scholarly journals Statistical analysis of the associations between phenolic monoterpenes and molecular markers, AFLPs and SAMPLs in the spice plant Oregano

2016 ◽  
Vol 62 (2) ◽  
pp. 42-56 ◽  
Author(s):  
Ali Azizi ◽  
Hamidreza Ardalani ◽  
Bernd Honermeier
Keyword(s):  
Molecular Markers ◽  
Essential Oils ◽  
Linear Model ◽  
Genetic Markers ◽  
Marker Assisted Selection ◽  
Molecular Breeding ◽  
Mixed Linear Model ◽  
Origanum Vulgare ◽  
Starting Point ◽  
Essential Oil Yield

Summary Introduction: Molecular markers are the examples of the contribution of genome technology to medicinal plant breeding through marker-assisted selection (MAS) for pharmaceutical quality. Objective: Forty-two accessions of Origanum vulgare L. originating from Europe were evaluated to detect genomic and chemotypic polymorphisms and to discover possible associations between them. Methods: A total of 477 molecular polymorphisms including 214 AFLP (Amplified Fragment Length Polymorphism) and 263 SAMPL (Selectively Amplified Microsatellite Polymorphic Loci) were used for genotyping. Components in the essential oils were identified and quantified by gas chromatography (GC) and two major compounds (two economically important monoterpenes: carvacrol and thymol) were investigated. Results: Based on results, a relatively high correlation between chemotypic patterns and genetic markers was identified. Associations between traits of interest for essential oils (carvacrol and thymol content) and genetic markers were tested using five statistical methods including three General Linear Model (GLM) and two unified Mixed Linear Model (MLM) approaches. Significant associations were found for 3 AFLP and 20 SAMPL with three key traits including essential oil yield, carvacrol and thymol content. Conclusion: These associations can constitute a useful starting point for marker-assisted selection. Therefore, the results provide the basis for molecular breeding of O. vulgare for pharmaceutical purposes.

scholarly journals On modeling and analyzing barley malt data in different years

2019 ◽  
Vol 56 (1) ◽  
pp. 45-57
Author(s):  
Iwona Mejza ◽  
Katarzyna Ambroży-Deręgowska ◽  
Jan Bocianowski ◽  
Józef Błażewicz ◽  
Marek Liszewski ◽  
...  
Keyword(s):  
Linear Model ◽  
Random Effects ◽  
Fixed Effects ◽  
Linear Models ◽  
Model Fitting ◽  
Mixed Linear Model ◽  
Barley Grain ◽  
Barley Malt ◽  
Starting Point ◽  
Quality Coefficient

SummaryThe main purpose of this study was the model fitting of data deriving from a three-year experiment with barley malt. Two linear models were considered: a fixed linear model with fixed effects of years and other factors, and a mixed linear model with random effects of years and fixed effects of other factors. Two cultivars of brewing barley, Sebastian and Mauritia, six methods of nitrogen fertilization and four germination times were analyzed. Three quantitative traits were observed: practical extractivity of the malt, malting productivity, and a quality coefficient Q. The starting point for the statistical analyses was the available experimental material, which consisted of barley grain samples destined for malting. The analyses were performed over a series of years with respect to fixed or random effects of years. Due to the strong differentiation of the years of the study and some significant interactions of factors with years, annual analyses were also carried out.

scholarly journals Genetic identification of the Putre’s oregano (Origanum vulgare L.) by ITS and microsatellites, a species recognized in Chile with Seal of Origin

2021 ◽  
Vol 20 (2) ◽  
pp. 177-194
Author(s):  
Roberto Contreras ◽  
◽  
Isabel Calle ◽  
Romulo Oses ◽  
Fernanda Aguayo ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Markers ◽  
Dna Barcode ◽  
Genetic Identification ◽  
Geographical Indication ◽  
Origanum Vulgare ◽  
Technological Support ◽  
Different Sources ◽  
Production Conditions ◽  
Organoleptic Attributes

Putre´s oregano (Origanum vulgare L.) is a variety of oregano that grown in the Arica-Parinacota Region. Its organoleptic attributes and unique production conditions have earned it a certification with Geographical Indication (GI). However, the demands of the markets require a scientific-technological support for identification and authentication of materials. In this context, was proposed to identify Putre's oregano by phylogenetic relationships based on the use of molecular markers SSR and "DNA Barcode". The results showed that when comparing materials from different sources of Putre´s oregano versus information from certified germplasms and GenBank sequences, added to the analysis with nuclear genetic markers, Putre´s oregano corresponds to the species Origanum vulgare L. subsp virens. This precise identification will support the correct differentiation and authentication of this genotype, serving in addition to supporting the GI.

scholarly journals Simulation of marker assisted selection in hybrid populations

1994 ◽  
Vol 63 (1) ◽  
pp. 39-47 ◽  
Author(s):  
A. Gimelfarb ◽  
R. Lande
Keyword(s):  
Molecular Markers ◽  
Linkage Disequilibrium ◽  
Population Size ◽  
Genetic Markers ◽  
Computer Model ◽  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Response To Selection ◽  
Molecular Information ◽  
Efficiency Of Selection

SummaryA computer model is developed that simulates Marker Assisted Selection (MAS) in a population produced by a cross between two inbred lines. Selection is based on an index that incorporates both phenotypic and molecular information. Molecular markers contributing to the index and their relative weights are determined by multiple regression of individual phenotype on the markers. The model is applied to investigate the efficiency of MAS as affected by several factors including total number of markers in the genome, number of markers contributing to the index, population size and heritability of the character. It is demonstrated that selection based on genetic markers can effectively utilize the linkage disequilibrium between genetic markers and QTLs created by crossing inbred lines. Selection is more efficient if markers contributing to the index are re-evaluated each generation than if they are evaluated only once. Increasing the total number of markers in the genome as well as the number of markers contributing to the index does not necessarily result in a higher efficiency of selection. Moreover, too many markers may result in a weaker response to selection. Population size is shown to be the most important factor affecting the efficiency of MAS.

scholarly journals Application of Markers Assisted Selection for Striga Hermonthica Resistance on Sorghum (Sorghum bicolor (L.) Moench

2021 ◽  
pp. 15-26
Author(s):  
Habtamu Demelash Tamir
Keyword(s):  
Molecular Markers ◽  
Sorghum Bicolor ◽  
Genetic Markers ◽  
Ssr Markers ◽  
Marker Assisted Selection ◽  
Smallholder Farmers ◽  
Striga Hermonthica ◽  
Resistant Cultivars ◽  
Germplasm Collections ◽  
Sorghum Bicolor L

Sorghum (Sorghum bicolor L. [Moench]) is a staple food crop for smallholder farmers in arid and semi-arid(ASALs) regions worldwide, feeding over 500 million of the world's most resource-poor. Development of Striga Hermonthica resistant cultivars by conventional breeding is slow and have been hampered by the lack of efficient and reliable screening techniques in breeding programs. Molecular markers that are linked to witchweed resistance can expedite the development of resistant cultivars through the adoption of appropriate marker-assisted selection (MAS) strategies. Marker-assisted selection involves the selection of genotypes carrying a desirable gene(s) via linked markers; through MAS more rapid transfer of traits from donor parents to more elite locally adapted crop cultivars is possible with simple-sequence repeat (SSR) markers which have been initially used to detect polymorphism between the parent cultivars. Although costly to develop relative to some other classes of genetic markers, once developed, analysis by SSR markers is both easy and inexpensive. The highly polymorphic nature (high information content) and other favorable characteristics make them excellent genetic markers for a number of studies including marker-assisted selection and fingerprinting of germplasm collections. In this review, we summarize the molecular markers that are linked to the inheritance trait or low germination stimulant production is one of the recognized mechanisms of witch weed resistance.

Identification and validation of functional markers in a global rice collection by association mapping

Genome ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 355-362 ◽  
Author(s):  
Mojtaba Jahani ◽  
Ghorbanali Nematzadeh ◽  
Behnaz Dolatabadi ◽  
Sayyed Hamidreza Hashemi ◽  
Ghasem Mohammadi-Nejad
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Association Mapping ◽  
Marker Assisted Selection ◽  
Multiple Testing ◽  
Morphological Traits ◽  
Mixed Linear Model ◽  
Width Ratio ◽  
Functional Markers ◽  
Population Structure Analysis

Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker–trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.

scholarly journals Combined application of essential oils from Origanum vulgare L. and Rosmarinus officinalis L. to inhibit bacteria and autochthonous microflora associated with minimally processed vegetables

2011 ◽  
Vol 44 (5) ◽  
pp. 1541-1548 ◽  
Author(s):  
Geíza Alves de Azeredo ◽  
Tânia Lúcia Montenegro Stamford ◽  
Pollyana Campos Nunes ◽  
Nelson Justino Gomes Neto ◽  
Maria Elieidy Gomes de Oliveira ◽  
...  
Keyword(s):  
Essential Oils ◽  
Rosmarinus Officinalis ◽  
Origanum Vulgare ◽  
Minimally Processed ◽  
Combined Application ◽  
Rosmarinus Officinalis L ◽  
Minimally Processed Vegetables

scholarly journals Multi-Targeting Bioactive Compounds Extracted from Essential Oils as Kinase Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2174 ◽  
Author(s):  
Annalisa Maruca ◽  
Delia Lanzillotta ◽  
Roberta Rocca ◽  
Antonio Lupia ◽  
Giosuè Costa ◽  
...  
Keyword(s):  
Essential Oils ◽  
Binding Affinity ◽  
Structural Changes ◽  
Kinase Inhibitors ◽  
Synergistic Effects ◽  
Data Bank ◽  
Binding Modes ◽  
Starting Point ◽  
Target Action ◽  
Potential Resource

Essential oils (EOs) are popular in aromatherapy, a branch of alternative medicine that claims their curative effects. Moreover, several studies reported EOs as potential anti-cancer agents by inducing apoptosis in different cancer cell models. In this study, we have considered EOs as a potential resource of new kinase inhibitors with a polypharmacological profile. On the other hand, computational methods offer the possibility to predict the theoretical activity profile of ligands, discovering dangerous off-targets and/or synergistic effects due to the potential multi-target action. With this aim, we performed a Structure-Based Virtual Screening (SBVS) against X-ray models of several protein kinases selected from the Protein Data Bank (PDB) by using a chemoinformatics database of EOs. By evaluating theoretical binding affinity, 13 molecules were detected among EOs as new potential kinase inhibitors with a multi-target profile. The two compounds with higher percentages in the EOs were studied more in depth by means Induced Fit Docking (IFD) protocol, in order to better predict their binding modes taking into account also structural changes in the receptor. Finally, given its good binding affinity towards five different kinases, cinnamyl cinnamate was biologically tested on different cell lines with the aim to verify the antiproliferative activity. Thus, this work represents a starting point for the optimization of the most promising EOs structure as kinase inhibitors with multi-target features.

scholarly journals Essential Oils of Four Virginia Mountain Mint (Pycnanthemum virginianum) Varieties Grown in North Alabama

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1397
Author(s):  
William N. Setzer ◽  
Lam Duong ◽  
Trang Pham ◽  
Ambika Poudel ◽  
Cuong Nguyen ◽  
...  
Keyword(s):  
Essential Oil ◽  
Essential Oils ◽  
University Research ◽  
Oil Yield ◽  
Research Station ◽  
Continuous Extraction ◽  
Chromatographic Techniques ◽  
Relative Differences ◽  
Essential Oil Yield ◽  
Very High

Virginia mountain mint (Pycnanthemum virginianum) is a peppermint-flavored aromatic herb of the Lamiaceae and is mainly used for culinary, medicinal, aromatic, and ornamental purposes. North Alabama’s climate is conducive to growing mint for essential oils used in culinary, confectionery, and medicinal purposes. There is, however, a need for varieties of P. virginianum that can be adapted and easily grown for production in North Alabama. Towards this end, four field-grown varieties with three harvesting times (M1H1, M1H2, M1H3; M2H1, M2H2, M2H3; M3H1, M3H2, M3H3, M4H1, M4H2, M4H3) were evaluated for relative differences in essential oil yield and composition. Thirty-day-old greenhouse-grown plants of the four varieties were transplanted on raised beds in the field at the Alabama A & M University Research Station in North Alabama. The plots were arranged in a randomized complete block with three replications. The study’s objective was to compare the four varieties for essential oil yield and their composition at three harvest times, 135, 155, and 170 days after planting (DAP). Essential oils were obtained by hydrodistillation with continuous extraction with dichloromethane using a Likens–Nickerson apparatus and analyzed by gas chromatographic techniques. At the first harvest, the essential oil yield of the four varieties showed that M1H1 had a yield of 1.15%, higher than M2H1, M3H1, and M4H1 with 0.91, 0.76, and 1.03%, respectively. The isomenthone concentrations increased dramatically through the season in M1 (M1H1, M1H2, M1H3) by 19.93, 54.7, and 69.31%, and M3 (M3H1, M3H2, M3H3) by 1.81, 48.02, and 65.83%, respectively. However, it increased only slightly in M2 and M4. The thymol concentration decreased slightly but not significantly in all four varieties; the thymol in M2 and M4 was very high compared with M1 and M3. The study showed that mountain mint offers potential for production in North Alabama. Two varieties, M1 and M3, merit further studies to determine yield stability, essential oil yield, composition, and cultivation development practices.

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