Abstract Detail

Classical Genetics

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

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

In direct comparisons, flowPloidy recovers parameter estimates that are very close to or indistinguishable from those from commercial model-fitting programs. We now use flowPloidy for all of our FCM analyses, allowing us to forego costly software licenses, without sacrificing analytical rigour.

Related Links:
flowPloidy GitHub repository

1 - Agriculture and Agri-Food Canada, Science and Technology, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
2 - University Of Guelph, Department Of Botany, GUELPH, ON, N1G 2W1, Canada

Keywords:
flow cytometry
Polyploidy
software
genome size.

Presentation Type: Oral Paper
Session: 4, Classical Genetics & Molecular Ecology
Location: Fort Worth Ballroom 8/Omni Hotel
Date: Monday, June 26th, 2017
Time: 8:30 AM
Number: 4002
Abstract ID:66
Candidate for Awards:None