Unraveling the genetic basis of Rhizobium rhizogenes-mediated transformation and hairy root formation in rose using a genome-wide association study.

Multiple QTLs reveal the polygenic nature of R. rhizogenes-mediated transformation and hairy root formation in roses, with five key regions explaining 12.0-26.

Automated image registration of RGB, hyperspectral and chlorophyll fluorescence imaging data.

Background: The early and specific detection of abiotic and biotic stresses, particularly their combinations, is a major challenge for maintaining and increasing plant productivity in sustainable agriculture under changing environmental conditions. Optical imaging techniques enable cost-efficient and non-destructive quantification of plant stress states. Monomodal detection of certain stressors is usually based on non-specific/indirect features and therefore is commonly limited in their cross-specificity to other stressors.

Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses.

Background: Due to genetic depletion in nature, gene banks play a critical role in the long-term conservation of plant genetic resources and the provision of a wide range of plant genetic diversity for research and breeding programs. Genetic information on accessions facilitates gene bank management and can help to conserve limited resources and to identify taxonomic misclassifications or mislabelling. Here, we developed SNP markers for genotyping 4,187 mostly polyploid rose accessions from large rose collections, including the German Genebank for Roses.

Genome-wide association study (GWAS) analyses of early anatomical changes in rose adventitious root formation.

Adventitious root (AR) formation is a genetically complex trait with high genotypic variability. Therefore, only a limited range of cultivars are currently propagated by cuttings in rose. In this study, we analysed the anatomy of in vitro shoots, the early formation of root primordia (RP) and the formation of ARs in a diverse set of 106 rose genotypes.

Genome-Wide Analysis of the WRKY Transcription Factor Family in Roses and Their Putative Role in Defence Signalling in the Rose-Blackspot Interaction.

WRKY transcription factors are important players in plant regulatory networks, where they control and integrate various physiological processes and responses to biotic and abiotic stresses. Here, we analysed six rose genomes of 5 different species (, , , , and ) and extracted a set of 68 putative genes, extending a previously published set of 58 sequences based on the genome. Analysis of the promoter regions revealed numerous motifs related to induction by abiotic and, in some cases, biotic stressors.

Robust markers associated with floral traits in roses are suitable for marker-assisted selection across gene pools.

Unlabelled: We investigated the potential of markers associated with floral traits for parental selection in a cut rose breeding program. We analysed six Kompetitive Allele Specific PCR (KASP) markers for three important floral traits, petal length, petal number and scent, derived from experiments in a garden rose population. The six markers were applied to genotype a collection of 384 parental genotypes used for commercial cut rose breeding.

Time course of changes in the transcriptome during russet induction in apple fruit.

Background: Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear.

Potato Wart Isolates from Europe and North America Form Distinct Clusters of Genetic Variation.

We have extended previously published sets of simple sequence repeat markers for selected to be polymorphic for the German-standard isolates of pathotypes P1, P2, P6, P8, and P18. These markers also complement the extensive published information on DNA polymorphisms for the mitogenomes of . This extended set of 35 markers representing 73 alleles differentiated 51 isolates from Europe and North America into three large, well-separated clusters and subclusters using dendrogram analysis, principal coordinates analysis (PCoA), and population substructure analysis using STRUCTURE 2.

GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection.

Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses.

Apple fruit periderms (russeting) induced by wounding or by moisture have the same histologies, chemistries and gene expressions.

Russeting is a cosmetic defect of some fruit skins. Russeting (botanically: induction of periderm formation) can result from various environmental factors including wounding and surface moisture. The objective was to compare periderms resulting from wounding with those from exposure to moisture in developing apple fruit.

P Starvation in Roses Leads to Strongly Genotype-Dependent Induction of P-Transporter Genes during Black Spot Leaf Disease.

Phosphorous starvation in plants has been reported to have contrasting effects on the interaction with pathogens in different plant pathogen systems and plant species. Both increases and decreases in susceptibility have been observed in numerous reports. Here, we analysed black spot infection and the leaf expression of two plant phosphate transporters and one defence marker gene in roses after phosphorous starvation.

First genome edited poinsettias: targeted mutagenesis of flavonoid 3'-hydroxylase using CRISPR/Cas9 results in a colour shift.

Unlabelled: The CRISPR/Cas9 system is a remarkably promising tool for targeted gene mutagenesis, and becoming ever more popular for modification of ornamental plants. In this study we performed the knockout of ' (') with application of CRISPR/Cas9 in the red flowering poinsettia ( cultivar 'Christmas Eve', in order to obtain plants with orange bract colour, which accumulate prevalently pelargonidin. F3'H is an enzyme that is necessary for formation of cyanidin type anthocyanins, which are responsible for the red colour of poinsettia bracts.

Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses.

The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated that major QTL could already be detected in small association panels. In this study, we analyzed petal number, petal size and fragrance in a small panel of 95 mostly tetraploid garden rose genotypes.

Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs.

Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses.

A highly mutable GST is essential for bract colouration in Euphorbia pulcherrima Willd. Ex Klotsch.

Background: Mutation breeding is an extraordinary tool in plant breeding to increase the genetic variability, where mutations in anthocyanin biosynthesis are targets to generate distinctive phenotypes in ornamental species. In poinsettia, ionizing radiation is routinely applied in breeding programs to obtaining a range of colours, with nearly all pink and white varieties being obtained after γ- or X-ray mutagenesis of red varieties. In the present study we performed a thorough characterization of a potential mutagenesis target gene as the main responsible for the 'white paradox' in poinsettia.

Russeting in Apple is Initiated after Exposure to Moisture Ends: Molecular and Biochemical Evidence.

Exposure of the fruit surface to moisture during early development is causal in russeting of apple ( × Borkh.). Moisture exposure results in formation of microcracks and decreased cuticle thickness.

Russeting in Apple Is Initiated After Exposure to Moisture Ends-I. Histological Evidence.

Russeting (periderm formation) is a critical fruit-surface disorder in apple ( × Borkh.). The first symptom of insipient russeting is cuticular microcracking.

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily.

The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae.

Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts.

Background: Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation.

Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors.

Rose black spot is one of the most severe diseases of field-grown roses. Though R-genes have been characterised, little information is known about the molecular details of the interaction between pathogen and host. Based on the recently published genome sequence of the black spot fungus, we analysed gene models with various bioinformatic tools utilising the expression data of infected host tissues, which led to the prediction of 827 secreted proteins.

Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation.

Transcriptomic analysis resulted in the upregulation of the genes related to common defense mechanisms for black spot and the downregulation of the genes related to photosynthesis and cell wall modification for powdery mildew. Plant pathogenic fungi successfully colonize their hosts by manipulating the host defense mechanisms, which is accompanied by major transcriptome changes in the host. To characterize compatible plant pathogen interactions at early stages of infection by the obligate biotrophic fungus Podosphaera pannosa, which causes powdery mildew, and the hemibiotrophic fungus Diplocarpon rosae, which causes black spot, we analyzed changes in the leaf transcriptome after the inoculation of detached rose leaves with each pathogen.

The rare orange-red colored Euphorbia pulcherrima cultivar 'Harvest Orange' shows a nonsense mutation in a flavonoid 3'-hydroxylase allele expressed in the bracts.

Background: Commercially available poinsettia (Euphorbia pulcherrima) varieties prevalently accumulate cyanidin derivatives and show intense red coloration. Orange-red bract color is less common. We investigated four cultivars displaying four different red hues with respect to selected enzymes and genes of the anthocyanin pathway, putatively determining the color hue.

Improved genetic resolution for linkage mapping of resistance to potato wart in monoparental dihaploids with potential diagnostic value in tetraploid potato varieties.

We achieved improved mapping resolution of the major wart resistance locus Xla-TNL containing also Sen1 in a dihaploid population using SNP data and developed additional markers with diagnostic value in tetraploid varieties. We analyzed a segregating monoparental dihaploid potato population comprising 215 genotypes derived from a tetraploid variety that is highly resistant to Synchytrium endobioticum pathotypes 18 and 6. The clear bimodal segregation for both pathotypes indicated that a major dominant resistance factor in a simplex allele configuration was present in the tetraploid donor genotype.