Development and characterization of microsatellite markers in Cynara cardunculus L.

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 217-225 ◽  
Author(s):  
Alberto Acquadro ◽  
Ezio Portis ◽  
David Lee ◽  
Paolo Donini ◽  
Sergio Lanteri
Keyword(s):  
Molecular Markers ◽  
Fold Increase ◽  
The United States ◽  
Enriched Library ◽  
Globe Artichoke ◽  
Cynara Cardunculus ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Novel Approach ◽  
Wild Cardoon

Cynara cardunculus L. is a species native to the Mediterranean basin that comprises 2 crops, globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC), as well as wild cardoon (var. sylvestris (Lamk) Fiori). Globe artichoke represents an important component of the South European agricultural economy but is also cultivated in North Africa, the Near East, South America, the United States, and China. Breeding activities and molecular marker studies have been, to date, extremely limited. Better knowledge of the genome of the species might be gained by developing a range of molecular markers. Here, we report on the development of 14 microsatellites (simple sequence repeats (SSRs)) through a novel approach that we have defined as the microsatellite amplified library (MAL). The approach represents a combination of amplified fragment length polymorphism and a primer extension based enriched library, is rapid, and requires no hybridization enrichment steps. The technique provided a ~40-fold increase in the efficiency of SSR identification compared with conventional library procedures. The developed SSRs were applied for genotyping 36 accessions of C. cardunculus, including a core of 27 varietal types of globe artichoke, 3 accessions of cultivated cardoon, and 6 Sicilian accessions of wild cardoon. Principal coordinates analysis made it possible to differentiate both cultivated and wild forms from each other.Key words: globe artichoke, wild and cultivated cardoon, molecular markers, AFLP, MAL (microsatellite amplified library).

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Zhao-Wei Liu ◽  
Robert L. Jarret ◽  
Ronny R. Duncan ◽  
Stephen Kresovich
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Seashore Paspalum ◽  
Principal Coordinates ◽  
Paspalum Vaginatum ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

The wild gene pool of globe artichoke

2015 ◽  
Vol 62 (1-2) ◽  
pp. 33-38 ◽  
Author(s):  
Aaron Rottenberg
Keyword(s):  
Molecular Markers ◽  
Gene Pool ◽  
Mediterranean Basin ◽  
Molecular Genetic ◽  
Globe Artichoke ◽  
Cynara Cardunculus ◽  
Primary Gene Pool ◽  
The Mediterranean ◽  
Primary Gene ◽  
The Mediterranean Basin

Globe artichoke is an important vegetable of the Mediterranean basin. Its primary gene pool (GP1) consists of wild types ofCynara cardunculus. Crosses between the wild types and the cultivars (artichoke and cardoon) are fully fertile. In accordance, analyses of molecular markers revealed high genetic identity between the wild types and the cultivars. Hence, all these taxa are grouped together as conspecific varieties withinC.cardunculus. Several other wildCynaraspecies thrive in the Mediterranean basin. Of these,C. syriaca,C. algarbiensis,C. baeticaandC. humiliswere tested and found to be part of the secondary gene pool (GP2) of artichoke, as they were rather difficult to cross with either wild or cultivatedC. cardunculusand the few hybrids obtained were semi-sterile. In accordance, molecular genetic markers suggest that these wildCynaraspecies indeed diverged fromC. cardunculus. Four additionalCynaraspecies thrive in the Mediterranean basin, namelyC. cornigera,C. cyrenaica,C. tournefortiiandC. makrisii. There is no information on the crossability of these four species with artichoke, but molecular markers suggest that they may also belong to the secondary gene pool of the crop. Considering some attractive, variable characteristics of each of the GP2 species, such as earliness, albinism, dwarfism and diverse flavors, these wild species might be of great interest for artichoke breeders.

scholarly journals Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1182 ◽  
Author(s):  
Meriem Miyassa Aci ◽  
Antonio Lupini ◽  
Giuseppe Badagliacca ◽  
Antonio Mauceri ◽  
Emilio Lo Presti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Protein Content ◽  
Structure Analysis ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content.

Retrotransposon-based S-SAP as a platform for the analysis of genetic variation and linkage in globe artichoke

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1149-1159 ◽  
Author(s):  
Alberto Acquadro ◽  
Ezio Portis ◽  
Andrea Moglia ◽  
Franco Magurno ◽  
Sergio Lanteri
Keyword(s):  
Copy Number ◽  
Genetic Linkage ◽  
Fragment Length Polymorphism ◽  
Sequence Polymorphism ◽  
Hybrid Population ◽  
Genetic Linkage Analysis ◽  
Globe Artichoke ◽  
Cynara Cardunculus ◽  
The Core ◽  
Wild Cardoon

A high copy number of retrotransposon sequences are present and widely dispersed in plant genomes. Their activity generates a considerable degree of sequence polymorphism. Here, we report the cloning of CYRE-5, a long-terminal repeat carrying retrotransposon-like sequence in Cynara cardunculus L., and its exploitation to develop a DNA fingerprinting assay across 22 accessions, including both cultivated (globe artichoke and cultivated cardoon) and wild (wild cardoon) types. The effectiveness of the sequence-specific amplified polymorphism (S-SAP) platform is compared with that of amplified fragment length polymorphism (AFLP). A genetic linkage analysis, based on a hybrid population between 2 globe artichoke varietal types, resulted in the inclusion of 29 S-SAP loci in the core genetic map, confirming their dispersed distribution across the globe artichoke genome.

Cynara cardunculus L., a potential source of inulin in the Mediterranean environment: screening of genetic variability

2004 ◽  
Vol 55 (6) ◽  
pp. 693 ◽  
Author(s):  
S. A. Raccuia ◽  
M. G. Melilli
Keyword(s):  
Genetic Variability ◽  
Sugar Content ◽  
Total Sugar ◽  
Total Biomass ◽  
Globe Artichoke ◽  
Cynara Cardunculus ◽  
Mediterranean Environment ◽  
Total Sugar Content ◽  
The Mediterranean ◽  
Wild Cardoon

Cynara cardunculus L. is a diploid (2n = 34) outcrossing perennial species, native to the Mediterranean basin, comprising the globe artichoke, the cultivated cardoon, and the wild cardoon. These species have potential as biomass, sugar, and oilseed crops. This paper aimed to study the genetic variability for sugar production and sugar composition in the roots of different C. cardunculus L. genotypes, in order to select those suitable for this specific purpose in the Mediterranean environment. At harvest the total biomass and root production, averaged for all genotypes, were 20.4 and 9.8 t DM/ha; they were influenced by genotype, with a CV of 37.4 and 38.5%, respectively. On average for all of the genotypes, the roots showed a total sugar content of 367 g DM/kg, with a CV of 17.1%; the main compound was inulin (85.0% of total sugars). The wild cardoon ‘SR1’ showed the highest total sugar content (470 g/kg DM). On average for all of the genotypes, the total sugar and inulin yields were 3.6 ± 0.20 and 3.0 ± 0.16 t/ha, respectively. It was possible to obtain total sugar yields higher than 4 t/ha in 6 genotypes (‘BH’, ‘VP’, ‘E438’, ‘L01’, ‘C2’, ‘P1’) of the 15 studied.

scholarly journals Allelopathic potential of leaf aqueous extracts from Cynara cardunculus L. on the seedling growth of two cosmopolitan weed species

2019 ◽  
Vol 14 (2) ◽  
pp. 78-83 ◽  
Author(s):  
Aurelio Scavo ◽  
Gaetano Pandino ◽  
Alessia Restuccia ◽  
Sara Lombardo ◽  
Gaetano Roberto Pesce ◽  
...  
Keyword(s):  
Root System ◽  
Aqueous Extract ◽  
Hplc Analysis ◽  
Globe Artichoke ◽  
Aqueous Extracts ◽  
Cynara Cardunculus ◽  
Weed Species ◽  
Allelopathic Potential ◽  
System Length ◽  
Wild Cardoon

The search for sustainable alternatives to synthetic herbicides for weed control, has led the scientific community to an increased interest for plant allelopathic mechanisms. The utilisation of plant extracts as possible bioherbicides represents an important solution. In the present study, laboratory experiments were carried out to investigate, for the first time, the differences in the allelopathic activity of the three Cynara cardunculus L. botanical varieties (globe artichoke, cultivated and wild cardoon) leaf aqueous extracts on the seedling growth of Amaranthus retroflexus L. and Portulaca oleracea L. In addition, the autoallelopathic effect on wild cardoon growth and the qualitative profile of the aqueous extract through high-performance liquid chromatograpy (HPLC) analysis were evaluated. Overall, the allelopathic effects were both genotype- and weed species-dependent. Wild cardoon showed the highest allelopathic potential (–23.4%), followed by cultivated cardoon and globe artichoke, and P. oleracea was the most sensitive target species (–32%). Besides, root system length was the most affected parameter (–32.6%). The autoallelopathic effect of wild cardoon extract was also demonstrated on root system length, hypocotyl and epicotyl length and total dry weight. C. cardunculus leaf aqueous extract was characterised by 5 sesquiterpene lactones, 2 caffeoylquinic acids, 6 flavones and 1 lignan. From the HPLC analysis we found that apigenin and luteolin 7-O-glucoronide were detected only in wild cardoon, apigenin 7-O-glucoside was typic of globe artichoke, and 11,13-dihydro-deacylcynaropicrin and 11,13-dihydroxi-8-deoxygrosheimin were characteristics of cultivated cardoon.

Forecasting Interconnections in International Housing Markets: Evidence from the Dynamic Model Averaging Approach

2020 ◽  
Vol 42 (1) ◽  
pp. 37-103
Author(s):  
Hardik A. Marfatia
Keyword(s):  
Dynamic Model ◽  
Model Averaging ◽  
Housing Markets ◽  
The United States ◽  
Forecasting Model ◽  
Change Over Time ◽  
The United Kingdom ◽  
Novel Approach ◽  
Dynamic Model Averaging ◽  
Over Time

In this paper, I undertake a novel approach to uncover the forecasting interconnections in the international housing markets. Using a dynamic model averaging framework that allows both the coefficients and the entire forecasting model to dynamically change over time, I uncover the intertwined forecasting relationships in 23 leading international housing markets. The evidence suggests significant forecasting interconnections in these markets. However, no country holds a constant forecasting advantage, including the United States and the United Kingdom, although the U.S. housing market's predictive power has increased over time. Evidence also suggests that allowing the forecasting model to change is more important than allowing the coefficients to change over time.

scholarly journals Orexin receptor antagonists reverse aberrant dopamine neuron activity and related behaviors in a rodent model of stress-induced psychosis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hannah B. Elam ◽  
Stephanie M. Perez ◽  
Jennifer J. Donegan ◽  
Daniel J. Lodge
Keyword(s):  
United States ◽  
Sensorimotor Gating ◽  
The United States ◽  
Dopamine Neuron ◽  
Neuron Activity ◽  
Sprague Dawley ◽  
Post Traumatic Stress ◽  
Neuron Population ◽  
Population Activity ◽  
Novel Approach

AbstractPost-traumatic stress disorder (PTSD) is a prevalent condition affecting approximately 8% of the United States population and 20% of United States combat veterans. In addition to core symptoms of the disorder, up to 64% of individuals diagnosed with PTSD experience comorbid psychosis. Previous research has demonstrated a positive correlation between symptoms of psychosis and increases in dopamine transmission. We have recently demonstrated projections from the paraventricular nucleus of the thalamus (PVT) to the nucleus accumbens (NAc) can regulate dopamine neuron activity in the ventral tegmental area (VTA). Specifically, inactivation of the PVT leads to a reversal of aberrant dopamine system function and psychosis-like behavior. The PVT receives dense innervation from orexin containing neurons, therefore, targeting orexin receptors may be a novel approach to restore dopamine neuron activity and alleviate PTSD-associated psychosis. In this study, we induced stress-related pathophysiology in male Sprague Dawley rats using an inescapable foot-shock procedure. We observed a significant increase in VTA dopamine neuron population activity, deficits in sensorimotor gating, and hyperresponsivity to psychomotor stimulants. Administration of selective orexin 1 receptor (OX1R) and orexin 2 receptor (OX2R) antagonists (SB334867 and EMPA, respectively) or the FDA-approved, dual-orexin receptor antagonist, Suvorexant, were found to reverse stress-induced increases in dopamine neuron population activity. However, only Suvorexant and SB334867 were able to reverse deficits in behavioral corelates of psychosis. These results suggest that the orexin system may be a novel pharmacological target for the treatment of comorbid psychosis related to PTSD.

scholarly journals Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Komal Jain ◽  
Teresa Tagliafierro ◽  
Adriana Marques ◽  
Santiago Sanchez-Vicente ◽  
Alper Gokden ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Fold Increase ◽  
The United States ◽  
Genomic Research ◽  
Babesia Microti ◽  
Hybridization Capture ◽  
Mouse Tissues ◽  
Genome Analyses ◽  
Capture Sequencing

AbstractInadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.

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