[!IMPORTANT] We moved and improved! Check out Qploidy2 at: https://github.com/Breeding-Insight/Qploidy2

Qploidy

Qploidy is an R package designed for ploidy and aneuploidy estimation using genotyping platform data.

When does the Qploidy methodology work?

The Qploidy approach is effective under the following conditions:

• Your marker data originates from Axiom or Illumina genotyping arrays.
• Your marker data is derived from targeted sequencing platforms (e.g., DArTag, GTseq, AgriSeq).
• All DNA samples were prepared following the same library preparation protocol.
• You know the ploidy of at least a subset of 60 samples or you know the most common ploidy in the dataset.
• Your dataset includes heterozygous samples.

When does the Qploidy methodology NOT work?

The methodology will not be effective under the following circumstances:

• Your marker data comes from RADseq or GBS (Genotyping-by-Sequencing) platforms.
• You intend to combine datasets from different sequencing batches.
  • For example: If you extracted DNA and sequenced two plates (192 samples) as one batch, and later sequenced an additional three plates (288 samples) as a second batch, you would need to analyze the two batches separately in Qploidy. Combining all 480 samples into a single analysis will lead to incorrect results.
• You do not have a subset of samples with known ploidy or lack a predominant ploidy in your dataset.
• Your samples consist of inbred lines (homozygous individuals).

Installation

# Install the latest stable version from CRAN
install.packages("Qploidy")

# Install the development version from GitHub
#install.packages("devtools")
# devtools::install_github("cristianetaniguti/Qploidy")
install.packages("Qploidy", repos = c('https://cristianetaniguti.r-universe.dev', 'https://cloud.r-project.org'))

Documentation

• Qploidy tutorial for directions on how to run

Bug Reports

If you find a bug or want an enhancement, please submit an issue here.

How to cite

Taniguti, C. H., Lau, J., Hochhaus, T., Arias, D. C. L., Hokanson, S. C., Zlesak, D. C., Byrne, D. H., Klein, P. E., & Riera-Lizarazu, O. (2025). Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy. The Plant Genome, e70044. https://doi.org/10.1002/tpg2.70044

Acknowledgments

Version 1.0.0

This work is funded in part by the Robert E. Basye Endowment in Rose Genetics, Dept. of Horticultural Sciences, Texas A&M University, and USDA’s National Institute of Food and Agriculture (NIFA), Specialty Crop Research Initiative (SCRI) projects: ‘‘Tools for Genomics-Assisted Breeding in Polyploids: Development of a Community Resource’’ (Award No. 2020-51181-32156); and ‘‘Developing Sustainable Rose Landscapes via Rose Rosette Disease Education, Socioeconomic Assessments, and Breeding RRD-Resistant Roses with Stable Black Spot Resistance’’ (Award No. 2022-51181-38330).

Versions > 1.0.0

Supported by Breeding Insight.