Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.

Centre for Functional Ecology Department of Life Sciences University of Coimbra Coimbra Portugal

Czech Academy of Sciences Institute of Botany Průhonice Czech Republic

Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Botany Faculty of Science University of South Bohemia České Budějovice Czech Republic

Henan University School of Life Sciences State Key Laboratory of Crop Stress Adaptation and Improvement State Key Laboratory of Cotton Biology Key Laboratory of Plant Stress Biology Kaifeng China

Kew Science Directorate Royal Botanic Gardens Kew Richmond Surrey UK

Laboratory of Molecular Biology and Cytometry Department of Agricultural Biotechnology UTP University of Science and Technology Bydgoszcz Poland

School of Plant Sciences BIO5 Institute Arizona Cancer Center Department of Biomedical Engineering University of Arizona Tucson Arizona USA

Swift Current Research and Development Centre Agriculture and Agri Food Canada Swift Current Saskatchewan Canada

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New estimates and synthesis of chromosome numbers, ploidy levels and genome size variation in Allium sect. Codonoprasum: advancing our understanding of the unresolved diversification and evolution of this section

Diploid and tetraploid cytotypes of the flagship Cape species Dicerothamnus rhinocerotis (Asteraceae): variation in distribution, ecological niche, morphology and genetics

Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes

The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae)

Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants

Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid Genus Neotinea