Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

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

Comparative transcriptomic and metabonomic analysis revealed the relationships between biosynthesis of volatiles and flavonoid metabolites in Rosa rugosa

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

Inheritance of Perpetual Blooming in Rosa chinensis ‘Old Blush’

Perpetual blooming is one of the most important biological and economical traits in modern rose, while the genetic basis underlining the control of this trait is poorly investigated. With an aim in dissecting the genetic determinism of perpetual blooming, we developed six rose populations (OB, W, F1, F2, BC1OB and BC1W) derived from a WOB population [interspecific diploid hybridization between Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basye’s Thornless’ (W)]. Perpetual blooming is absent both in a F1 population with 296 individuals and a BC1W population (W as the backcross parent) with 150 individuals. However, the perpetual blooming trait showed a typical 3:1 segregation in a backcross population BC1OB with OB as the backcross parent. In this population with 300 individuals, 83 plants had the perpetual blooming phenotype while the other 217 featured non-perpetual blooming, indicating that the perpetual blooming trait is very likely controlled by two recessive genes in R. chinensis (rpb1 and rpb2). These genetic data suggest that the inheritance of rose perpetual blooming may be controlled by a complex mechanism

The rosa chinensis cv. viridiflora phyllody phenotype Is associated with misexpression of flower organ identity genes

International audiencePhyllody 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 homologs 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 homolog 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

Transcriptome and gene expression analysis during flower blooming in Rosa chinensis 'Pallida'

International audienceRosa chinensis ‘Pallida’ (Rosa L.) is one of the most important ancient rose cultivars originating from China. It contributed the ‘tea scent’ trait to modern roses. However, little information is available on the gene regulatory networks involved in scent biosynthesis and metabolism in Rosa. In this study, the transcriptome of R. chinensis ‘Pallida’ petals at different developmental stages, from flower buds to senescent flowers, was investigated using Illumina sequencing technology. De novo assembly generated 89,614 clusters with an average length of 428 bp. Based on sequence similarity search with known proteins, 62.9% of total clusters were annotated. Out of these annotated transcripts, 25,705 and 37,159 sequences were assigned to gene ontology and clusters of orthologous groups, respectively. The dataset provides information on transcripts putatively associated with known scent metabolic pathways. Digital gene expression (DGE) was obtained using RNA samples from flower bud, open flower and senescent flower stages. Comparative DGE and quantitative real time PCR permitted the identification of five transcripts encoding proteins putatively associated with scent biosynthesis in roses. The study provides a foundation for scent-related gene discovery in roses

Comparative transcriptomics identifies patterns of selection in roses

Abstract Background Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. Results Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basye’s Thornless’ (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. Conclusions We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Abstract Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis ‘Old Blush’ (OB) and R. wichuraiana ‘Basyes’ Thornless’ (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose

Smoking and smoking cessation in relation to risk of diabetes in Chinese men and women: a 9-year prospective study of 0·5 million people

Summary: Background: In developed countries, smoking is associated with increased risk of diabetes. Little is known about the association in China, where cigarette consumption has increased (first in urban, then in rural areas) relatively recently. Moreover, uncertainty remains about the effect of smoking cessation on diabetes in China and elsewhere. We aimed to assess the associations of smoking and smoking cessation with risk of incident diabetes among Chinese adults. Methods: The prospective China Kadoorie Biobank enrolled 512 891 adults (59% women) aged 30–79 years during 2004–08 from ten diverse areas (five urban and five rural) across China. Participants were interviewed at study assessment clinics, underwent physical measurements, and had a non-fasting blood sample taken. Participants were separated into four categories according to smoking history: never-smokers, ever-regular smokers, ex-smokers, and occasional smokers. Incident diabetes cases were identified through linkage with diabetes surveillance systems, the national health insurance system, and death registries. All analyses were done separately in men and women and Cox regression was used to yield adjusted hazards ratios (HRs) for diabetes associated with smoking. Findings: 68% (n=134 975) of men ever smoked regularly compared with 3% (n=7811) of women. During 9 years' follow-up, 13 652 new-onset diabetes cases were recorded among 482 589 participants without previous diabetes. Among urban men, smokers had an adjusted HR of 1·18 (95% CI 1·12–1·25) for diabetes. HRs increased with younger age at first smoking regularly (1·12, 1·20, and 1·27 at ≥25 years, 20–24 years, and <20 years, respectively; p for trend=0·00073) and with greater amount smoked (1·11, 1·15, 1·42, and 1·63 for <20, 20–29, 30–39 and ≥40 cigarettes per day; p for trend<0·0001). Among rural men, similar, albeit more modest, associations were seen. Overall, HRs were more extreme at higher levels of adiposity. Among men who stopped by choice, there was no excess risk within 5 years of cessation, contrasting with those who stopped because of illness (0·92 [0·75–1·12] vs 1·42 [1·23–1·63]). Among the few women who ever smoked regularly, the excess risk of diabetes was significant (1·33 [1·20–1·47]). Interpretation: Among Chinese adults, smoking was associated with increased risk of diabetes, with no significant excess risk following voluntary smoking cessation. Funding: Wellcome Trust, Medical Research Council, British Heart Foundation, Cancer Research UK, Kadoorie Charitable Foundation, Ministry of Science and Technology, National Natural Science Foundation of China, and China Scholarship Council