Development of STS and CAPS markers for identification of three tall larkspurs (Delphinium spp.)

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 229-235 ◽  
Author(s):  
Xiaomei Li ◽  
Dale R Gardner ◽  
Michael H Ralphs ◽  
Richard R-C Wang
Keyword(s):  
Rapd Markers ◽  
Poisonous Plants ◽  
Plant Materials ◽  
Sts Markers ◽  
Hybrid Plants ◽  
Tall Larkspur ◽  
Caps Markers ◽  
Species Specific ◽  
Delphinium Occidentale

One cleaved amplified polymorphic sequence (CAPS) and nine sequence tagged site (STS) markers were developed for identifying tall larkspur (Delphinium spp.) plants in three species based on the DNA sequence of known species-specific RAPD markers. Four STS markers were used for identification of Delphinium occidentale, three STS markers for Delphinium barbeyi, and one CAPS and two STS markers for Delphinium glaucum. One hundred sixty-six individual plants collected at 19 locations in the western U.S.A. were tested using the STS and CAPS markers. Over 95% of the D. occidentale plants contained all four D. occidentale specific STS markers, whereas the remaining plants contained three of the four STS markers. Approximately 97% of D. barbeyi plants contained all three D. barbeyi specific STS markers, and the rest had two of the three STS markers. A small percentage of D. barbeyi plants contained one D. occidentale specific STS marker. Hybrid populations were characterized as having more D. occidentale specific than D. barbeyi specific STS markers, suggesting that the three hybrid populations are composed not of F1 hybrid plants of the parental species but of segregating offspring of different generations from original hybrids. This set of STS and CAPS markers for larkspur species should be useful in classification of unknown plant materials and the identification of hybrid populations.Key words: poisonous plants, RAPD, molecular marker, PCR.

scholarly journals Reexamining the Classification of Theobroma cacao L. Using Molecular Markers

1994 ◽  
Vol 119 (5) ◽  
pp. 1073-1082 ◽  
Author(s):  
Antonio Figueira ◽  
Jules Janick ◽  
Morris Levy ◽  
Peter Goldsbrough
Keyword(s):  
Molecular Markers ◽  
Theobroma Cacao ◽  
Rapd Markers ◽  
Continuous Variation ◽  
Clear Distinction ◽  
Species Separation ◽  
Theobroma Cacao L ◽  
Rdna Polymorphism

Genetic similarities among eight Theobroma and two Herrania species, including 29 genotypes of T. cacao, were estimated by rDNA polymorphism. A phenogram based on these genetic similarities significantly separated two clusters: one cluster included all Herrania and Theobroma species, except T. cacao, while the second contained 28 of 29 T. cacao genotypes. There was no clear distinction between Herrania and Theobroma species. Separation of 29 T. cacao genotypes, representing all races and various origins, had no congruency with the conventional classification into three horticultural races: Criollo, Forastero, and Trinitario. Genetic similarities in T. cacao, estimated with RAPD markers, indicated continuous variation among the generally similar but heterogeneous genotypes. The wild genotypes formed an outgroup distinct from the cultivated genotypes, a distinction supported by the rDNA data. The phenograms constructed from RAPD and rDNA data were not similar within the wild and cultivated cacao subsets.

scholarly journals Pollination Ecology and Breeding System of Delphinium Occidentale

1993 ◽  
Vol 17 ◽  
pp. 87-90
Author(s):  
Ron Scogin
Keyword(s):  
Flower Color ◽  
Pollination Ecology ◽  
Seed Collection ◽  
Local Populations ◽  
Balanced Polymorphism ◽  
Flower Color Polymorphism ◽  
Tall Larkspur ◽  
Alternative Hypotheses ◽  
Flower Form ◽  
Delphinium Occidentale

Delphinium occidentale Nutt. (Ranunculaceae), the tall larkspur, occurs sporatically as isolated local populations in moist locations at lower and middle elevations of Grand Teton National Park. Individual plants of this species exhibit flowers which occur as one of three distinct color morphs and which occur mixed in the local populations. The three floral morphs are 1) plants exhibiting the most familiar, uniformly dark purple pigmented flower form, 2) plants exhibiting an all white, nonpigmented, albino form, and 3) plants whose flowers are intermediate in form between the extremes of 1) and 2), a semi-albino form which exhibits normally pigmented petals, but white, nonpigmented sepals. The occurrence of mixed, polymorphic populations of D. occidentale floral morphs can be rationalized by two alternative hypotheses: 1. A stable, balanced polymorphism exists among the three morphs. This polymorphism is actively maintained by selective pressures, probably on some aspect of the reproductive biology (perhaps pollination ecology) of the floral morphs, or 2. The distribution of polymorphs is merely a founder effect, reflecting the distribution of morphs present in the seed collection which initially established the colonizing population. The research undertaken during 1993 represents an effort to discriminate between these alternative explanations of flower color polymorphism in D. occidentale.

scholarly journals Species-Specific Identification of Human Adenoviruses by a Multiplex PCR Assay

2000 ◽  
Vol 38 (11) ◽  
pp. 4114-4120 ◽  
Author(s):  
WanHong Xu ◽  
Mike C. McDonough ◽  
Dean D. Erdman
Keyword(s):  
Multiplex Pcr ◽  
Human Adenovirus ◽  
Cost Effective ◽  
Pcr Assay ◽  
Multiplex Pcr Assay ◽  
Amplicon Size ◽  
Species Specific ◽  
Fiber Gene ◽  
Amplification Reaction

A multiplex PCR assay was developed by using primers to the fiber gene that could differentiate human adenovirus (Ad) species A through F in a single amplification reaction. The assay correctly identified the species of all 49 recognized Ad prototype strains as well as 180 geographically and temporally diverse Ad field isolates. Ad serotype 6 (Ad6) (species C), Ad16 (species B), Ad31 (species A), and Ad40 and Ad41 (species F) could also be distinguished by amplicon size within each respective species. In comparison, a previously described Ad species-specific multiplex PCR assay that used primers to the Ad hexon gene gave equivocal results with several serotypes of species B, whereas our multiplex assay amplified all species B serotypes equally well. Our multiplex PCR assay will permit rapid, accurate, and cost-effective classification of Ad isolates.

scholarly journals A Bead-Based Flow Cytometric Assay for MonitoringYersinia pestisExposure in Wildlife

2018 ◽  
Vol 56 (7) ◽  
Author(s):  
Jeffrey C. Chandler ◽  
Laurie A. Baeten ◽  
Doreen L. Griffin ◽  
Thomas Gidlewski ◽  
Thomas J. DeLiberto ◽  
...  
Keyword(s):  
Analytical Sensitivity ◽  
Flow Cytometric Assay ◽  
Passive Hemagglutination ◽  
Content Type ◽  
Spatially Correlated ◽  
Flow Cytometric ◽  
Standard Tool ◽  
Specific Igg ◽  
Species Specific

ABSTRACTYersinia pestisis the causative agent of plague and is considered a category A priority pathogen due to its potential for high transmissibility and the significant morbidity and mortality it causes in humans.Y. pestisis endemic to the western United States and much of the world, necessitating programs to monitor for this pathogen on the landscape. Elevated human risk of plague infection has been spatially correlated with spikes in seropositive wildlife numbers, particularly rodent-eating carnivores, which are frequently in contact with the enzootic hosts and the associated arthropod vectors ofY. pestis. In this study, we describe a semiautomated bead-based flow cytometric assay developed for plague monitoring in wildlife called the F1 Luminex plague assay (F1-LPA). Based upon Luminex/Bio-Plex technology, the F1-LPA targets serological responses to the F1 capsular antigen ofY. pestisand was optimized to analyze antibodies eluted from wildlife blood samples preserved on Nobuto filter paper strips. In comparative evaluations with passive hemagglutination, the gold standard tool for wildlife plague serodiagnosis, the F1-LPA demonstrated as much as 64× improvement in analytical sensitivity for F1-specific IgG detection and allowed for unambiguous classification of IgG status. The functionality of the F1-LPA was demonstrated for coyotes and other canids, which are the primary sentinels in wildlife plague monitoring, as well as felids and raccoons. Additionally, assay formats that do not require species-specific immunological reagents, which are not routinely available for several wildlife species used in plague monitoring, were determined to be functional in the F1-LPA.

scholarly journals The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation

2013 ◽  
Vol 70 (3) ◽  
pp. 636-649 ◽  
Author(s):  
Ian H. McQuinn ◽  
Maxime Dion ◽  
Jean-François St. Pierre
Keyword(s):  
Model Validation ◽  
Fishery Management ◽  
Noise Removal ◽  
Trophic Levels ◽  
Angle Distribution ◽  
Acoustic Frequency ◽  
Frequency Responses ◽  
Meganyctiphanes Norvegica ◽  
Species Specific

Abstract McQuinn, I. H., Dion, M., and St. Pierre, J.-F. 2013. The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation. – ICES Journal of Marine Science, 70: 636–649. The ecosystem approach to fishery management requires monitoring capabilities at all trophic levels, including pelagic organisms. However, the usefulness of active acoustics for ecosystem monitoring has been limited by ambiguities in the identification of scattering layers. Increasingly, multifrequency acoustic methods are being developed for the classification of scattering layers into species or species groups. We describe a method for distinguishing between sympatric northern and Arctic krill (Meganyctiphanes norvegica and Thysanoessa raschii) using sv amplitude ratios from 38, 120, and 200 kHz data which were pre-processed through a self-noise removal algorithm. Acoustic frequency responses of both euphausiid species were predicted from species-specific parameterizations of a SDWBA physical model using specific body forms (shape, volume, and length) for Arctic and northern krill. Classification and model validation were achieved using macrozooplankton samples collected from multiple-sampler (BIONESS) and ringnet (JackNet) hauls, both equipped with a strobe light to reduce avoidance by euphausiids. SDWBA frequency responses were calculated for a range of orientations (± 45°) and compared with observed frequency responses, solving for orientation by least squares. A tilt angle distribution of N[9°,4°] and N[12°,6°] for T. raschii and M. norvegica, respectively resulted in best fits. The models also provided species-specific TS–length relationships.

scholarly journals Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

2014 ◽  
Vol 80 (11) ◽  
pp. 3341-3349 ◽  
Author(s):  
Tony Campillo ◽  
Sébastien Renoud ◽  
Isabelle Kerzaon ◽  
Ludovic Vial ◽  
Jessica Baude ◽  
...  
Keyword(s):  
Ferulic Acid ◽  
Protocatechuic Acid ◽  
Coenzyme A ◽  
Degradation Pathway ◽  
Hydroxycinnamic Acid ◽  
Plant Materials ◽  
Toxic Compounds ◽  
Content Type ◽  
Acid Degradation ◽  
Species Specific

ABSTRACTThe soil- and rhizosphere-inhabiting bacteriumAgrobacterium fabrum(genomospecies G8 of theAgrobacterium tumefaciensspecies complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genesatu1416,atu1417, andatu1420have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genesatu1415andatu1421have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that theA. fabrumhydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transformp-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

scholarly journals Classification of Lytic Bacteriophages Attacking Dairy Leuconostoc Starter Strains

2013 ◽  
Vol 79 (12) ◽  
pp. 3628-3636 ◽  
Author(s):  
Yahya Ali ◽  
Witold Kot ◽  
Zeynep Atamer ◽  
Jörg Hinrichs ◽  
Finn K. Vogensen ◽  
...  
Keyword(s):  
Host Range ◽  
Detection System ◽  
Structural Genes ◽  
Phage Group ◽  
Content Type ◽  
Phage Types ◽  
Species Specific ◽  
Leuconostoc Pseudomesenteroides ◽  
Different Sources

ABSTRACTA set of 83 lytic dairy bacteriophages (phages) infecting flavor-producing mesophilic starter strains of theLeuconostocgenus was characterized, and the first in-depth taxonomic scheme was established for this phage group. Phages were obtained from different sources, i.e., from dairy samples originating from 11 German dairies (50Leuconostoc pseudomesenteroides[Ln. pseudomesenteroides] phages, 4Ln. mesenteroidesphages) and from 3 external phage collections (17Ln. pseudomesenteroidesphages, 12Ln. mesenteroidesphages). All phages belonged to theSiphoviridaefamily of phages with isometric heads (diameter, 55 nm) and noncontractile tails (length, 140 nm). With the exception of one phage (i.e., phage ΦLN25), allLn. mesenteroidesphages lysed the same host strains and revealed characteristic globular baseplate appendages. Phage ΦLN25, with different Y-shaped appendages, had a unique host range. Apart from two phages (i.e., phages P792 and P793), allLn. pseudomesenteroidesphages shared the same host range and had plain baseplates without distinguishable appendages. They were further characterized by the presence or absence of a collar below the phage head or by unique tails with straight striations. Phages P792 and P793 with characteristic fluffy baseplate appendages could propagate only on other specific hosts. AllLn. mesenteroidesand allLn. pseudomesenteroidesphages were members of two (host species-specific) distinct genotypes but shared a limited conserved DNA region specifying their structural genes. A PCR detection system was established and was shown to be reliable for the detection of allLeuconostocphage types.

scholarly journals 676 PB 160 IDENTIFICATION AND CLASSIFICATION OF PISTACHIO (Pistacia vera L.) CULTIVARS WITH RAPD MARKERS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 529f-529
Author(s):  
J.I. Hormaza ◽  
L. Dollo ◽  
V.S. Polito
Keyword(s):  
Rapd Markers ◽  
Geographical Origin ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Pistacia Vera ◽  
Polymorphic Markers ◽  
Molecular Phenotype ◽  
And Cluster Analysis

The Random Amplified Polymorphic DNA (RAPD) technique was used to characterize 15 cultivars of pistachio (Pistacia vera L.). A total of 37 polymorphic markers were considered in this study. Each cultivar exhibited a unique molecular phenotype and, as a consequence, can be uniquely fingerprinted. A similarity and cluster analysis based on the amplified fragments produced two distinct groups which are consistent with the known geographical origin of the cultivars. Our results suggest that RAPD analysis can provide a new alternative for cultivar identification and classification of pistachio.

scholarly journals Genetic Relationships of Pyrus Species and Cultivars Native to East Asia Revealed by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (2) ◽  
pp. 262-270 ◽  
Author(s):  
Yuanwen Teng ◽  
Kenji Tanabe ◽  
Fumio Tamura ◽  
Akihiro Itai
Keyword(s):  
East Asia ◽  
Clustering Analysis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Randomly Amplified Polymorphic Dna ◽  
Pyrus Calleryana ◽  
Chinese White ◽  
Species Specific ◽  
Kochi Prefecture

A total of 118 Pyrus sp. (pear) and cultivars native mainly to east Asia were subjected to randomly amplified polymorphic DNA (RAPD) analysis to evaluate genetic variation and relationships among the accessions. Two hundred fifty RAPD markers were scored from 20 decamer primers. RAPD markers specific to species were identified. Clustering analysis revealed two divisions: one comprising cultivars of P. communis L., and the other including all accessions of Pyrus native to east Asia. The grouping of the species and cultivars by RAPD data largely agrees with morphological pear taxonomy. However, some noted incongruence existed between two classification methods. Pyrus calleryana Dcne. clustered together with P. koehnei Schneid., P. fauriei Schneid. and P. dimorphophylla Makino. Pyrus betulaefolia Bge. clustered with P. ×hopeiensis Yu and P. ×phaeocarpa Rehd. A noncultivated clone of P. aromatica Kikuchi et Nakai grouped with P. aromatica cultivars. Pyrus hondoensis Nakai et Kikuchi and cultivars of P. ussuriensis Max. formed a single group. Some accessions from Korea (named Korean pear) had species-specific RAPD markers and comprised an independent group. Most of the Chinese white pears clustered together with most of the Chinese sand pears. Based on the present results, the new nomenclature P. pyrifolia var. sinensis (Lindley) Teng et Tanabe for Chinese white pear was suggested. Most accessions of Japanese pears fell into one main group, whereas pear cultivars from Kochi Prefecture of Japan subclustered with some Chinese sand pears and one accession from Korea. Our results infer that some local Japanese pear cultivar populations may have been derived from cultivars native to Kochi Prefecture in Shikoku region, and that the latter may have been introduced from ancient China and/or Korea.

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