Compiling molecular evidence from a tetraploid rose genome into a near-saturated map for the identification of pigment-related genes

With their high economic value and cultural significance, modern roses are one of the most important ornamental plants. Because of their complicated genetic background and tetraploid nature, the creation of high-density genetic maps of roses has been a challenge that has slowed the pace of molecular breeding for modern roses. The current construction of tetraploid genetic maps based on existing diploid rose genomes could lead to inaccurate marker information and genotyping results. Therefore, we generated the first high-quality tetraploid genome of Rosa chinensis ‘Yunzheng Xiawei.’ Utilizing Illumina, PacBio, and Hi-C sequencing technologies, we assembled a genome of 858.59 Mb with 14 pseudo-chromosomes. Mode of inheritance analysis using PolyOrigin indicated that modern roses show both quadrivalent and bivalent pairing. Based on this reference genome, high-density genetic maps were constructed using MSTmap with nearly saturated markers. Quantitative trait locus (QTL) analysis was conducted using WinQTLCart and R/qtl for flavonoids and carotenoids, and 11 QTL clusters were identified. By combining the genome annotation, phylogenetic analyses, and gene expression analyses, we were able to identify several key genes related to flavonoid and carotenoid biosynthesis. This study provides the basis for further genetic analyses of highly heterozygous tetraploid roses and could facilitate the progress of marker-assisted selection in modern roses.