Arabidopsis thaliana a Medicinal Plant as a Genetic Model System in Crop Science And Scientific Fields

2020 ◽  
Vol 13 (3) ◽  
pp. 1527-1535
Author(s):  
Rania M. Makki
Keyword(s):  
Arabidopsis Thaliana ◽  
Medicinal Plant ◽  
Genetic Model ◽  
Model System ◽  
Crop Science ◽  
Scientific Fields

scholarly journals The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits

2021 ◽  
Author(s):  
Anthony D Long ◽  
Alan Barbour ◽  
Phillip N Long ◽  
Vanessa J Cook ◽  
Arundhati Majumder
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Peromyscus Leucopus ◽  
False Positive Rate ◽  
Model System ◽  
Sequencing Data ◽  
Power Estimate ◽  
Genome Wide ◽  
Low Pass ◽  
Closed Colony

Although Peromyscus leucopus (deermouse) is not considered a genetic model system, its genus is well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and its ability to serve as a disease vector. Here we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a non-traditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals between 1982 and 1985 and subsequently maintained for 35+ years (~40-60 generations). From 405 low-pass (~1X) short-read sequenced deermice we accurately imputed genotypes at 17,751,882 SNPs. Conditional on observed genotypes for a subset of 297 individuals, simulations were conducted in which a QTL contributes 5% to a complex trait under three different genetic models. The power of either a haplotype- or marker-based statistical test was estimated to be 15-25% to detect the hidden QTL. Although modest, this power estimate is consistent with that of DO/HS mice and rat experiments for an experiment with ~300 individuals. This limitation in QTL detection is mostly associated with the stringent significance threshold required to hold the genome-wide false positive rate low, as in all cases we observe considerable linkage signal at the location of simulated QTL, suggesting a larger panel would exhibit greater power. For the subset of cases where a QTL was detected, localization ability appeared very desirable at ~1-2Mb. We finally carried out a GWAS on a demonstration trait, bleeding time. No tests exceeded the threshold for genome-wide significance, but one of four suggestive regions co-localizes with Von Willebrand factor. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice in much the same manner as founders-known DO/HS mice and rats, with genotypes obtained from low pass sequencing data. Our results further suggest that the DO/HS approach can be powerfully extended to any system in which a founders-unknown closed colony has been maintained for several dozen generations.

scholarly journals Arabidopsis sepals: A model system for the emergent process of morphogenesis

2021 ◽  
Vol 2 ◽  
Author(s):  
Adrienne H. K. Roeder
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Cell Division ◽  
Slow Growth ◽  
Expression Patterns ◽  
Giant Cells ◽  
Model System ◽  
Gene Expression Patterns ◽  
Emergent Properties ◽  
Correct Size

Abstract During development, Arabidopsis thaliana sepal primordium cells grow, divide and interact with their neighbours, giving rise to a sepal with the correct size, shape and form. Arabidopsis sepals have proven to be a good system for elucidating the emergent processes driving morphogenesis due to their simplicity, their accessibility for imaging and manipulation, and their reproducible development. Sepals undergo a basipetal gradient of growth, with cessation of cell division, slow growth and maturation starting at the tip of the sepal and progressing to the base. In this review, I discuss five recent examples of processes during sepal morphogenesis that yield emergent properties: robust size, tapered tip shape, laminar shape, scattered giant cells and complex gene expression patterns. In each case, experiments examining the dynamics of sepal development led to the hypotheses of local rules. In each example, a computational model was used to demonstrate that these local rules are sufficient to give rise to the emergent properties of morphogenesis.

Arabidopsis Thaliana: A Model System for Plant Molecular Biology

1987 ◽  
Vol 5 (11) ◽  
pp. 1177-1181 ◽  
Author(s):  
Patty P. Pang ◽  
Elliot M. Meyerowitz
Keyword(s):  
Arabidopsis Thaliana ◽  
Molecular Biology ◽  
Plant Molecular Biology ◽  
Model System

scholarly journals High-Resolution Ecosystem Model of the Puck Bay (Southern Baltic Sea)—Hydrodynamic Component Evaluation

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2057 ◽  
Author(s):  
Dawid Dybowski ◽  
Jaromir Jakacki ◽  
Maciej Janecki ◽  
Artur Nowicki ◽  
Daniel Rak ◽  
...  
Keyword(s):  
Cross Sections ◽  
Ecosystem Model ◽  
Model System ◽  
Computational Power ◽  
Model Simulations ◽  
Hydrodynamic Parameters ◽  
Raster Maps ◽  
Dedicated Service ◽  
Scientific Fields ◽  
Puck Bay

In recent years, thanks to the enormous computational power of modern supercomputers, modeling has become one of the most highly evolving scientific fields. It is now possible to describe relatively large physical bodies and to study the changes occurring in these bodies with resolution never attainable before. The paper describes the initial implementation of the EcoPuckBay model system and presents the results of the model simulations compared to observations from monitoring stations and other model reanalyses. High correlation between model results and observations has been confirmed both in terms of spatial and temporal approach. Data acquired via simulations of the EcoPuckBay model was deployed in the project archive database. The dedicated service was created, allowing the user to visualize all produced hydrodynamic parameters as raster maps, time series, and/or cross-sections. This functionality is available online via the official WaterPUCK project website in the services web section. In the next stage of the project, this service will be upgraded to an operational state and forecasts will be added.

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