Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted in the need to further improve the diversity and quality of traits. However, frequent hybridization leads to highly heterozygous nature, including the allelic variants. Therefore, the absence of comprehensive genomic information leads to them making it challenging to molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis ‘Chilong Hanzhu’ (2n = 14) which is high heterozygous diploid old Chinese rose are generated. An amount of genetic variation (1,605,616 SNPs, 209,575 indels) is identified. 13,971 allelic genes show differential expression patterns between two haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms of traits. RcMYB114b can influence cyanidin-3-glucoside accumulation and the allelic variation in its promoter leads to differences in promoter activity, which as a factor control petal color. Moreover, gene family expansion may contribute to the abundance of terpenes in floral scents. Additionally, RcANT1, RcDA1, RcAG1 and RcSVP1 genes are involved in regulation of petal number and size under heat stress treatment. This study provides a foundation for molecular breeding to improve important characteristics of roses.

The double flower developmental process is regulated via a complex transcriptional regulatory network. To understand this highly dynamic and complex developmental process of Dianthus spp., we performed a comparative analysis of floral morphology and transcriptome dynamics in simple flowers and double flowers. We found that the primordium of double flowers of ‘X’ was larger in size compared to that of simple flowers of ‘L’ in Dianthus chinensis. RNA-seq and Weighted Gene Co-expression Network Analysis (WGCNA) during flower development, identified stage-specific gene network modules. Expression analysis by RNA-seq indicated that a group of genes related to floral meristem identity, primordia position and polarity were highly expressed in double flowers genotypes compared to simple flowers genotypes, suggesting their roles in double-petal formation. A total of 21 DEGs related to petal number were identified between simple and double flowers. The experiments of in situ hybridization revealed that DcaAP2L, DcaLFY and DcaUFO genes were expressed in the intra-sepal boundary and petal boundary. We proposed a potential transcriptional regulatory network for simple and double flower development. This study provides novel insights into the molecular mechanism underlying double flower formation in Dianthus spp.