Prickles act against herbivores, pathogens or mechanical injury, while also preventing water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remain poorly explored. Here, we generated a high-quality reference genome assembly for ‘Basye's Thornless’ (BT), a prickle-free cultivar of Rosa wichuraiana, to identify genetic elements related to stem prickle development. The BT genome harbors a high level of sequence diversity in itself and with cultivar ‘Old Blush’ (R. chinensis), a founder genotype in rose domestication. Inheritance of stem prickle density was determined and two QTL were identified. Differentially expressed genes in QTL were involved in water-related functions, suggesting that prickle density may hitchhike with adaptations to moist environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, the expression variation of key candidate genes was associated with prickle density. Our study provides fundamental resources and insights for genome evolution in the Rosaceae. Ongoing efforts on identification of the molecular bases for key rose traits may lead to improvements for horticultural markets.

Genus Rosa (Rosaceae) has a base chromosome number of x = 7. Ploidy levels of wild species range from 2n= 2x= 14 to 2n= 8x=56. In this paper, one decaploid, the highest naturally occurring ploidy never reported before in the genus was detected in the karyological study of an endemic wild species, R. praelucens Byhouwer to Zhongdian Plateau, Yunnan, China. Its karyotype formula was 2n=10x=70=2st+6sm+62m and the karyotype was 2B. Chromosome No. 6 was subterminal. Chromosome No. 15, No. 22 and No. 23 were submedian. According to its karyomorphology, R. praelucens derived not from auto polyploidization directly but from inter-specific hybridization. Polyploidization and inter-species hybridization both might have played important roles in the origin of R. praelucens associated with effect of high altitude environment. Further research on this species is warranted to provide helpful evidences to understand the differentiation and evolution of the Genus Rosa, and even clues to trace the process of speciation in Sino-Himalayan region.