosity ranged from 0.150 to 1.000 and the expected heterozygosity ranged from 0.185 to 0.796. ? Conclusions: The microsatellite loci developed and characterized in this study will facilitate future analyses of the genetic diversity of T. jackii. Such information will aid in designing strategies to conserve this currently endangered species.     

Eight microsatellite markers for the San Esteban chuckwalla,Sauromalus varius

We characterize eight polymorphic microsatellite loci for the San Esteban chuckwalla, Sauromalus varius, which are being used as markers in a study of the genetic results from a decade of captive breeding in this endangered species. Observed heterozygosity estimates for S. varius ranged from 0.00 to 0.30, whereas expected heterozygosity estimates ranged from 0.06 to 0.58.     

dbEST-derived SSR markers in sea urchin (Hemicentrotus pulcherrimus)

Sea urchin is an important model organism for evolutionary biology, embryology, and gene regulation study. We developed and evaluated simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Strongylocentrotus purpuratus and Hemicentrotus pulcherrimus. Characteristics of nine EST-SSR loci were investigated using 41 Hemicentrotus pulcherrimus individuals. The number of alleles per locus ranged from two to five. The observed heterozygosity ranged from 0.122 to 0.7805, while the expected heterozygosity ranged from 0.4472 to 0.7696. These loci and markers will be useful for population genetics and systemic evolution among species of sea urchin.     

Isolation and characterization of polymorphic microsatellite loci from the pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)

Thirteen polymorphic microsatellite markers were developed from an enriched partial genomic library for the pink bollworm, Pectinophora gossypiella (Saunders), one of the most important cotton pests in the world. The total number of alleles ranged from two to 12 for a sample of 50 individuals and the expected heterozygosity at these loci ranged from 0.042 to 0.830. Although the presence of null alleles in some loci is suspected, these polymorphic markers are likely to provide useful tools for the population genetic studies of this species.