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Mutants lacking wild-type MLO (Mildew resistance Locus O) proteins show broad-spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants, we analysed systematically genome-wide data from Fragaria vesca, Prunus persica, Prunus mume, Malus domestica, Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods. Using three phylogenetic methods (the neighbour-joining, maximum likelihood, and Bayesian methods), we identified 117 MLO genes from 6 Rosaceae species. The results of all three phylogenetic analysis methods supported that these genes were divided into six clades. Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues. The findings indicated that motif 2 might be shared by the MLO gene family. The structural features of these genes showed large variations in sequence length among different species, although the lengths and the numbers of exons exhibited high degrees of similarity. Selective pressure analysis showed extremely significant differences in all 6 clades, with 2, 1, and 1 site(s) under significant positive selection detected in clades III, IV, and VI, respectively. These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes. Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes. Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process. However, clade I may have undergone extensive altered functional constraints as a specialised functional role. Moreover, the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew, which then gradually evolved into functions such as the regulation of flower development, the control of root morphology, and seed evolution due to the different evolutionary rates after gene duplication. These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

Abstract Background Rose is one of the most popular flowers in the wold. Its field growth and quality are negatively affected by aphids. However, the defence mechanisms used by rose plants against aphids are unclear. Therefore, to understand the defence mechanism of rose under aphid stress, transcriptome and metabolome techniques were used to investigate the regulation mechanism in R. longicuspis infected with M. rosivorum. Result In our study, after inoculation with M. rosivorum, M. rosivorum quickly colonized R. longicuspis. A total of 34,202 genes and 758 metabolites were detected in all samples. Under M. rosivorum stress, R. longicuspis responded by MAPK cascades, plant hormone signal transduction pathway activation, RlMYBs and RlERFs transcription factors expression and ROS production. Interestingly, the ‘brassinosteroid biosynthesis’ pathway was significantly enriched in A3 d-vs.-A5 d. Further analysis showed that M. rosivorum induced the biosynthesis of secondary metabolites such as terpenoids, tannins and phenolic acids, among others. Importantly, the ‘glutathione metabolic’ and ‘glucosinolate biosynthesis’ pathways were significantly enriched, which involved in the rose against aphids. Conclusion Our study provides candidate genes and metabolites for Rosa defence against aphids. This study provides a theoretical basis for further exploring the molecular regulation mechanism of rose aphid resistance and aphid resistance breeding in the future.

Abstract Background Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants defend themselves against this fungal pathogen. Here, we used transcriptomic, metabolomic and VIGS analyses to explore the mechanism of resistance to Botrytis c. Result In this study, a protein activity analysis revealed a significant increase in defence enzyme activities in infected plants. RNA-Seq of plants infected for 0 h, 36 h, 60 h and 72 h produced a total of 54 GB of clean reads. Among these reads, 3990, 5995 and 8683 differentially expressed genes (DEGs) were found in CK vs. T36, CK vs. T60 and CK vs. T72, respectively. Gene annotation and cluster analysis of the DEGs revealed a variety of defence responses to Botrytis c. infection, including resistance (R) proteins, MAPK cascade reactions, plant hormone signal transduction pathways, plant-pathogen interaction pathways, Ca2+ and disease resistance-related genes. qPCR verification showed the reliability of the transcriptome data. The PTRV2-RcTGA1-infected plant material showed improved susceptibility of rose to Botrytis c. A total of 635 metabolites were detected in all samples, which could be divided into 29 groups. Metabonomic data showed that a total of 59, 78 and 74 DEMs were obtained for T36, T60 and T72 (T36: Botrytis c. inoculated rose flowers at 36 h; T60: Botrytis c. inoculated rose flowers at 60 h; T72: Botrytis c. inoculated rose flowers at 72 h) compared to CK, respectively. A variety of secondary metabolites are related to biological disease resistance, including tannins, amino acids and derivatives, and alkaloids, among others; they were significantly increased and enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways. This study provides a theoretical basis for breeding new cultivars that are resistant to Botrytis c. Conclusion Fifty-four GB of clean reads were generated through RNA-Seq. R proteins, ROS signalling, Ca2+ signalling, MAPK signalling, and SA signalling were activated in the Old Blush response to Botrytis c. RcTGA1 positively regulates rose resistance to Botrytis c. A total of 635 metabolites were detected in all samples. DEMs were enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways.

Rosa chinensis var. spontanea and R. lucidissima complex are the morphologically very similar key ancestors of modern roses with high importance in rose research and breeding. Although widely distributed in subtropical central and southwestern China, these two taxa are highly endangered. We sampled a total of 221 specimens and 330 DNA samples from 25 populations across the two taxa's whole range. Leaf morphological traits were compared. Two chloroplast DNA intergenic spacers (trnG-trnS, petL-psbE) and ITS were used for population genetics and phylogenetic study to delimit the boundary between the two taxa, assess the genetic variation, uncover the possible evolutionary mechanism responsible for the differentiation within the complex, and make the conservation recommendations. The complex exhibited high levels of genetic variation (hTcpDNA = 0.768, hTITS = 0.726) and high population differentiation even over small geographic distance. We suggest R. chinensis var. spontanea and R. lucidissma be treated as independent taxa, and the northern populations around and within the Sichuan Basin being R. chinensis var. spontanea, having broader leaflets and paler full-blooming flowers, while those in the middle and southern Yunnan-Guizhou Plateau and the adjacent regions being R. lucidissma, having narrower leaflets and darker full-blooming flowers. Transitional areas between the southeastern Sichuan Basin and northeastern Guizhou are the contact or the hybridization zone of the two taxa. Ancestral haplotypes of the complex (R. lucidissma) evolved at about 1.21–0.86 Mya in southeastern Yunnan-Guizhou Plateau and its adjacent regions and survived there during the Quaternary Oscillation. Ancestral haplotypes of R. chinensis var. spontanea deviated from R. lucidissma at about 0.022–0.031 Mya at the transitional areas (Daloushan and Wulingshan Mountains) between the northeastern edge of Yunnan-Guizhou Plaeteau and the southeastern border of Sichuan Basin, where they survived the LGM. The evolution of the complex included spatial isolation and inter-species hybridization. The complex's endangered status might be the result of over-exploitation for its ornamental and medical value, or due to reforestation of some originally open habitats. We provide specific recommendations for the two taxa's in situ and ex situ conservation.

Rosa rugosa is not only cultivated as a landscaping plant, but also used in cosmetics, the medical and food industries. However, little information is currently available on the gene regulatory networks involved in its scent and color biosynthesis and metabolism. In this study, R. rugosa Thunb. f. rosea Rehd with red petals (RR) and its white petal variant (WR), were used to study the molecular mechanisms in flower color and scent. Sixty-five differential flavonoid metabolites and 15 volatiles were found to have significant differences between RR and WR. Correspondingly, the key regulators (MYB-bHLH-WD40) of anthocyanin synthesis pathway and their structural genes involved in flavonoid biosynthesis, benzenoid/phenylpropanoid biosynthesis, terpenoid biosynthesis pathways were also found to be differentially expressed by comparative transcriptome. Further, qPCR permitted the identification of some transcripts encoding proteins that were putatively associated with scent and color biosynthesis in roses. Particularly, the results showed that the ACT gene (encoding CoA geraniol/citronellol acetyltransferase, GeneID: 112190420), which expressed lower in WR, was involved in three pathways: flavonoid biosynthesis, phenylpropanoid biosynthesis and terpenoid biosynthesis, however, GT5 (anthocyanin glycosylation gene, GeneID:112186660), expressed higher in WR, was involved in both flavonoid and phenylpropanoid biosynthesis pathways. These results suggested that ACT and GT5 might play important roles in regulating the relationship of color pigmentation and volatile emission.

Rose (Rosa L.) is an economically important ornamental genus that has been cultivated for its scent for the perfume industry since antiquity. However, most modern roses have lost their fragrance during the later stages of the breeding process. Here, 59 species of Rosa, including 24 wild Rosa species, 20 Chinese old garden roses, and 15 modern roses, were examined by headspace solid-phase microextraction and gas chromatography–mass spectrometry. Fifty-three volatile organic compounds (VOCs), including terpenoids, benzenoids/phenylpropanoids, and fatty acid derivatives, were detected with qualitative and quantitative analyses. Thirteen common components, including geraniol, citronellol, 2-phenylethanol, 3,5-dimethoxytoluene, 1,3,5-trimethoxybenzene, germacrene D, and cis-3-hexenyl acetate, were found. Furthermore, different wild species or cultivars showed different characteristic compounds. 3,5-Dimethoxytoluene and 1,3,5-trimethoxybenzene were the main compounds in Rosa odorata and Rosa chinensis, which are the original parents of modern roses. 2-Phenylethanol, citronellol, and geraniol were the main aromatic compounds in Rosa damascene and Rosa centifolia. Methyl salicylate, eugenol, methyl eugenol, and benzyl acetate were lost during domestication and breeding of wild Rosa species to Chinese old garden roses and then to modern cultivars. Geranyl acetate, neryl acetate, and dihydro-β-ionol were gained during this time and showed higher amounts across the rose breeding process. Natural and breeding selection may have caused volatile compound gains and losses. These findings provide a platform for mining scent-related genes and for breeding improved ornamental plants with enhanced flower characteristics to develop new essential oil–producing plants.

Phyllody is a flower abnormality in which leaf-like structures replace flower organs in all whorls. Here we investigated the origin and the molecular mechanism of phyllody phenotype in Rosa chinensis cv. Viridiflora, an ancient naturally occurring Chinese mutant cultivar. Reciprocal grafting experiments and microscopy analyses, demonstrated that the phyllody phenotype in Viridiflora is not associated with phytoplasmas infection. Transcriptome comparisons by the mean of RNA-Seq identified 672 up-regulated and 666 down-regulated genes in Viridiflora compared to its closely related genotype R. chinensis cv. Old Blush. A fraction of these genes are putative homologues of genes known to be involved in flower initiation and development. We show that in flower whorl 2 of Viridiflora, a down-regulation of the floral organ identity genes RcPISTILLATA (RcPI), RcAPETALA3 (RcAP3) and RcSEPALLATA3 (RcSEP3), together with an up-regulation of the putative homologue of the gene SUPPRESSOR of OVEREXPRESSION of CONSTANS1 (RcSOC1) are likely at the origin of the loss of petal identity and leaf-like structures formation. In whorl 3 of Viridiflora, ectopic expression of RcAPETALA2 (RcAP2) along with the down regulation of RcPI, RcAP3 and RcSEP3 is associated with loss of stamens identity and leaf-like structures formation. In whorl 4, the ectopic expression of RcAP2 associated with a down-regulation of RcSEP3 and of the C-class gene RcAGAMOUS correlate with loss of pistil identity. The latter also suggested the antagonist effect between the A and C class genes in the rose. Together, these data suggest that modified expression of the ABCE flower organ identity genes is associated with the phyllody phenotype in the rose Viridiflora and that these genes are important for normal flower organs development.

The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity (Ht), Shannon index (I), and heterozygosity value within populations (Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient (Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River.

Roses are one of the economically most important groups of ornamental plants. The internal transcribed spacers (ITS) of the nuclear ribosomal DNA and the chloroplast gene matK were used to investigate the genetic diversity and genetic relationships among Rosa germplasm including 39 wild species, 21 old garden roses, and 29 modern cultivars. Three dendrograms based on ITS and matK clustering data indicated that 1) 39 wild genotypes were consistent with their classification into botanical sections with only a few exceptions; 2) most of the wild genotypes were separated from rose cultivars. However, three sections, Synstylae, Chinenses, and Rosa, that contributed to the modern roses generally gathered together with almost all old garden and modern roses on the molecular level; and 3) the relationships between cultivated roses as inferred by ITS and matK sequences do not correlate with horticultural groups. Results demonstrated that both sequence techniques can contribute to clarifying the genetic relationships of rose accessions and germplasm conservation to enhance the ornamental and economic value of rose. [ABSTRACT FROM AUTHOR]