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

Authors: TANIGUITI, CRISTIANE - Breeding Insight; Lau, Jeekin; HOCHHAUS, TESSA - Texas A&M University; LOPEZ ARIAS, DIANA - University Of Minnesota; HOKANSON, STAN - University Of Minnesota; ZLESAK, DAVID - University Of Wisconsin-River Falls, Department Of Plant And Earth Science; BYRNE, DAVID - Texas A&M University; KLEIN, PATRICIA - Texas A&M University; RIERA-LIZARAZU, OSCAR - Texas A&M University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2025
Publication Date: 6/23/2025
Citation: Taniguiti, C.H., Lau, J., Hochhaus, T., Lopez Arias, D.C., Hokanson, S., Zlesak, D., Byrne, D., 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. 18(2).Article e70044. https://doi.org/10.1002/tpg2.70044.
DOI: https://doi.org/10.1002/tpg2.70044

Interpretive Summary: Roses are important ornamental plants with varying chromosome sets(ploidy levels). Most rose cultivars are either diploid, triploid, or tetraploid (2, 3, and 4 sets of chromosomes respectively). To study these variations, we developed a software package, Qploidy, which helps us estimate the number of sets of chromosomes a rose plant has. Qploidy was used to analyze 1,809 rose samples, revealing that most samples in a germplasm collection were tetraploid, with fewer diploids and triploids. Aneuploids, individuals with abnormal chromosome numbers (different than the expected diploid, triploid, and tetraploid levels), were more common in mapping populations than in commercially available cultivars. Qploidy will help scientists be able to more efficiently determine ploidy, which is important in a breeding program. In tetraploid populations, pentasomy (having an extra chromosome) was more frequent than trisomy (missing a chromosome), and aneuploidy was mainly transmitted through the female parent. Also, Qploidy can be used to guide the removal of aneuploid data, improving downstream genetic analyses. This tool can also be applied to other polyploid species.

Technical Abstract: Roses (Rosa L.) are among the most economically important ornamentals worldwide, with ploidy ranging from diploid (2x) to decaploid (10x), 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 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 1,809 samples consisting of 483 samples from a germplasm collection and 1,326 samples from 14 bi-parental mapping populations. The majority of genotypes in the germplasm collection were tetraploid (56%), followed by diploids (20%) and triploids (11%). The percentage of aneuploids was lower in the germplasm collection (2%) compared to bi-parental mapping populations (16%). Reduced fitness likely explains the higher frequency of aneuploids in mapping populations compared to the germplasm collection, where stronger selective pressures normally act. In tetraploid bi-parental populations, pentasomy (65%) was significantly more common than trisomy (19%). Also, aneuploid states were predominantly transmitted through the female parent (87%), suggesting greater male gametophyte sensitivity to chromosome number variation, particularly the loss of a chromosome. Since aneuploidy disturbs linkage and QTL analyses, Qploidy may also be used to guide the removal of aneuploid-affected data prior to downstream analysis. Besides roses, Qploidy can be used to study ploidy and aneuploidy in other polyploid species.