Rose without prickle: genomic insights linked to moisture adaptation

Abstract

Prickles act against herbivores, pathogens or mechanical injury, while also prevent water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remains 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 between 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 the improvement of horticultural markets.

Rosoideae-specific duplication and functional diversification of FT-like genes in Rosaceae

“…Clade I contained FT1-like genes from all 12 Rosaceae species and jujube, whereas clade II contained FT2-like genes from only Rosoideae ( Rosa , Fragaria , and Rubus ). Consistent with the recent WGD in Maloideae, Malus , Eriobotrya , and Pyrus have two FT1-like genes ( Figure 1E ) [ 5 ]. Because no recent WGD event is present in the Rosoideae, these data indicate that a Rosoideae-specific duplication of FT2-like genes may have occurred prior to the separation of all Rosoideae plants from their common ancestor but after the separation of Rosoideae from Rosaceae ( Fig.…”

“…Here, we report the duplication and expression diversification of FT in rose, an emerging woody model for flowering regulation. We identified two copies of FT via BLAST in the genomes of R. wichuraiana ‘Basye’s Thornless’ (BT; RwFT1 , Rw3g00010 ; and RwFT2 , Rw0G011750 ) [ 5 ] and Rosa chinensis ‘Old Blush’ (OB; RcFT1 , RchiOBHm_Chr3g0447431 ; and RcFT2 , RchiOBHm_Chr4g0439111 ) [ 6 ] ( Fig. 1 ).…”

“…1C ). Rose FT2 was also not listed in the syntenic gene pairs generated via the WGD event in Rosaceae [ 5 ]. A subsequent BLAST scan with reduced criteria in the genomes of these two species detected no sign of FT2 - like sequences, implying that FT2-like genes may have arisen from random duplication in Rosoideae or may have been lost in the common ancestor that gave rise to the Maloideae and Prunoideae lineages.…”

Integrated multi‐omic data and analyses reveal the pathways underlying key ornamental traits in carnation flowers

“…The genome of the carnation referred to as ‘Scarlet Queen’ was highly heterozygous. Therefore, we examined sequence polymorphisms within our newly assembled genome using a previously published method (Zhong et al ., 2021 ). We found 1.79 million single nucleotide polymorphisms (SNPs), of which 1.15 million were transitions and 0.74 million were transversions (Tables S14 and S15 , Figures S9–S11).…”

Fine mapping a single nucleotide transversion in AUXIN RESPONSE FACTOR 18 controls prickle absence/presence on various organs in eggplant (Solanum melongena L.)

“…Based on this acknowledgment, GWAS (genome-wide association study), QLT (quantitative trait locus) analysis, homologous cloning, and comparative transcription methods were employed to explore some genes homologous to glandular trichome development-related genes in horticultural plants (such as rose, red raspberry, and eggplant). They were considered candidate genes for the regulation of prickle initiation (Khadgi and Weber, 2020b;Pandey et al, 2018;Zhong et al, 2021;Swarnkar et al, 2021;Khadgi and Weber, 2021;Zhou et al, 2020b;Feng et al, 2015;Saint-Oyant et al, 2018). GWAS analysis was carried out to identify the QTLs associated with stem prickles in red raspberry (Rubus idaeus L.) and rose (Rosa chinensis).…”