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Abstract Detail



Functional Genetics/Genomics

Smith, Tyler [1], Kron, Paul [2], Martin, Sara [3].

flowPloidy: An R Package for determining Genome Size and Ploidy from Flow Cytometry Histograms.

Flow cytometry (FCM) is a key technology for assessing genome size and ploidy in plants. Where cytology was once limited to time-consuming and laborious chromosome squashes, we can now process dozens of FCM samples in a single day. Determining DNA content relative to a co-chopped standard is an intuitive process. In practice, however, extracting accurate DNA estimates from FCM data in a rigorous and repeatable way is a difficult task. Several widely used programs rely on users to manually select peaks, a process that is inherently subjective. Alternative model-fitting approaches are not widely used in botany, in part due to their limited availability in inexpensive software packages. To address this issue, we have developed flowPloidy, an R package that provides a robust, non-linear regression-based procedure for determining DNA content from FCM histograms. It offers several features that distinguish it from available alternatives: - non-linear regression analysis for FCM histograms, with automated extraction of DNA ratios, CV values and other parameters - a graphical interface for interactively reviewing analyses - simple gating for dealing with high-debris samples, while retaining the power of model-fitting to extract parameter estimates - part of the R programming environment, allowing results to be seamlessly integrated into downstream analyses - open-source, providing users with complete access to study and extend the code - cross-platform and freely available


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1 - Agriculture And Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
2 - Dept Of Botany, University Of Guelph, Guelph, ON, N1G 2W1, Canada
3 - Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada

Keywords:
flow cytometry
software.

Presentation Type: Poster
Session: P, Functional Genetics and Genomics
Location: Grand Ballroom - Exhibit Hall/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 5:30 PM This poster will be presented at 5:30 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PCG005
Abstract ID:727
Candidate for Awards:None


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