Ploidy is defined as the number of complete chromosome sets in a cell’s nucleus. In animal cells, chromosomes are typically found in pairs and cells are considered diploid. In contrast, plant cells can tolerate higher levels of genome duplication and can exist in various states of polyploidy. Understanding and characterizing ploidy in diverse organisms, from bacteria to mammals, has been greatly facilitated by flow cytometry-based ploidy measurements. Consider these three P’s of ploidy as you decide if ploidy analysis could be a valuable addition to a current or upcoming study.

1. Polyploid Plants: Agriculture and horticulture research is heavily dependent on ploidy measurements, as polyploid plants have been shown to have greater pest and disease resistance and improved stress tolerance. Ploidy modification also improves fruit and flower characteristics, such as generating seedless fruit varieties. Flow cytometry analysis of ploidy involves staining nuclei from cells with a fluorescent dye that binds to DNA and analyzing samples such that a histogram plot distinguishes different ploidy patterns based on DNA content. These ploidy measurements can be used to select for plant progeny with different desired traits.
2. Purity of samples: Flow cytometry-based ploidy is based on staining DNA. Different DNA dyes can be used, such as DAPI, propidium iodide, and Hoechst 33258, and each dye reacts differently with DNA, which affects how DNA content is measured and what type cytometer can be used. Staining is dependent on using nuclei extracted from cells, but different tissues, particularly those rich in tannins or starch granules, can be difficult to process and can cause nonspecific staining. It is critical to optimize nuclei preparation and staining to attain accurate ploidy measurements.
3. Problematic Ploidy: Ploidy measurements are valuable for characterizing cellular abnormalities. Aneuploidy arises when chromosomes are abnormally distributed between daughter cells, and many birth defects and tumor mutations have been linked to aneuploidy. Ploidy analysis can be used as a diagnostic in these settings and flow cytometry-based ploidy analysis is advancing these studies as a rapid method that requires relatively small amounts of sample.

Flow cytometry-based ploidy analysis is being used in many areas of basic and applied research. Consider consulting with a flow cytometry expert to integrate this analysis into your next study.