Agropolis Resource Center for Crop Conservation, Adaptation and Diversity

Jean-Louis PhamJean-Pierre Labouisse

arcad@agropolis.fr

Research on plant genetic resources and agrobiodiversity in Montpellier

•Conservation•Evolution•Genetic diversity•Genomics•Information technology•Plant breeding•Social Sciences•Economics•Farming systems•Seed systems•...

Initiative oncrop biological resources

Financial support to new infrastructure/facilitiesfor the conservation and analysis of crop biological resources

Flagship scientific programme

Give Montpellier - Languedoc-Roussillon Regionworld-wide visibility in the field of agrobiodiversity,

plant genetics and genomics

Nurturing the future of crop biodiversity

•An open platform for genetic and genomic resource conservation, management and analysis

•A research programme addressing key challenges on Mediterranean and tropical crop diversity for agriculture and sustainable development

•A demand-oriented training platform for Southern scientific communities

Crop biodiversity research and resource center

• New facilities on the La Valette campus (> € 10M)(on-going decision process)– Conservation (PGR, genomic resources)– DNA analysis– Scientific exchanges, Training

• Scientific project (€ 3M, operational costs) 2009-2013– Agrobiodiversity preservation and exploration: going beyond the

freezer– Understand how human societies and environment have shaped plant

agrobiodiversity over time : Crop domestication and adaptation– Africa + Mediterranean regions

Crop biodiversity research and resource center

Why so much focuson crop domestication ?

12 000 BP TDWG 2009

AgricultureCrop domestication

Crop domestication :

How a never-ending story started

Farmers’ practicesIndigenous and non-indigenous knowledge

Genetic content and structure of crop species

Wild forms

migration

cultivationhybridizations

selectionmigration

etc

cultivation

Selectively neutral

under selection

Allele diversityCrop history

Crop genetic diversity has been shaped by domestication and successive events

Courtesy of JC Glaszmann

Association genetics : linking genotype and phenotype

History ofcrop populations

SP1 Comparative crop population genomics

SP2 Crop Adaptation

SP3 Cereals in Africa

Conservation of biological resources

Mediterranean and tropical plant genetic resources(Vitis, Medicago, Zea, rice, millets, Coffea, …)

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domestication bottlenecks, LD evolution…

rate of divergenceselection footprints…

SP1. Comparative crop population genomics :a phylogenetic and genome-wide approach of crop adaptation

Identify genomic selective patterns within and across crops

•High throughput bulk cDNA sequencing of a wide range of crops and wild relatives

•Bioinformatics analysis

>>mechanisms governing genome evolution>>influence of life history traits>>detection of selection footprints>>identification of agronomical genes

crop

wild

ancestor

relative 1

relative 2

molecular evolution

Crop Phylogeny Units Domestication Cultivated taxon Mating Life form

African Rice Poaceae old Oryza glaberrima A self Herb

Banana Musacées old Musa acuminata P out Herb

Cocoa Malvaceae DAP old Theobroma cacao P mixed tree

Coffea Rubiaceae recent C. canephora P out tree

Einkorn wheat Poaceae old A self Herb

Grapevine Vitaceae DIAPC old P Herm vine

Medicago Fabaceae DIAPC old medicago sativa P out Herb

Palm Arecaceae unknown Elaeis guineenis P out tree

Pearl millet Poaceae DIAPC old A out Herb

Sorghum Poaceae DAP old A self Herb

Tomato Solanaceae UGAFL old A self Herb

Life span

GDP/DAP/ UR AIVADAP / BGPI / UR 75

DIAPC/RPB/DAP

DIAPC /ISEM

Triticum monococcum

Vitis vinifera ssp. sativa

UPR 28/ DAP/ DIAPC

Pennisetum glaucum

Sorghum bicolor ssp bicolor

Solanum lycopersicum

SP1. Comparative crop population genomics-Studied crops

Studying genetic and evolutionary processes of adaptation a focus on phenological responses

Spatial gradients: populations/varieties collected along climatic gradients.

• M. truncatula : Latitudinal variation around the Mediterranean basin• rice : altitudinal variation (Madagascar)• pearl millet and sorghum : latitudinal gradient in West Africa.

Temporal gradients : comparing current populations/varieties and populations collected 20-30 years ago in the same sites • M. truncatula• pearl millet• rice

>>> Develop statistical and methodological tools to detect selection footprints along environmental gradients and over time.>>> Ecogeographical distribution of alleles of agronomical interest

SP2. Crop adaptation to climate change

1976 germplasm collection 2003 Sampling in the same locations

Changes in pearl millet diversity in Niger (1976-2003)

Conservation at 4ºCfor 27 years

DNA markeranalysis

Morphological and phenological analysis

Conservation at 4ºCfor 27 years

Passeport dataon landraceaccessions

Bezancon et al. 2008, Vigouroux et al. submitted .

1976 2003

Pluviometry isohyetes from 1950 to 1976 Pluviometry isohyetes from 1977 to 2003

cycle duration

Rapid changes in phenology of pearl millet landraces in Niger

Flowering time of Pearl millet in Niger

1976

2003

50-55 days55-60 days60-65 days65-70 days70-75 days

75-80 days

80+ days

Saidou et al. 2009, Vigouroux et al, submitted

2005 field trial

2004 field trial

F=7.4, P<0.001 F=10.4, P<0.001

F=11.8, P<0.001 F=7.8, P<0.001

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Flowering time Panicle length

Phytochrome C gene -- SNP 101

candidate gene, association analysis (pearl millet)

Association between PhyC and flowering time

Flowering in Arabidopsis, Komeda, 2004. Ann. Rev. Plant Biol.

Rice

Pearl Millet

Sorghum

Corn

SP3. Cereals in Africa

• Rice, Millet, Sorghum, Corn, Durum Wheat

•Domestication history•Diffusion, Adoption

•Impact of cultural and socioeconomic factors on crop diversity

>>> In situ diversity of crops and wild relatives>>> Diffusion of innovation>>> From advanced to underutilized crops

Guinea, 2007

Durum wheat

media-2.web.britannica.com

SP8 Training

Conservation of biological resources

- PGR - passeport data - New entries and data - Conservation strategies

SP7 CryopreservationSP6 DNA bank- samples conservation- traceability- transferable technology

Methods for detection of selection

Additional data on crop adaptation

Comparative crop population genomics

SP2 Crop Adaptation

SP3 Cereals in Africa

Genome wide SNP Knowledge on genome evolution

Intra-specific effects of selectionSP4

Bioinformatics

- Databases- Assembling- Sequence annotation- SNP detection- Web interfaces - Methodology

- Methodology- Population structure- Validation

SP5Linkage

Disequilibrium

SP8. Training

• Already planned– Bioinformatics

– Molecular evolution

– Cryopreservation

– Agrobiodiversity analysis (multidisciplinary approach)

• Involve South and international partners– International course on Agrobiodiversity

• 2008: Montpellier• 2010: Morocco (IAV Hassan II)

AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse

Montpellier-Carnon17-28 novembre 2008

Ecole thématique internationale

AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse

Montpellier-Carnon17-28 novembre 2008

Ecole thématique internationale

AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse

Montpellier-Carnon17-28 novembre 2008

Ecole thématique internationale

ARCAD : study countries (2009)

As an open platform, ARCAD will continuously seek new partnerships

• Data– Germplasm collections, DNA collections– Genotypes (SSR, SNPs, sequences), Phenotypes– Environmental data– Indigenous knowledge

• Technical and legal issues– Data management– Data access/sharing

• Plant, DNA, society and data explorers,“cross-disciplinary pollinators”, …

• Ontologists• Data quality managers• Information disseminators• …

Information: a key issue for ARCAD

Thank you