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


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
Number: PCG005
Abstract ID:727
Candidate for Awards:None


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