Quantitative trait loci for flowering time and inflorescence architecture in rose

The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F 1 diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose

Kernel methods for phenotyping complex plant architecture

The Quantitative Trait Loci (QTL) mapping of plant architecture is a critical step for understanding the genetic determinism of plant architecture. Previous studies adopted simple measurements, such as plant-height, stem-diameter and branching-intensity for QTL mapping of plant architecture. Many of these quantitative traits were generally correlated to each other, which give rise to statistical problem in the detection of QTL. We aim to test the applicability of kernel methods to phenotyping inflorescence architecture and its QTL mapping. We first test Kernel Principal Component Analysis (KPCA) and Support Vector Machines (SVM) over an artificial dataset of simulated inflorescences with different types of flower distribution, which is coded as a sequence of flower-number per node along a shoot. The ability of discriminating the different inflorescence types by SVM and KPCA is illustrated. We then apply the KPCA representation to the real dataset of rose inflorescence shoots (n=1460) obtained from a 98 F1 hybrid mapping population. We find kernel principal components with high heritability (>0.7), and the QTL analysis identifies a new QTL, which was not detected by a trait-by-trait analysis of simple architectural measurements. The main tools developed in this paper could be use to tackle the general problem of QTL mapping of complex (sequences, 3D structure, graphs) phenotypic traits

3D phenotyping and QTL analysis of a complex character: rose bush architecture

Plant shape, and thereby plant architecture, is a major component of the visual quality of ornamental plants. We have been developing a new method for analyzing the entire plant architecture by 3D digitalization that allows an almost exhaustive description of rose bush architecture and generates a large number of variables, many of them inaccessible manually. We carried out a QTL analysis using this original phenotyping method. In order to evaluate a broader allelic variability as well as the effect of the genetic background on QTL detection, we used two connected, segregating, recurrent blooming populations. The number of QTLs per variable varied from three for the number of determined axes (NbDetA) to seven for the branching angle of order 2 long axes (AngLA2), the two populations taken together. Five new QTLs, located on the linkage groups (LGs) 2, 6, and 7, were detected for the branching angle of axes, and the QTL located on LG7 co-localized with RhBRC1, a branching repressor. Branching and stem elongation QTLs also co-located with RhBRC1, suggesting its pleiotropic nature. Year-specific QTLs were also revealed, that explained the genotype × year interactions observed for the number of order 3 short axes (NbSA3) and AngLA2 from a genetic point of view. We also evidenced an effect of the genetic background on QTL detection. This new knowledge should help to better reason the genetic improvement programs for rose bush architecture and, therefore, rose bush shape

Effect of GA 3 and paclobutrazol on adventitious shoot regeneration of two Pelargonium sp

This study had two aims. The first was to improve the regeneration efficiency of Pelargonium leaf discs by adventitious budding. The second was to test the effect of gibberellic acid (GA 3) and paclobutrazol (PBZ) on callus formation and adventitious shoot regeneration in Pelargonium before using genetic transformation of this species for functional validation of genes involved in the process of GA regulation. GA 3 and paclobutrazol (an inhibitor of GA synthesis pathway) were added (together or separately) in the shoot regeneration media of two Pelargonium species, Pelargonium * hortorum \u27Panache sud\u27 (\u27P.sud\u27) and Pelargonium * domesticum \u27Autumn haze\u27 (\u27 P.dom\u27). In both cases, GA 3 applied alone, completely inhibited the bud regeneration. Moreover, the rate of callus formation decreased drastically when 5 M of GA 3 was applied to \u27 P. dom\u27 explants. Similar result was obtained with \u27P.sud\u27 explants using 20 M GA 3. Paclobutrazol (0.3 M) applied at the same time as GA 3 (10 M) could partially restore regeneration process of \u27 P. dom\u27. For \u27 P. dom\u27, the use of paclobutrazol alone increased callus formation and slightly improved the rate of regeneration. Moreover, initiated buds had a better appearance. For \u27P. sud\u27, which had an abundant callusing, paclobutrazol did not improve regeneration and led to hyperhydric shoots

Genotype of FLOWERING LOCUS T homologue contributes to flowering time differences in wild and cultivated roses

Rose flowers have long delighted humans as ornamental plants. To improve the ornamental value of roses it is necessary to understand the regulatory mechanisms of flowering. We previously found that flowering time is controlled by three minor quantitative trait loci (QTLs) and a major QTL co-localised with RoFT. In this study, we isolated three RoFT alleles encoding completely identical amino acid sequences from the parents of a mapping population. Correlation analysis of the RoFT genotypes and flowering time phenotypes in the mapping population showed that the RoFT_f and RoFT_g alleles contribute to the early-flowering phenotype, while the RoFT_e allele contributes to the late-flowering phenotype. We developed two novel cleaved amplified polymorphic sequence (CAPS) markers based on the genomic sequences of the RoFT alleles and clearly showed that the relationship between RoFT genotype and flowering time was applicable to 12 of 13 cultivated roses grown at the Higashiyama Botanical Gardens, Japan. Allele-specific expression analysis using a reverse transcription CAPS assay suggested that these RoFT alleles are regulated differentially at the transcription level. Furthermore, transgenic Arabidopsis thaliana plants ectopically expressing the RoFT gene showed an early-flowering phenotype. Conversely, in roses, RoFT was continuously expressed after floral bud formation, and RoFT transcript accumulation reached its peak after that of the floral meristem identity gene RoAP1b. These data suggest that RoFT may be essential not only for floral transition but also for normal floral development and flowering in roses

The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry

Flowering is a key event in plant life, and is finely tuned by environmental and endogenous signals to adapt to different environments. In horticulture, continuous flowering (CF) is a popular trait introduced in a wide range of cultivated varieties. It played an essential role in the tremendous success of modern roses and woodland strawberries in gardens. CF genotypes flower during all favourable seasons, whereas once-flowering (OF) genotypes only flower in spring. Here we show that in rose and strawberry continuous flowering is controlled by orthologous genes of the TERMINAL FLOWER 1 (TFL1) family. In rose, six independent pairs of CF/OF mutants differ in the presence of a retrotransposon in the second intron of the TFL1 homologue. Because of an insertion of the retrotransposon, transcription of the gene is blocked in CF roses and the absence of the floral repressor provokes continuous blooming. In OF-climbing mutants, the retrotransposon has recombined to give an allele bearing only the long terminal repeat element, thus restoring a functional allele. In OF roses, seasonal regulation of the TFL1 homologue may explain the seasonal flowering, with low expression in spring to allow the first bloom. In woodland strawberry, Fragaria vesca, a 2-bp deletion in the coding region of the TFL1 homologue introduces a frame shift and is responsible for CF behaviour. A diversity analysis has revealed that this deletion is always associated with the CF phenotype. Our results demonstrate a new role of TFL1 in perennial plants in maintaining vegetative growth and modifying flowering seasonality

The continuous flowering gene in rose is a floral inhibitor

In rose, RoKSN, a TFL1 homologue, is a key regulator of continuous flowering. To study the function of this gene in planta, protocols of plant transformation are needed. We complemented tfl1 Arabidopsis mutants and ectopically expressed RoKSN in a continuous-flowering rose. In Arabidopsis, RoKSN complemented the tfl1 mutant by rescuing late flowering and indeterminate growth. In continuous-flowering rose, the ectopic expression of RoKSN led to the absence of flowering. In these transgenic roses, a study of genes implied in the floral regulation was carried out. The floral activator transcripts decreased whereas the FD transcription factor is up-regulated. We conclude that RoKSN is a floral repressor and could regulate the expression of transcripts as RoFT and RoFD. These results could strengthen a mechanism of competitive interactions of RoFT and RoKSN with a common partner, FD to move towards flowering or vegetative developments

Overexpression of RoDELLA impacts the height, branching, and flowering behaviour of Pelargonium × domesticum transgenic plants

Key message We reported the cloning of a rose DELLA gene. We obtained transgenic Pelargonium lines overexpressing this gene which presented several phenotypes in plant growth, root growth, flowering time and number of inflorescences. Abstract Control of development is an important issue for production of ornamental plant. The plant growth regulator, gibberellins (GAs), plays a pivotal role in regulating plant growth and development. DELLA proteins are nuclear negative regulator of GA signalling. Our objective was to study the role of GA in the plant architecture and in the blooming of ornamentals. We cloned a rose DELLA homologous gene, RoDELLA, and studied its function by genetic transformation of pelargonium. Several transgenic pelargonium (Pelargonium × domesticum ‘Autum Haze’) lines were produced that ectopically expressed RoDELLA under the control of the 35S promoter. These transgenic plants exhibited a range of phenotypes which could be related to the reduction in GA response. Most of transgenic plants showed reduced growth associated to an increase of the node and branch number. Moreover, overexpression of RoDELLA blocked or delayed flowering in transgenic pelargonium and exhibited defects in the root formation. We demonstrated that pelargonium could be used to validate ornamental gene as the rose DELLA gene. RoDELLA overexpression modified many aspects of plant developmental pathways, as the plant growth, the transition of vegetative to floral stage and the ability of rooting

RoKSN, a floral repressor, forms protein complexes with RoFD and RoFT to regulate vegetative and reproductive development in rose

FT/TFL1 family members have been known to be involved in the development and flowering in plants. In rose, RoKSN, a TFL1 homologue, is a key regulator of flowering, whose absence causes continuous flowering. Our objectives are to functionally validate RoKSN and to explore its mode of action in rose.We complemented Arabidopsis tfl1 mutants and ectopically expressed RoKSN in a continuous-flowering (CF) rose. Using different protein interaction techniques, we studied RoKSN interactions with RoFD and RoFT and possible competition. In Arabidopsis, RoKSN complemented the tfl1 mutant by rescuing late flowering and indeterminate growth. In CF roses, the ectopic expression of RoKSN led to the absence of flowering. Different branching patterns were observed and some transgenic plants had an increased number of leaflets per leaf. In these transgenic roses, floral activator transcripts decreased. Furthermore, RoKSN was able to interact both with RoFD and the floral activator, RoFT. Protein interaction experiments revealed that RoKSN and RoFT could compete with RoFD for repression and activation of blooming, respectively. We conclude that RoKSN is a floral repressor and is also involved in the vegetative development of rose. RoKSN forms a complex with RoFD and could compete with RoFT for repression of flowering

In the name of the rose: a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions