High-density genetic map construction and QTL analysis of flower color traits based on a tetraploid rose genome

Bixuan Cheng is in the first year of her Ph.D. studies at the School of Landscape Architecture, Beijing Forestry University, China, under the supervision of Prof. Chao Yu. Based on genomics and linkage analysis, she is seeking to discover the molecular mechanism of important traits for tetraploid roses. China has been cultivating Rosa species for many centuries. More than a hundred Chinese rose cultivars are recorded in "The Rose Anthology" compiled by Chuanchuo Liu in the Qing Dynasty (1636-1912). Some of them have excellent ornamental traits and strong adaptability. R. ‘Yunzheng Xiawei’ is a tetraploid, with pink to light pink petals and a moderate fragrance. In previous breeding work, this ancient germplasm was used as maternal material to generate an F1 tetraploid rose YS population. However, due to the complex genetic background and inefficiency in polyploid mapping, the construction of tetraploid genetic maps based on existing diploid rose genomes was leading to inaccurate marker information and genotyping results. Combining PacBio, Illumina and Hi-C scaffolding technologies, Bixuan and her colleagues presented the first highly heterozygous tetraploid rose genome for R. ‘Yunzheng Xiawei.’ Based on this reference genome and tools for polyploids, they performed inheritance analyses, which showed that tetraploid roses had both tetrasomic and preferential pairing events. By aligning the previous whole genome re-sequencing data to the reference R. ‘Yunzheng Xiawei’ genome, an average of 13,113,819 SNPs were developed for each offspring. Then they used MSTmap to cluster and assign markers into linkage groups and finally obtained three near-saturated genetic linkage maps. Based on 67 pigment content data, 11 QTL clusters were identified for each pigment, including three QTL clusters for anthocyanins, four clusters for flavonols and four clusters for carotenoids. Combing genome annotation and RT-qPCR results, four differentially expressed genes were identified within the confidence intervals, including CHYB, CCD4, PDS and NXS. The 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.

Bixuan Cheng won the ISHS Young Minds Award for the best oral presentation at the XVII International Eucarpia Symposium Section Ornamentals: From Nature to Culture – Breeding Ornamentals for Sustainability in Italy in July 2023.

Bixuan Cheng, School of Landscape Architecture, Beijing Forestry University, 100083 Beijing, e-mail: chengbixuan@126.com

The article is available in Chronica Horticulturae