(17) TRAP Markers Help Categorizea Pelargonium Collection

The Ornamental Plant Germplasm Center (OPGC) maintains a collection of herbaceous ornamental plants in order to protect future breeders from a loss of genetic diversity. The current Pelargonium collection includes ≈870 accessions. Our preliminary studies showed that TRAP (Target Region Amplified Polymorphism) has promise for analyzing the variation in our collection, and so we have expanded the study to analyze the entire Pelargonium collection. We have used the same primers for this screening of the Pelargonium collection as were used on sunflowers, and TRAP results run on a sequencing gel showed 90–150 bands that segregate the population into groups of similar accessions. In order to facilitate analysis of OPGC's large population, we have converted the method to a high throughput technique that efficiently analyzed the entire population. We used a 96-well DNA extraction kit from Qiagen that produced high quality DNA in spite of the high phenol levels in some Pelargonium species. Also, the use of labeled primers allowed analysis of the gels to be aided by a computer. These results produce a categorization of the collection that, combined with morphology and taxonomy, will form the basis for future studies that will use target genes specific to Pelargonium.

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Target Region Amplification Polymorphism (TRAP) as a Tool for Detecting Genetic Variation in the Genus Pelargonium

HortScience ◽

10.21273/hortsci.42.5.1118 ◽

2007 ◽

Vol 42 (5) ◽

pp. 1118-1123 ◽

Cited By ~ 6

Author(s):

Rose Palumbo ◽

Wai-Foong Hong ◽

Guo-Liang Wang ◽

Jinguo Hu ◽

Richard Craig ◽

...

Keyword(s):

Genetic Diversity ◽

Ornamental Plant ◽

The Other ◽

Sequence Information ◽

Extraction Techniques ◽

Large Collection ◽

Target Region ◽

Breeding Lines ◽

Target Region Amplification Polymorphism

Pelargonium was a priority genera collected by the Ornamental Plant Germplasm Center (OPGC) until a recent reorganization. To preserve genetic diversity for future breeders, OPGC collects heirloom cultivars, breeding lines, and wild species. The current Pelargonium collection at OPGC consists primarily of cultivars originating from P. ×hortorum and P. ×domesticum. Target region amplification polymorphism (TRAP) has the advantage of producing a large number of markers through use of sequence information that is already available. Our first goal was to determine the feasibility of TRAP for the analysis of this large collection, so that in the future the most diverse genotypes may be retained. To achieve this goal, we first modified existing DNA extraction techniques to account for the high levels of phenolic compounds present in some Pelargonium species by combining several washes to remove the phenolics with the addition of high levels of antiphenolic compounds. Second, we evaluated the TRAP procedure using the DNA isolated from 46 accessions. For 44 accessions, one or two primer combinations generated enough fragments to discriminate each of the accessions, and similar clades were produced by cluster analysis of the polymorphic fragments amplified by different primer combinations. All the scorable fragments were polymorphic, for one primer combination there were 148 markers from one image and the other produced 160 markers on two images. These results demonstrate that TRAP is an effective method for molecular characterization of ornamental collections.

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Contribuição ao estudo de insetos (Arthropoda: Insecta) associados ao gênero Ixora L. (Angiospermae: Rubiaceae) no Brasil

Ornamental Horticulture ◽

10.14295/aohl.v21i2.733 ◽

2015 ◽

Vol 21 (2) ◽

pp. 161

Author(s):

Thiago Dias Trindade ◽

Liliane Kiffer Figueira do Nascimento ◽

Ana Carolina Muniz

Keyword(s):

Bemisia Tabaci ◽

Ornamental Plants ◽

Ornamental Plant ◽

Future Studies ◽

Toxoptera Citricida ◽

First Time ◽

Chrysomphalus Aonidum ◽

Aspidiotus Destructor

This study aimed to register insects (Arthropoda: Insecta) associated with genus Ixora L. (Angiospermae: Rubiaceae) and contribute the knowledge about this popular tropical ornamental plant in Brazil. For this study, we detected the presence of insects in solid or isolated plants of Ixora spp., and greenhouses, between the period 2004 and 2012. It was pointed out for the first time on I. chinensis Lam.: Syntermes dirus (Burmeister, 1839) (Isoptera: Termitidae), Aspidiotus destructor (Signoret, 1869) and Chrysomphalus aonidum (Linnaeus, 1758) (Hemiptera: Diaspididae), Praelongorthezia praelonga (Douglas, 1891) (Hemiptera: Ortheziidae) and Camponotus sp. (Hymenoptera: Formicidae). Studies registered for the first time on I. coccinea L.: Aleurothrixus aepim (Goeldi, 1886) and Bemisia tabaci (Gennadius, 1889) (Hemiptera: Aleyrodidae) Eucalymnatus sp., Parasaissetia nigra (Nietner, 1861) and Saissetia olae (Olivier, 1791) (Hemiptera: Coccidae), and Camponotus sp. It was observed first on I. macrothyrsa Teijsm. & Binn.) N. E. Br.: Aleurothrixus floccosus (Maskell, 1895), Aleurotrachelus sp. (Aleyrodidae), Aphis (Toxoptera) citricida (Kirkaldy, 1907) and Myzus (Nectarosiphon) persicae (Sulzer, 1778) (Hemiptera: Aphididae) Harmonia sp. (Coleoptera: Coccinellidae), Camponotus sp. This paper contributes to the study of these important ornamental plants, presenting for the first time a list of associated insects. This work also creates conditions for future studies.

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Every beach an island—deep population divergence and possible loss of genetic diversity in Tylos granulatus, a sandy shore isopod

Marine Ecology Progress Series ◽

10.3354/meps12882 ◽

2019 ◽

Vol 614 ◽

pp. 111-123 ◽

Cited By ~ 1

Author(s):

NA Mbongwa ◽

C Hui ◽

A Pulfrich ◽

S von der Heyden

Keyword(s):

Genetic Diversity ◽

Population Divergence ◽

Sandy Shore ◽

Loss Of Genetic Diversity

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Evolutionary genetics of small populations

10.1093/oso/9780198783398.003.0002 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Evolutionary Genetics ◽

Small Population ◽

Small Populations ◽

Effective Population ◽

Genetic Management ◽

Evolutionary Genetic ◽

Loss Of Genetic Diversity ◽

Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

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From Multiplex Serology to Serolomics—A Novel Approach to the Antibody Response against the SARS-CoV-2 Proteome

Viruses ◽

10.3390/v13050749 ◽

2021 ◽

Vol 13 (5) ◽

pp. 749

Author(s):

Julia Butt ◽

Rajagopal Murugan ◽

Theresa Hippchen ◽

Sylvia Olberg ◽

Monique van Straaten ◽

...

Keyword(s):

Antibody Response ◽

High Throughput ◽

Large Population ◽

High Sensitivity ◽

Population Based ◽

Antibody Responses ◽

Hek293 Cells ◽

Novel Approach ◽

Assay Performance ◽

Multiplex Serology

The emerging SARS-CoV-2 pandemic entails an urgent need for specific and sensitive high-throughput serological assays to assess SARS-CoV-2 epidemiology. We, therefore, aimed at developing a fluorescent-bead based SARS-CoV-2 multiplex serology assay for detection of antibody responses to the SARS-CoV-2 proteome. Proteins of the SARS-CoV-2 proteome and protein N of SARS-CoV-1 and common cold Coronaviruses (ccCoVs) were recombinantly expressed in E. coli or HEK293 cells. Assay performance was assessed in a COVID-19 case cohort (n = 48 hospitalized patients from Heidelberg) as well as n = 85 age- and sex-matched pre-pandemic controls from the ESTHER study. Assay validation included comparison with home-made immunofluorescence and commercial enzyme-linked immunosorbent (ELISA) assays. A sensitivity of 100% (95% CI: 86–100%) was achieved in COVID-19 patients 14 days post symptom onset with dual sero-positivity to SARS-CoV-2 N and the receptor-binding domain of the spike protein. The specificity obtained with this algorithm was 100% (95% CI: 96–100%). Antibody responses to ccCoVs N were abundantly high and did not correlate with those to SARS-CoV-2 N. Inclusion of additional SARS-CoV-2 proteins as well as separate assessment of immunoglobulin (Ig) classes M, A, and G allowed for explorative analyses regarding disease progression and course of antibody response. This newly developed SARS-CoV-2 multiplex serology assay achieved high sensitivity and specificity to determine SARS-CoV-2 sero-positivity. Its high throughput ability allows epidemiologic SARS-CoV-2 research in large population-based studies. Inclusion of additional pathogens into the panel as well as separate assessment of Ig isotypes will furthermore allow addressing research questions beyond SARS-CoV-2 sero-prevalence.

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Genetic diversity and evolution of hepatitis C virus – 15 years on

Journal of General Virology ◽

10.1099/vir.0.80401-0 ◽

2004 ◽

Vol 85 (11) ◽

pp. 3173-3188 ◽

Cited By ~ 564

Author(s):

Peter Simmonds

Keyword(s):

Genetic Diversity ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Human Liver ◽

Large Population ◽

Sequence Divergence ◽

Selection Pressures ◽

Host Interactions ◽

Persistent Viruses ◽

The Face

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus–host interactions may represent key components in establishing its ‘ecological niche’ in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

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