On the characterization of flowering curves using Gaussian mixture models

In this paper, we develop a statistical methodology applied to the characterization of flowering curves using Gaussian mixture models. Our study relies on a set of rosebushes flowering data, and Gaussian mixture models are mainly used to quantify the reblooming properties of each one. In this regard, we also suggest our own selection criterion to take into account the lack of symmetry of most of the flowering curves. Three classes are created on the basis of a principal component analysis conducted on a set of reblooming indicators, and a subclassification is made using a longitudinal $k$--means algorithm which also highlights the role played by the precocity of the flowering. In this way, we obtain an overview of the correlations between the features we decided to retain on each curve. In particular, results suggest the lack of correlation between reblooming and flowering precocity. The pertinent indicators obtained in this study will be a first step towards the comprehension of the environmental and genetic control of these biological processes.Comment: 28 pages, 27 figure

PREMS / ELVIS : A local plant biological resource management system ELVIS PREMS

International audienceThe management of biological resources collection is a major key for quality of research results. It is also mandatory to keep trace from data to studied organism through every experimental steps including sampling, culture conditions and description of the subject of the study. To achieve this goal in the context of plant science, there are some notable software such as Doriane Labkey and GreenGlobal. After evaluating these solutions with other laboratories we ended with the conclusion that, for different reasons, neither fulfill our needs especially when dealing with perennial plants such as fruit trees (apple or pear trees) or ornamental bush (rose). We then decided to provide our own solution based on the needs and feedbacks from the different teams of the IRHS in the fields of biological resources management, breeding, genetics, molecular biology, physiology and phenotyping. We introduce here two pieces of software:-ELVIS: an information system that takes care of data management and provides an extensible set of python libraries to interact with. These libraries are used here to provide a JSON-RPC API exposed as web services. This is the foundation of the LIMS of our laboratory.-PREMS: a dynamic web interface for biological resources management. This is one of the interfaces developed to interact with ELVIS. ELVIS The laboratory information system Main features:-3 levels of storage: Variety, Accession, Lot (as plant or seeds)-Notations on each level-Grouping of lot for actions (notation, transfer)-Multi-criteria search-Usergroup level data partitioning-Single value or batch importation for material introduction-Single value or batch notations with the ability of exporting field notation forms that can be uploaded back in the database Technology: Qooxdoo (Javascrip framwork) Bioinformatic team HTTP(S) Postgresql JSON-RPC Web API Pyhon libraries ELVIS Qooxdoo libraries PREMS PREMS The plant resource management system Multi-criteria Variety search gives a list of Varieties. A selection in that list displays a detailed view of the Lots and Accessions for that Variety. This view provides quick access to denomination and passport data. On Lots, the view gives access to phenotyping notations and location of the plants or the seeds bag. The user can also enter new notations. ELVIS and PREMS are made available to the community through the SourceSup forge under CeCILL license. ELVIS can provide access to the data by implementing compatible API to interact with other tools. For instance, we are deploying a PHIS installation with the integration of IRHS team in the PHENOM project and are working on ways to make the two applications interact. https://sourcesup.renater.fr/projects/elvis/ https://sourcesup.renater.fr/projects/prems

Inheritance of garden rose architecture and its association with flowering behaviour

International audienceUnderstanding the genetic basis of plant architecture is limited for woody plants due to the challenges of assessing the inheritance of their complex architecture. We aimed to evaluate the genetic variability of plant form and stature in a garden rose population, analyse the inheritance of plant architecture and its linkage with flowering behaviour and identify the quantitative trait loci (QTLs) controlling garden rose architecture. A total of 98 F 1 hybrids were derived from the cross between two diploid roses, The Fairy (TF) and Rosa × wichurana (RW) that differed in stature and flowering behaviour. The TF exhibits continuous flowering (CF) and has erect stature. The RW is once flowering (OF) and prostrate in stature. Three clones per genotype were multiplied, and a total of 300 plants were cultivated in a field. Flowering behaviour, plant form, plant height, stem diameter and internode length were scored during each of 2&nbsp;years. All architectural traits had significant genetic variances (29–61&nbsp;% of their respective phenotypic variances), and their broad-sense heritability estimates were 0.76–0.92. The majority of CF progeny was erect, whereas the OF progeny was prostrate, suggesting a linkage between plant form and flowering behaviour. The QTL analysis identified eight major QTLs controlling architectural traits. Several candidate genes involved in gibberellin biosynthesis and auxin signalling were identified in the vicinity of the QTLs. High heritability estimates obtained for garden rose architecture indicated that architectural characteristics are feasible targets of rose breeding. Linkage of plant form and flowering behaviour, however, prevents independent selection of these traits. The candidate genes identified can be good targets for future physiological studies.</p

The Continuous Flowering Gene in Rose Is a Floral Inhibitor

International audienceIn 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

Impacts of light and temperature on shoot branching gradient and expression of strigolactone synthesis and signalling genes in rose

Article de revue (Article scientifique dans une revue à comité de lecture)International audienceLight and temperature are two environmental factors that deeply affect bud outgrowth. However, little is known about their impact on the bud burst gradient along a stem and their interactions with the molecular mechanisms of bud burst control. We investigated this question in two acrotonic rose cultivars. We demonstrated that the darkening of distal buds or exposure to cold (5°C) prior to transfer to mild temperatures (20°C) both repress acrotony, allowing the burst of quiescent medial and proximal buds. We sequenced the strigolactone pathway MAX-homologous genes in rose and studied their expression in buds and internodes along the stem. Only expressions of RwMAX1, RwMAX2 and RwMAX4 were detected. Darkening of the distal part of the shoot triggered a strong increase of RwMAX2 expression in darkened buds and bark-phloem samples, whereas it suppressed the acropetal gradient of the expression of RwMAX1 observed in stems fully exposed to light. Cold treatment induced an acropetal gradient of expression of RwMAX1 in internodes and of RwMAX2 in buds along the stem. Our results suggest that the bud burst gradient along the stem cannot be explained by a gradient of expression of RwMAX genes but rather by their local level of expression at each individual position.</p

The rose genome sequencing initiative.

International audienc

The rose genome sequencing initiative.

International audienc

Blooming and blooming again : what we learn from rose and strawberry

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