RICE

Rice, Interspecies Comparison & Evolution

Research focuses

RICE team's activities are focused on biological questions in relation to interspecific hybrids in rice and the identification and transfer of genes of interest. Asian cultivated rice, Oryza sativa, is a staple food for a large part of the world population and yield increase is one of the major challenges of coming years. Wild rice species or African cultivated rice, O. glaberrima, particularly adapted to biotic and abiotic stresses specific to Africa, constitute major sources of genes or alleles of interest. We aim at studying some of these genes or traits, using adapted genetic and genomic resources we have developed. However, their transfer to O. sativa is often impaired by interspecific sterility barriers and possible genomic instability. We also aim at understanding these mechanisms and developing resources able to facilitate interspecific introgressions.

 

Main projects

 

Development of genetic resources

We have gathered a collection of nearly 300 accessions of cultivated and wild African rice. This collection was characterized by SNP genotyping and high-depth sequencing of about 200 accessions is underway. We also developed interspecific bridges or "iBridges" based on the counter-selection of a sterility gene (see 4) and aiming at facilitating the interspecific introgression of  O. glaberrima alleles into O. sativa. Finally, NAM (Nested Association Mapping) populations derived from crosses between indica and japonica subspecies were developed and genotyped by sequencing.

Arbreglabbarthii anglais

Major resistance genes against RYMV. Localization of the genes on rice genetic map and nature of two of them

Pan core genome

Pan and Core-genomes analyses for African Rices

The whole set of genomic sequences from a complete species is called the pan-genome, and gather the core-genome, which represents the set of sequences shared between all individuals from the considered species, and the dispensable, which is the variable part between individuals. Through massive sequencing, we analyse those pan and core genomes for cultivated and wild African rice species. We will then be able to identify allelic and genic variation linked to local adaptations or specific environmental conditions. Moreover, the analysis of the two compartments through the domestication process will allow us to better understand the effect of a speciation upon a plant genome.

Real time analysis of transposable element mobility

We have established a method to specifically sequence the extrachromosomal fraction of the mobile genome, or mobilome, in different species, and we applied the technique to identify active transposable elements in different rice varieties during development and in stress conditions. Candidate mobile transposable elements help us decipher the role of the epigenome in the control of genome stability in rice.

 

Genetic bases of the O. sativa et O. glaberrima hybrid sterility

The S1 gene is the main genetic factor involved in the reproductive barrier that separates the two cultivated species of rice, O. sativa et O. glaberrima. However, its mode of action remains largely unknown. We are studying the nature and biology of the S1 gene using approaches of expression analysis (in situ and Q-PCR), genetics, histology and transformation, carried out on interspecific materials.

 

Characterization of the genetic basis of resistance to Rice yellow mottle virus (RYMV) and its breakdown

Breeding for natural resistance against RYMV is considered as one of the most efficient way to control  this disease, endogenous to Africa. Resistance sources are rare in O. sativa, while they are both more frequent and more diverse in O. glaberrima. We aim at characterizing the resistance sources and genes, and their breakdown by the virus, to optimize resistance deployment strategies at field level.

Carte genes rymv angais

Genetic diversity of a collection of O. glaberrima and O. barthii  African rices, based on 235 SNP markers

Data integration for functional genomics

Data management in the context of the RICE team (data integration and multi-scale knowledge management) requires the deployment of particular architectures (distributed architectures, cloud, semantic integration via ontologies). We are particularly interested in massive data management (NGS, high throughput phenotyping, workflows) within the framework of collaboration with the Institute of Computational Biology in Montpellier (IBC).

Permanent staff, IRD

  • Laurence Albar, CR, head of team
  • Sophie Chéron, TR
  • Harold Chrestin, TR
  • Christine Dubreuil, IE
  • Alain Ghesquière, DR
  • Pierre Larmande, IE
  • Mathias Lorieux, DR, based at CIAT, Cali, Colombia
  • Marie Mirouze, CR, based at UPVD, Perpignan, France
  • François Sabot, CR

 

Non permanent staff and PhD students

  • Andres Gutiérrez, PhD student, 2011-2015
  • Cécile Monat, PhD student, 2013-2016
  • Hélène Pidon, PhD student, 2013-2016
  • Sophie Lanciano, PhD student, 2014-2017

Main collaborations

Upvd 1

Ibc

Ciat 1

Africa rice 2

Grisp

Southgreen 1

 

Other collaborations

  • CIRAD, SouthGreen
  • Laboratoire Mixte International LAPSE, IRD/UCAD, Sénégal
  • Laboratoire Mixte International PathoBios, IRD/INERA, Burkina Faso
  • Laboratoire Mixte International RICE, Vietnam
  • IRRI, Philippines
  • FAST/Dassa – Université D' Abomey-Calavi, Bénin
  • Université de Naples, Italie
  • Universidade Federal do Rio Grande do Sul, Brésil
  • The University of Sheffield
  • Yale University

 

Ongoing or recently funded projects

  • ANR JCJC, EXTRACHROM, coordination, 2014-2017
  • BBSRC, STRiGA, co-PI, 2013-2016
  • France Génomique Massive Sequencing, IRIGIN project, coordination, 2013-2017
  • ANR Blanc, AfriCrop, participant, 2013-2017
  • LABEX NUMEV, LANDPan-TOGGLE, coordination, 2015-2016
  • SPIRALES, MENERGEPdb, coordination, 2015
  • OpenScience Agropolis Fundation, SURvEY, coordination, 2015
  • FIRST Cariplo/Agropolis Fondation, EvoReprice, participant, 2013-2015
  • SPIRALES, Framboisine, coordination, 2014
  • OpenScience Agropolis Fondation, RETROCROP, coordination, 2013-2014
  • Global Rice Science Partnership, MENERGEP, participant, 2012-2014
  • OpenScience Agropolis Fondation, ChloroDiv, participant, 2013-2014

 

Publications >>>