The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. The consortium has established a high-quality reference for the sunflower genome (3.6 Gb). The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. The genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Collaborators

Dr Stéphane Muños - Institut National de la Recherche Agronomique, “INRA”, France

Dr Loren RIESEBERG - University of British Columbia, Canada     

Dr John BURKE - University of Georgia, USA

Dr Sariel HUBNER - Galilee Research Institute (MIGAL), Israel

Articles

• Badouin H, et al., (2017) The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature. 546 (7656):148-152. doi: 10.1038/nature22380.
• Kane, N.C., Gill, N., King, M.G., Bowers, J.E., Bergès, H., Gouzy, J., Bachlava, E., Langlade, N.B., Lai, Z., Stewart, M., Burke, J.M., Vincourt, P., Knapp, S.J., and Rieseberg L.H. (2011) Progress towards a reference genome for sunflower. Botany (89:429-437)

CNRGV's responsible

Sonia Vautrin

Project coordinator:

Judith BURSTIN
INRA
UMR AgroEcologie
17 rue Sully
BP 86510
21065 DIJON
Email : judith.burstin@dijon.inra.fr

Website:  https://www.peamust-project.fr/Le-projet

Project partner:

The PeaMUST project combines 26 public and private partners.

Abstract

•    Develop novel pea varieties and optimize plant-symbiotic interactions for stabilizing seed yield and quality, in the context of pesticide reduction and climate change
•    Enhance national and international research and competitiveness of the French breeders and pea production

Objectives

•    Undertake a program of genomic selection targeted to low-input cropping systems
•    Discover molecular determinants of disease, insect and frost partial resistance in pea and faba bean
•    Investigate the potential of architecture and plant-symbiote interactions in breeding for multiple stress tolerance
•    Provide enhanced platforms for gene validation in pea
•    Devise best breeding strategies towards optimized yield and stress tolerance

Methodology

•    Federate actors gathering various complementary competencies (quantitative genetics, breeding, genomics, biochemistry, biotechnology, plant /pathogen, pests and symbiots interactions, agronomy, socio-economy)
•    Use associated phenotyping platforms (PPHD Dijon, DIAPHEN Montpellier, UE Epoisses, UE Le Rheu, UE Mons, UE Clermont-Theix, UE Lusignan, UE Toulouse, SNES) and national sequencing and genotyping platforms (GENOTOUL, GENTYANE, GENOSCOPE)

Main Results

•    Acquire original basic knowledge on the genetic control of multiple stress tolerance (QTL cloning, impact of plant architecture, phenology and symbiotic interactions on multiple-stress tolerance)
•    Develop unique tools for gene identification: high throughput sequence-based genotyping, translational genomic tools, association genetics panels, TILLING and VIGS platforms, user-friendly databases
•    Develop enhanced breeding methods and lines, optimizing yield under varying stress conditions

CNRGV's responsibles:

Sonia Vautrin - Genséric Beydon

CNRGV involvement:

 Bac libraries construction

Publication related to the project:

Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.).

Abstract:

This project intends to fine-map one of the most effective Fusarium-resistance quantitative trail locus (QTL) Qfhs.ifa-5A in wheat. Qfhs.ifa-5A is located on the short arm of chromosome 5A supposedly close to the centromere. The region exhibits a very low recombination rate. To generate a high-resolution map for this region we will employ several strategies from screening for meiototic recombination events to physical mapping approaches that will provide additional breakpoints in this poor-recombining region. Using markers close to the physical position of the QTL, we will screen a non-gridded BAC library of the resistant wheat cultivar CM-82036. Selected BACs will be sequenced and investigated for more markers and candidate genes underlying the QTL.

CNRGV involvement:

• Construction and screening of a Non Gridded BAC library
• Physical map of the genomic region of interest

CNRGV's responsible

• Sonia Vautrin

Publication related to the project:

• Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat.

The world oilseed production will be faced to an increasing demand in the next thirty years catapulted by a combination of factors, including: i) an additional demand of edible oil, ii) the development of the biofuels industry and more specifically biodiesel around the world, and iii) the needs for green chemistry.

Sunflower represents a major renewable resource for food (oil), feed (meal), and green energy. France is a major sunflower producer. French breeders are ranked first in terms of sunflower seed production. World leading seed companies and SME involved in sunflower breeding are based in France and are creating a wide range of employments in France – from molecular breeders to farmers involved in seed production - , while ensuring a continuous genetic progress in integrating new technologies in their breeding programs.
During the past ten years, the impact of genetic advance on sunflower yield increase has been lower than expected, suggesting that current breeding resources and methods might not bring future solutions to the requested need in a context of climate changes. In order to face the challenges of delivering safe and high-quality food while maintaining yield and stability across different environments affected by climatic change, a paradigm shift is needed in sunflower breeding.
The near availability of the genome sequences of Helianthus annuus together with the breakthrough created by the new sequencing technologies, the development of phenotypic platforms and of bioinformatic tools allowing the integration of such high throughput data, are offering a favorable context to reinforce, through an optimization of the breeding process of hybrid cultivars, the competitiveness of French seed industry.
In an unprecedented effort (8 years project, 10 public and 7 private partners), SUNRISE offers unique opportunities to accelerate genetic gain and improve oil yield of sunflower hybrids grown under limited water supply through a better use of the outstanding genetic diversity of wild and domesticated Helianthus annuus genetic resources.

As the result of climate changes, more variability is expected in the timing and quantity of water availability for crop production from location to location. Sunflower is seen as a water stress tolerant crop, but wastes available water. On the long term period, due to the cost of investments all along the oil industry chain, the competitiveness of the sunflower chain is highly depending on the stability of oil yield across years and locations. SUNRISE will decipher the genes and genes networks involved in both the sunflower oil yield potential and its stability across years and locations, and then identify in the wide Helianthus annuus gene pool which alleles would be of interest for sunflower breeding.
Moreover, SUNRISE will devote a particular effort in the improvement of sunflower hybrid breeding process. SUNRISE will identify the loci and/or the heterosis mechanisms which are the most involved in homeostasis, depending on the parental alleles, and then build new gene pools exhibiting between themselves the better specific combining ability for homeostasis, i.e. yield stability.
All together, these two objectives will result in the definition of a new sunflower ideotype.
Full benefit of present possibilities requires (i) the better characterization of genetic diversity in order to optimize dense genotyping needed for genome wide association and linkage mapping, (ii) the development of appropriate detailed or high throughput phenotyping strategies, including molecular phenotyping, to characterize the sunflower response to the variation of the abiotic environment, (iii) the involvement of appropriate genetic design to decipher the genetic factors involved in this response, (iv) the integration of the knowledge into a crop model for in silico testing of the genotype environment interactions and for ideotypes design, (v) the development of innovative tools and methods to optimize the utilization of genetic resources and breed for new improved sunflower varieties for the concerned traits.
It relies on a large partnership between the key players of sunflower economy in France and in particular a strong private partnership unique to date in the history of sunflower research in France. This partnership will ensure that the new knowledge, resources and methods resulting from the project will be translated into products and varieties supporting the sunflower economy in France.

SUNRISE will ultimately enable efficient molecular based improvement to reduce the time from trait to commercialization. Indeed, SUNRISE will not only produce new resources, data and material, but will also follow their valorization by partners (usually competitors) that agree to synergize their efforts within the partnership of this project and give a feedback of their value in their programs. The project also integrates socio-economic analyses that will enable to evaluate the benefit of innovative genetic and ecophysiological results for the breeding sector and transfer of knowledge to agriculture.

Project coordinator:

Patrick VINCOURT
INRA UMR INRA-CNRS 441-2559
Chemin de Borde Rouge
31326 Castanet Tolosan

Patrick.Vincourt@toulouse.inra.fr

Project partner:

10 public and 7 private partners (CETIOM, BIOGEMMA,CAUSSADE SEMENCES, MAISADOUR, RAGT, SOLTIS,SYNGENTA SEEDS)

CNRGV involvement:

Responsible:
Arnaud Bellec
William Marande
Sonia Vautrin
Production and analysis of new genomic resources

Coordinateur du projet :

Prof. Frederic Bourgaud
Directeur du laboratoire Agronomie et Environnement

Dr Sandro ROSELLI -  Post-Doctorant

Partenaire :

Laboratoire Agronomie et Environnement
UMR 1121 Université de Lorraine – INRA
ENSAIA, 2 Avenue Forêt de Haye
F-54500 Vandoeuvre

Résumé :

Les furocoumarines sont des composés secondaires issus du métabolisme des phenylpropanoïdes et principalement distribués chez quatre familles de végétaux supérieurs : Apiacées (céleri), Moracées (ficus), Rutacées (citrus) et Fabacées (coronilles). Certaines de ces plantes, comme les Apiacées (carotte, céleri, persil) ou les Rutacées (Citrus), ont un intérêt agronomique évident. Chez ces espèces à usage alimentaire, les furocoumarines ont fait l’objet d’études car elles présentent un risque de toxicité majeur pour les consommateurs de ces produits végétaux. D’une manière plus générale, les plantes à furocoumarines présentent un intérêt fondamental dans le domaine de la biologie végétale dans la mesure où elles constituent un des modèles les mieux compris de co-évolution avec des insectes herbivores. Ces molécules de défense chez la plante sont utilisées en médecine pour soigner un certain nombre d’affections comme des maladies de la peau (bergaptène, utilisé contre le psoriasis), ou le traitement de cancers (xanthotoxine contre le lymphome T). L’équipe Métabolites Secondaires du Laboratoire Agronomie et Environnement cherche à caractériser au niveau moléculaire et enzymatique l’ensemble des réactions impliquées dans la voie de biosynthèse et ainsi à comprendre quels sont les processus évolutifs mis en œuvre dans leur apparition au sein des 4 familles de plantes phylogénétiquement très distinctes. Des éléments de réponses ont été apportés par l’identification de la psoralène synthase (Larbat et al JBC 2007) et de l’angélicine synthase (Larbat et al JBC 2009), enzymes appartenant à la famille des P450.
Le projet vise à la caractérisation de l’ensemble des enzymes de cette voie de biosynthèse particulière par la construction d’une banque BAC de panais et le repérage et séquençage des BACs porteurs des gènes recherchés. Les connaissances générées permettront de révéler le fonctionnement complet de la voie de biosynthèse des phénylpropanoïdes et de comprendre la manière dont les plantes appartenant à des familles très distinctes ont pu évoluer pour s’adapter à un environnement hostile en produisant le même type de molécules. A terme, cela pourrait également permettre par des approches de génie métabolique de moduler/améliorer la synthèse des furocoumarines dans des plantes transgéniques et ainsi générer des plantes transformées dédiées à la production de ces molécules à usage thérapeutique. 

Responsable: Sonia VAUTRIN

Implication du CNRGV :

• Construction et Criblage d’une banque BAC de panais
• Séquençage

Publication issue du projet:

• A bacterial artificial chromosome (bac) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip

Représentation schématique de la voie de biosynthèse des furocoumarines. Les flèches rouges correspondent à des étapes catalytiques P450 dépendantes

Project coordinator:

Anete Pereira de Souza
Depto de Biologia Vegetal (DBV)
Instituto de Biologia (IB)
Lab. Análise Genética Molecular
Centro de Biol Mol e Eng Gen (CBMEG)
Univ. Est de Campinas (UNICAMP)
Fone: 19-3521-1132
Fax:19-3521-1089

Website: http://www.cbmeg.unicamp.br/

Abstract:

The aim of this project is the caracterization of five genomic regions associated with genes of interest to reveal the allelic organization among different hom(e)ologous regions; and also to identify markers (SSR and SNP) through the sequencing. These markers will be integrated to the map developed by RIDESA, IAC and UNICAMP-ESALQ/USP. To meet this goal two BAC libraries will be constructed for two genotypes of sugarcane in collaboration with CNRGV-INRA. BAC libraries will be organized as 3D pool for one genotype  and as macroarrays to find positive clones carrying these five genes. In addition, twenty BAC clones will be sequenced and analyzed.

At UNICAMP, the Center for Molecular Biology and Genetic Engineering, several projects have been developed related to genetic mapping using molecular markers in sugarcane. Therefore these 2 new BAC libraries will also be an essential tool to complement and accelerate the development of genetic maps, facilitating the localization of quantitative traits in them, thus contributing to the improvement of new varieties.

CNRGV involvement:

Responsible: Sonia Vautrin

The project aims at strengthening the competitiveness of the French breeding sector while addressing the societal demand for sustainability, quality and safety. Bringing together 26 partners from the public and private research and breeding sectors, it has a total budget of €34 million for 9 years.

Led by Catherine Feuillet, Research Director at INRA Clermont-Theix, Breedwheat will combine structural and functional genomics, genetics, and ecophysiology with high throughput phenotyping and genotyping to identify markers and genes underlying yield and quality traits under abiotic and biotic stress. Moreover, the project will characterize and tap unexploited genetic resources to expand the diversity of French gene banks. Finally, new breeding methods will be developed and evaluated for their socio-economic impact. .This project will enhance the sustainability of wheat production through the development of new varieties that are more robust and less demanding in water and fertilizer, towards a more environmentally friendly agriculture that is adapted to climate change.

Breedwheat will reinforce the French position in the “Wheat-Global Alliance” for world food security led by the international research centers CIMMYT and ICARDA. It will also enable new collaborations with other large scale national projects in the framework of the new international “Wheat Initiative” for the coordination of wheat research, supported by the G20, co-led by INRA and launched on September 15th, 2011 at the French Ministry of Agriculture.

Breedwheat is the 1st French Stimulus Initiative project coordinated by INRA in the category “Biotechnologies and Bioresources” to be launched. Announced on February 23rd, 2011 by the French Minister of Higher Education and Research and the French Minister of Agriculture, Breedwheat is one of the five laureates of the “Biotechnologies and Bioresources” call for proposals. The project represents a total investment of €34 million for 9 years, of which €9 million were granted by the French Stimulus Initiative through the French National Research Agency (ANR). The project gathers the competencies of 26 French partners, including 11 private companies, to develop and use efficient genome sequence-based tools and new methodologies for breeding wheat varieties with improved quality, sustainability, and productivity.

Project coordinator:

INRA - UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC)
5, chemin de Beaulieu
63100 Clermont-Ferrand
France

Website

Project partners:

The project involves 26 French partners, including 11 private companies.

CNRGV's responsible

• Arnaud Bellec

CNRGV involvement:

• 3D pool production and screening
• BAC libraires construction

In collaboration with :

Bruno Delbreil
UMR USTL INRA 1281, Stress abiotiques et différenciation des végétaux cultivés
Université des Sciences et technologies de Lille, Bâtiment SN2
59650 Villeneuve d’Ascq
France
Phone: +33 320434022
E-mail: bruno.delbreil@univ-lille1.fr

Isabelle Lejeune
UMR USTL INRA 1281, Stress abiotiques et différenciation des végétaux cultivés
80200 Estrées-Mons
France
Phone: +33 322857507
E-mail: Lejeune@mons.inra.fr

Nasser Bahrman
UMR USTL INRA 1281, Stress abiotiques et différenciation des végétaux cultivés
Université des Sciences et technologies de Lille, Bâtiment SN2
59650 Villeneuve d’Ascq
France
Phone: +33 322857854
E-mail: nasser.bahrman@mons.inra.fr

Abstract :

Dry pea is an important field crop in France. The sowing of dry pea in autumn allows a longer life cycle than in a spring sowing, associated with a higher biomass production that would help to improve and stabilize this crop productivity. However, to release winter varieties, winter survival has still to be improved and particularly the freezing tolerance component. On pea, the genetic determinism of frost tolerance has been studied. Three major QTLs have been mapped on linkage groups 3, 5 and 6.

Pea BAC-library are important genomic tools suitable for physical mapping and map-based cloning. This library is being screened with probes corresponding to markers in the QTL interval. The physical map of the corresponding region is under construction and BACs covering the reduced confidence interval of the QTL will be sequenced. This approach that combine fine mapping and positional cloning will lead us to identify potential candidate genes underlying the three freezing tolerance pea QTLs. 

Recent publications :

E. Dumont, N. Bahrman, E. Goulas, B. Valot, H. Sellier, JL. Hilbert, C. Vuylsteker, I. Lejeune-Hénaut, B. Delbreil. A proteomic approach to decipher chilling response from cold acclimation in pea (Pisum sativum L.)  Plant Sci. 2011 (180-1) pp 86-98

E. Dumont, V. Fontaine, C. Vuylsteker, H. Sellier, S. Bodèle, N.Voedts, R.Devaux, M.Frise, K. Avia, JL Hilbert, N.Bahrman, E.Hanocq, I.Lejeune-Hénaut, B.Delbreil. Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions. TAG 2008 (118-8) pp 1561-1571

CNRGV's responsible: Sonia Vautrin

Project

Dr Karen Aitken

CSIRO Plant Industry

Queensland Bioscience Precinct

306 Carmody Road                                                                     

St Lucia

4068

QLD Australia

Abstract

Over the last decade a number of genetic maps have been constructed and quantitative trait loci (QTL) studies carried out for agronomically important traits. These have included traits related to sugar content (Brix, Pol), as well as yield and biomass related traits such as stem diameter, height and stalk number. In parallel a large association study using the parental population of the Australian sugarcane breeding program has also been conducted targeting disease resistance. These studies have identified many markers that contribute to the phenotypic variation of these traits. The next step is to determine the genetic structure of these regions, and which genes or regulatory elements underlie these QTL. In the last five years a consortium of scientists from a number of countries including Australia have grouped together to form the Sugarcane Genome Sequencing Initiative (SUGESI). The goal of this consortium is to generate a combined monoploid genome sequence of sugarcane. The Australian contribution to this consortium is sequenced BAC clones from the R570 BAC library that underlie the QTLs identified in the numerous studies. The R570 BAC library will be screened at INRA-CNRGV to identify the BAC clones that underlie these QTL of agronomic importance.

The aims of this project are:

1) To establish a strategy to identify which QTL regions to target.

QTL regions were selected that had been identified at a significance level of less than p=0.001 and contained more than one marker. Ideally, the selected QTL should also have been identified in more than one population. In the next stage, sets of linked markers were selected to test across the whole QTL region. The selected markers were in most cases SNP or DArT markers with a known sequence. The sequenced markers were BLASTn aligned to the sorghum genome to determine the abundance of the sequence. Only those markers that aligned to a single location in sorghum were selected to screen the BAC clones and preference was given to those that also showed alignment to the sugarcane EST collection.

2) Screen the R570 BAC library with the selected markers linked to QTL.

Two different approaches: macroarray membrane hybridisation and qPCR using 3-D BAC pools will be used to screen the library. In total 112 primer pairs were developed to screen the R570 BAC library. These will be used to identify BAC clones which will then be characterised and ultimately sequenced to identify genes in these regions. Once the sequence is obtained a major outcome will be the development of robust markers, closely linked to causal genes, for use in the Australian sugarcane breeding program.

CNRGV's responsible

Sonia Vautrin

The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds (Dempewolf et al. 2008). Despite its size and economic importance, genomic characterization has lagged behind that of comparable groups such as the grass, legume, crucifer, and tomato families. In particular, the lack of a reference sequence for the Compositae impedes research and improvement efforts. We will dramatically enhance Compositae genomic resources by sequencing the genome of cultivated sunflower ( Helianthus annuus), the most important crop in the family. In addition to its global importance as an oil crop, sunflower has tremendous potential for cellulosic biomass production, both as a primary source and via the residue of oilseed production. Thus, the proposed large-scale sequencing effort will be accompanied by the development of genomic resources, genetic stocks, and knowledge for manipulating agronomically important traits in sunflower hybrid breeding programs.

The scientific objectives of the project are to :
 1) Extend the genetic map for sunflower;
 2) Construct a physical map of the sunflower genome based on fingerprinting and end-sequencing of BAC clones from deep-coverage libraries;
 3) Generate a reference sequence for sunflower using a hybrid strategy involving whole genome shotgun sequencing (40x depth) and sequencing of BAC pools (20x depth) with nextgeneration sequencing platforms;
 4) Determine the genetic basis of agriculturally important traits using an association mapping approach; and
 5) Develop a xylem EST database and determine the genetic basis of cellulosic biomass traits.

The project will create an unparalleled resource for sunflower and the Compositae and yield a wealth of data for functional and comparative genomic analyses and agricultural, biological, and environmental research. Candidate gene and SNP discovery will facilitate public and private crop improvement efforts, as well as the ongoing development of sunflower as a biofuel. With climate change, drought tolerant Compositae species are likely to become increasingly important as food and biofuel crops in Canada and elsewhere, as well as biological factories for the production of pharmaceuticals (Maloney 2000). Also because many of the most noxious weeds in Canada are Compositae species (e.g., thistles, napweeds, and ragweeds), a reference genome for the family will aid ongoing efforts to understand and control these invasive species. Finally, our results will allow us to test a new theory about the role of genomic redundancy in the establishment of chromosomal rearrangements and possibly solve a longstanding mystery in plant genome evolution.

Website :

http://www.sunflowergenome.org/

Partners :

Loren Rieseberg
Botany Department University of British Columbia
3529-6270 University Blvd Vancouver,
B.C. V6T 1Z4
CANADA
Phone: 604-827-4540
Fax: 604-822-6089

LIPM "SUNFLOWER" Team
INRA
Chemin de Borde Rouge
31326 Castanet Tolosan
FRANCE
Tel : 05 61 28 54 58
Mob : 06 73 69 23 72

Steven J. Knapp
Professor and Georgia Research Alliance Eminent Scholar
Institute of Plant Breeding, Genetics, and Genomics
Center for Applied Genetic Technologies
111 Riverbend Road
The University of Georgia
Athens, Georgia 30602
USA
Tel: (706) 542-4021
Fax (706) 583-8120
E-mail: sjknapp@uga.edu

Publications related to the project :

• Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome
•  Progress towards a reference genome for sunflower

CNRGV's responsible

• Sonia Vautrin

Sugarcane cultivars derive from recent interspecific hybrids obtained by crossing Saccharum officinarum and Saccharum spontaneum and represent relevant feedstock used worldwide for biofuel production. The challenge in a sugarcane sequencing project is the size (10 Gb) and complexity of its genome structure that is highly polyploid and aneuploid with a complete set of homo(eo)logous genes predicted to range from 8 to 10 copies (alleles). Although sugarcane’s monoploid genome is about 1 Gb, its highly polymorphic nature represent another significant challenge for obtaining a genuine assembled monoploid genome. A sugarcane R570 BAC library whose construction was funded by ICSB is available for sequencing. The genome coverage of this library is believed to be around 1,3x suggesting that recovery of all alleles would not be always efficient. In any case, BAC screening can be undertaken using a fast and efficient 3D-pool approach which has been developed at CNRGV followed by PCR amplification of genes of interest.

The Sugarcane Genome Sequencing Initiative – A particularly attractive initial strategy that lies at the intersection of the common interests of virtually all of the sugarcane research community is to capture much of the gene-rich recombinationally-active euchromatin. The Sugarcane Genome Sequencing Initiative (SUGESI) was envisaged to join efforts to produce a reference sequence of a sugarcane cultivar ( Saccharum hybrid) and ancestor genotypes ( Saccharum officinarum and  Saccharum spontaneum) using a combination of approaches but mainly focused on BAC sequencing. The SUGESI Consortium aggregates researchers from Australia, Brazil, France, South Africa and United States. The SUGESI Initiative intends to make sequences public as soon as minimum assemblies permit.

Publications related to the project :

• A mosaic monoploid reference sequence for the highly complex genome of sugarcane
• Building the sugarcane genome for biotechnology and identifying evolutionary trends
• The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome

List of partners:

Dr Marie-Anne Van Sluys, Professor of Botany GaTE Lab (Genomics and Transposable elements)
Departamento de Botânica-IBUSP
rua do Matao, 277 05508-900;
São Paulo, SP, BRASIL

Dr Glaucia Souza
Associate Professor
BIOEN Program Coordinator Instituto de Química
Universidade de São Paulo

Dr Angélique D'Hont
CIRAD, UMR 1098 DAP Equipe "Structure et évolution des génomes" TAA96/03,
Avenue Agropolis
34398 Montpellier cedex 5, FRANCE

Dr Andrew Paterson
Plant Genome Mapping Laboratory Center for Applied Genetic Technologies
111 Riverbend Road, Athens, GA 30606

Dr Ray Ming
University of Illinois at Urbana-Champaign
1201 W. Gregory Drive 148 ERML, MC-051

Dr Robert Henry
Southern Cross University
Centre for Plant Conservation Genetics Bioenergy Research Institute/Lismore, NSW Australia

Dr Rosanne Casu
Queensland Bioscience Precinct -
St Lucia 306 Carmody Road
St Lucia QLD 4067 Australia

Dr Bernard Potier
South African Sugarcane Research Institute
Private Bag X02 Mount Edgecombe
4300 South Africa

CNRGV's responsible

• Sonia Vautrin

In collaboration with:

•  Italian National Agency for New technologies, Energy and Environment (ENEA).
   ENEA-Casaccia RC, BAS BIOTEC-GEN
   Via Anguillarese, 301
   00123 Rome
   Italy

Website : http://www.enea.it/com/ingl/default.htm

Laboratory Leader: Dr. P. Galeffi
 Principal Researcher: Dr. A. Latini

Abstract

The Triticum durum Dehydration Responsive Factor 1 gene, TdDRF1,  belonging to the DREB gene family, is  expressed in response to dehydration and encodes for abiotic stress responsive transcription factors that impart stress endurance to the plants (Latini et al. 2007). Recently, the expression profile of this gene was finely examined in several wheat varieties in both greenhouse and in field conditions, during a water stress time-course (Latini et al. 2008). All obtained data spotlighted that the targeting of this gene could help the selection of cultivars for improving plant tolerance to drought.

The fine mapping of this gene, determining the exact locus position on chromosomes will be very interesting and useful. Actually, it is already established that homeologous loci of this gene exist in 1A, 1B chromosomes of durum wheat and 1A, 1B and 1D chromosomes of bread wheat; in addiction, there are some evidences about the existence of some paralogous gene copies and also pseudogenes without introns.

The collaboration with the CNRGV is highly fruitful, because it holds the most relevant BAC genomic DNA collections of wheat. In addiction to several collections of bread wheat, at CNRGV, durum wheat (Cenci et al. 2003) and chromosome-specific (such as 1D, 4D, 6D and 1AS or 1AL of hexaploid wheat – Janda et al. 2004) genomic BAC libraries are also available.

Actually, the bread wheat Chinese Spring BAC library (Tae-B-CS) was screened by both PCR on pools and microarray hybridization techniques with primers specific for the TdDRF1 sequence. A durum wheat library is still under screening. Several clones containing the target sequence were identified and are being characterized by restriction analyses, chromosome walking and complete BAC sequencing.

From the positive BAC clones, the upstream and downstream TdDRF1 gene regions will be sequenced, allowing the identification of the promoter and other regulatory sequences (enhancers, alternative splicing signals, and so on). Furthermore, the complete sequence of a selected BAC clone will reveal if some other dehydration-responsive gene is located next to the target locus and this information will be precious for developing applications in molecular assisted breeding programs aimed to the release of drought tolerant wheat cultivars.

- Latini A, Rasi C, Sperandei M, Cantale C, Iannetta M, Dettori M, Ammar K, Galeffi P: Identification of a DREB-related gene in Triticum durum and its expression under water stress conditions. Annals of Applied Biology (2007), 150: 187-195.
 - Latini A, Sperandei M, Sharma S, Cantale C, Iannetta M, Dettori M, Ammar K, Galeffi P: Molecular analyses of a dehydration-related gene from the DREB family in durum wheat and triticale. In Biosaline Agriculture and High Salinity Tolerance. Published by Birkhäuser and Verlag. Edited by Abdelly C, Öztürk M, Ashraf M, Grignon C. (2008), 286-295.
 - Cenci a, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld, Dubcovsky J: Construction and characterization of a half million clone BAC library of durum wheat ( Triticum turgidum ssp. durum). Theoretical and Applied Genetics (2003), 107: 931-939.
 - Janda J, Bartoš J, Šafář J, Kubaláková M, Valárik M, Čihalíková J, Šimková H, Caboche M, Sourdille P, Bernard M, Chalhoumb B, Doležel J: Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of Hexaploid wheat. Theoretical and Applied Genetics (2004) 109: 1337-1345.

This collaboration was also supported by a COST-STSM-FA0604 grant, given to A. Latini.

CNRGV involvement

Responsible : Elisa PRAT/ Sonia VAUTRIN

- Macroarray production/ screening
 - 2D DNA pools screening

Gestion des banques BAC de la tomate et définition du minimum tilling path pour le séquençage du chromosome 7

Projet développé dans le cadre du Solanaceae Genome Network

En collaboration avec

•  Dr. Monder Bouzayen
   Laboratoire de Génomique et Biotechnologies des fruits
   UMR990
   Chemin de Borde Rouge
   31326 Castanet Tolosan

Site internet: http://gbf.ensat.fr/gbf_projects.html

Résumé

Un projet international, International Solanaceae Genome Initiative, s’est mis en place dans le but de séquencer le génome de la tomate. La stratégie qui a été adoptée consiste à séquencer les régions riches en gènes. Elle découle de résultats qui montrent que chez la tomate la grande majorité des séquences géniques se trouvent concentrée dans des régions euchromatiques contiguës et constituant environ 25% des 950 Mb du génome de la tomate. La démarche choisie consiste à identifier et à séquencer un minimum tilling path de clones BAC présent dans ces 220Mb d’euchromatine. Le génome de la tomate est constitué de 12 chromosomes. Chaque pays partenaire participe à cet effort en prenant en charge le séquençage d’un ou plusieurs chromosomes ( http://www.sgn.cornell.edu/about/tomato_sequencing.pl ). En France, le laboratoire GBF de Monder Bouzayen, est responsable du séquençage du chromosome 7.

Résultats

La première version de la séquence complète du génome de la tomate vient d’être obtenue par le consortium international et une première version de ces données est disponible sur le site SGN ( http://solgenomics.net/tomato/ ).

Techniques utilisées par le CNRGV

Responsable : Sonia VAUTRIN

- Criblage sur Macroarrays
 - Production de pools en 3D DNA: banque SL_MboI et SL_HindIII
 - Criblage sur pools

Seventh framework programmeFood Agriculture and Fisheries, Biotechnology

Coordinateur du projet

• Dr. Catherine Feuillet
   Institut National de la Recherche Agronomique-ASP
   Domaine de Crouelle
   234 Avenue du Brezet
   63100 Clermont-Ferrand
   France
    www.clermont.inra.fr/umr-asp

  E-mail : catherine.feuillet@clermont.inra.fr

Résumé

Depuis de nombreuses années, la grandeur et la complexité des génomes du blé, de l'orge et du seigle ont ralenti le développement des approches génomiques et de leurs applications dans l’amélioration de la production et la qualité des récoltes. Cependant, récemment, de nouvelles approches technologiques plus efficaces ont été développées et de nouvelles ressources on été générées qui permettent que des programmes de génomiques robustes puissent être envisagés pour les Triticeae.

TriticeaeGenome est conçu pour accomplir des progrès significatifs dans la génomique des Triticeae et soutenir la reproduction efficace de variétés améliorées pour l'agriculture européenne. Ce projet sera développé par :

•  La construction et l’ancrage des cartes physiques du blé et de l'orge pour les chromosomes 1 et 3 qui portent un grand nombre de caractères agronomiques importants (par ex. la résistance de maladie, la production et la qualité)

•  L’isolement de gènes et QTLs liés à la résistance à des maladies, le rendement et les caractères de qualité pour le blé et l'orge

•  L’identification et l’exploitation de nouveaux allèles pour les gènes isolés par l'utilisation de variants naturels et de populations mutées aussi bien que le germplasm sauvage

•  Le développement de nouvelles variétés pour les besoins des consommateurs et des agriculteurs à travers des approches moléculaires

•  Le développement de nouveaux outils bioinformatiques pour structurer, centraliser et analyser à grande échelle les données génomiques qui seront générées dans ce projet

•  La mise en place de formation pour ces nouvelles approches technologiques, le partage des résultats et les transferts technologiques à l'industrie et aux collaborateurs internationaux.

Triticeaegenome est mis en place comme une contribution majeure aux efforts de consortiums internationaux dans le fait de construire des cartes physiques d'orge et de blé hexaploïde pour l’amélioration de l’agriculture, l'accélération de l'isolement de gènes et QTL et la mise en place de bases solides pour les prochains programmes de séquençage de ces génomes.

Triticeaegenome donnera des informations et des outils originaux aux éleveurs et aux scientifiques pour une meilleure compréhension de l'organisation des génomes des Triticeae, leur évolution et leur fonction, en fournissant une meilleure compréhension de la biologie de ces plantes cultivées essentielles.
liens utiles :

http://tritigen.ari.gov.cy/
http://www.wheatgenome.org/
http://urgi.versailles.inra.fr/Projects/TriticeaeGenome

Implications du CNRGV

Responsable : Arnaud Bellec/ Sonia Vautrin

- Conservation de banques BAC chromosome spécifique du blé.
 - Rearrangement du Minimum Tilling Path
 - Production de pools 3D sur les banques BACs chromosomes spécifiques Blé et sur la banque BAC Orge

Laboratoires partenaires

•  Institut National de la Recherche Agronomique - INRA - France
•  Leibniz Institute of Plant Genetics and Crop Plant Research - IPK - Germany
•  Institute of Experimental Botany - IEB - Czech Republic
•  GSF- National Research Center for Environment and Health - GSF - Germany
•  Università degli Studi di Milano - UMIL - Italy
•  University of Haifa - HU - Israel
•  MTT (Maa- ja elintarviketalouden tutkimuskeskus) - MTT - Finland
•  Scottish Crop Research Institute - SCRI - UK
•  Sabanci University - SABA - Turkey
•  National Institute of Agricultural Botany - NIAB - UK
•  John Innes Centre - JIC - UK
•  Universität Zürich - UZH - Switzerland
•  INRA Transfert - IT - France
•  Biogemma - BGA - France
•  Lochow-Petkus GmbH - LP - Germany
•  Istituto di Genomica Applicata - IGA - Italy
•  University of Bologna -UNBO - Italy

Etude de la Résistance du tournesol au mildiou (  Plasmopara halstedii )

Coordinateur du projet

•  Dr. Patrick Vincourt

  LIPM (UMR 441-2594 INRA-CNRS)
  BP 52627
  Chemin de Borde Rouge - Auzeville
  31326 Castanet Tolosan
  Email :   patrick.vincourt@toulouse.inra.fr

Résumé

Le mildiou du Tournesol causé par Plasmopara Halstedii est l’une des affections les plus potentiellement dangereuses en Europe. Son développement est favorisé par les pluies de printemps, dont la fréquence peut s’accroître du fait de la tendance à encourager les semis précoces pour faire bénéficier la culture, à des fins d’augmentation de la productivité, d’un apport en eau plus important. De façon concomitante au développement de culture, les variétés ont apporté des facteurs de résistance très efficaces à court-moyen terme, mais ceux-ci ont été peu à peu contournés par l’apparition de nouvelles races du parasite. Ce projet se propose de développer des outils et des connaissances dont la prise en compte globale permettra d’élaborer des stratégies de mise en œuvre d’une résistance durable, par la création et l’exploitation de ressources génétiques de Plasmopara halstedii en vue d’analyser la variabilité naturelle des populations du parasite et de progresser dans la connaissance et l’identification des pathotypes, l’identification et la cartographie de nouvelles sources de résistance race spécifique déjà recensées au sein d’un vaste ensemble de ressources génétique du genre Helianthus, la cartographie fine et les premières étapes du clonage positionnel d’un QTL de résistance quantitative partielle, Et la construction d’une ressource génétique Tournesol qui permettra ultérieurement l’analyse plus fine de l’interaction hôte-parasite dans l’espace et dans le temps.

Liens: 

http://lipm-helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start

http://www.heliagene.org/

http://www.heliagene.org/cgi/heliagene.cgi?__wb_session=WB12046189474944&__wb_main_menu=Collections&__wb_function=Collections
 

Implications du CNRGV

Responsable : Sonia VAUTRIN

Laboratoires partenaires

•  Laboratoire “ Interactions Plantes Microorganismes”, UMR 441-2594(INRA-CNRS)
   INRA-CNRS
   31326 CASTANET TOLOSAN

  Directeur du laboratoire : Pascal GAMAS
  Responsable scientifique : Patrick VINCOURT

•  UMR 1095 “ Amélioration et Santé des Plantes ”
   INRA – Université Blaise Pascal
   63100 CLERMONT-FERRAND

  Directeur du laboratoire : Gilles CHARMET
  Responsable scientifique : Felicity VEAR - D.TOURVIEILLE

•  UMR 1065 « Santé végétale »des Plantes
   INRA/ENITA Bordeaux
   33883 VILLENAVE-D'ORNON CEDEX

  Directeur du laboratoire : D. THIERRY
  Responsable scientifique : F. DELMOTTE

•  UR 1258 Centre National de Ressources Génomiques Végétales
   CNRGV -INRA
   31326 CASTANET TOLOSAN

  Directeur du laboratoire/Responsable scientifique : Helène BERGES

Validation fonctionnelle de gènes candidats pour un QTL à spectre large agissant sur la résistance aux Phytophthora  chez les Solanacées

Projet ANR - Réseau de Génomique Végétale - Génoplante 2010

Coordinateur du projet :

Dr. Véronique Lefebvre
 INRA-UR1052-GAFL
 Caractérisation Fonctionnelle des interactions Plantes-Bioagresseurs
 BP94 - 84140 Montfavet - France
 Email: veronique.lefebvre@avignon.inra.fr

Site web:
  http://www.avignon.inra.fr/les_recherches__1/liste_des_unites/genetique_et_amelioration_des_fruits_et_legumes

Résumé :

Les Phytophthora sont les parasites les plus dévastateurs des Dicotylédones. La lutte chimique a été interdite par la commission européenne. Les résistances monogéniques sont fréquemment contournées. Bien que les résistances polygéniques aient été démontrées plus durables, leurs bases moléculaires demeurent inconnues.
 Nous avons pour objectif de déterminer la nature moléculaire d’un QTL impliqué dans la résistance à plusieurs espèces de Phytophthora chez les Solanacées. Ce QTL, Phy-P5, confère un niveau élevé de résistance à plusieurs isolats de P. capsici chez le piment et montre une position colinéaire avec des QTL de résistance à P. infestans chez la tomate et la pomme de terre. L’analyse génétique du locus Phy-P5 a permis d’identifier deux QTL finement liés dans 0.57 cM. Deux clones BAC contenant chacun un des deux gènes sous-jacents à Phy-P5 seront séquencés, annotés, et ancrés à la carte génétique en 2007, afin de sélectionner les gènes candidats.
 Les objectifs du projet PHYTOSOL-2 sont de valider les gènes candidats identifiés pour le QTL Phy-P5, et de développer un système modèle facilitant la caractérisation fonctionnelle des gènes impliqués dans l’interaction Phytophthora/Solanacées.
 La variation naturelle dans les séquences des gènes candidats sera analysée chez les lignées parentales et plusieurs accessions de piment (EcoTILLING). Nous identifierons les domaines fonctionnels des gènes par analyse de recombinants intragéniques et séquençage d’allèles chimères. La validation des gènes candidats sera réalisée par transformation via Agrobacterium rhizogenes chez le piment, et par transformation stable chez la tomate. L’expression spatio-temporelle des gènes identifiés et les cascades de transduction du signal induites seront déterminées chez le piment et/ou la tomate. La validation fonctionnelle des gènes impliqués dans les réponses induites sera réalisée par génétique inverse en exploitant la plateforme TILLING de la tomate. Enfin, les résultats obtenus seront exploités pour améliorer la sélection de plantes résistantes aux Phytophthora.

Techniques utilisées par le CNRGV :

Responsable : Sonia Vautrin

- Construction de pools piment "Capsicum annum HD208" en deux dimensions
 - Criblage des pools d' ADN, par PCR Quantitative en temps réel
 - Séquençage des BACs Ends
 - Agencement des clones BACs sur la carte physique du QTL phy-P5

Laboratoires partenaires :

•  Unité de Génétique et Amélioration des Fruits et Légumes
   INRA-GAFL, UR1052
   84143 Montfavet Cedex
    Directeur du laboratoire : Mathilde Causse
    Responsable scientifique : Véronique Lefebvre

•  Unité de Recherche en Génomique Végétale
   URGV, UMR1165
   INRA-CNRS-Univ
   91057 Evry Cedex
    Directeur du laboratoire : Michel Caboche
    Responsable scientifique :Abdelhafifid Bendahmane

•  Centre National de Ressources Génomiques Végétales
   INRA-CNRGV, UR1258
   31326 Castanet Tolosan Cedex
    Directeur du laboratoire / Responsable scientifique :  Hélène Bergès