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

Area of Science:

• Plant genetics and genomics
• Computational biology and bioinformatics

Background:

• Roses (Rosa L.) exhibit diverse ploidy levels, complicating genetic studies.
• Accurate ploidy and aneuploidy assessment is crucial for understanding rose genetics and breeding.

Purpose of the Study:

• To develop Qploidy, an R package for high-throughput ploidy and aneuploidy analysis in roses.
• To analyze ploidy and aneuploidy in a large rose germplasm collection and mapping populations.

Main Methods:

• Development of the Qploidy R package utilizing allele dosage estimation and copy number variation methods.
• Standardization of allele intensity and B allele frequency for ploidy levels above 2x.
• Analysis of 1944 rose samples, including germplasm and biparental populations, using SNP array data.

Main Results:

• The germplasm collection predominantly consisted of tetraploids (56%), diploids (20%), and triploids (11%).
• Aneuploidy was more frequent in biparental populations (16%) than in the germplasm collection (2%).
• Pentasomy was more common than trisomy in tetraploid populations, and aneuploidies were mainly maternally inherited.

Conclusions:

• Qploidy provides a robust tool for ploidy and aneuploidy analysis in roses and other polyploids.
• Aneuploidy is more prevalent in mapping populations, likely due to reduced fitness, and its maternal inheritance suggests gametophyte sensitivity.
• Qploidy can aid in data curation for linkage and QTL analyses by identifying and facilitating the removal of aneuploid-affected data.