Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy.

ABSTRACT: Roses (Rosa L.) are among the most economically important ornamentals worldwide, with ploidy ranging from diploid (2x) to hendecaploid (11x), though most cultivars are diploid (2x), triploid (3x), or tetraploid (4x). To enable large-scale analyses of ploidy and aneuploidy in roses using high-density single nucleotide polymorphism (SNP) array data, we developed Qploidy, an R package. Qploidy leverages tools for estimating allele dosage, adapts methods from human genetics for copy number estimation, and optimizes the standardization of allele intensity (R) and B allele frequency (BAF) for ploidy levels greater than 2x. With Qploidy, we analyzed a dataset of 1944 samples consisting of 588 samples from a germplasm collection and 1356 samples from 14 biparental mapping populations. The majority

SUBMITTER: Taniguti CH 

PROVIDER: S-EPMC12185385 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature