JEAI ModelCaf: Integration of a genetic module within the GreenLab model, 2015-2017, funding from IRD, C2D-AGURES (J Lorougnon Guédé University, Ivory Coast), CIRAD and SCAC. http://modelcaf.net/
Leader : Selastique D. Akaffou (J Lorougnon Guédé University, UJLoG, Ivory Coast)
Partners from the North: Perla Hamon and Serge Hamon (IRD, DIADE), Romain Guyot (IRD, IPME), Sylvie Sabatier, Marc Jaeger and Philippe de Reffye (CIRAD, AMAP), Véronique Letort (CentraleSupelec, MICS)
Partners from the South: Hyacinthe Legnaté and Désiré Pokou (CNRA), Kouassi H Kouadio, Olivier N Konan and Amadou Kamagaté (UJLoG)
Key words: GreenLab, Coffee, architecture, functioning, simulation, genetic module
The overall objective of the project is to increase the performance of the GreenLab model in terms of forecasting and optimizing coffee production. In more details the project aim to i)- identify QTLs of architecture, production and estimated endogenous parameters, and iii) to implement the GreenLab model with genetic data.
Genome13: Comparative genomics in coffee trees. 2015-2020. Funding: contributions from the public and private partners of the consortium.
Leaders: Perla Hamon (DIADE ) and shared coordination with R Guyot (IPME) since 2017.
Partners from the North : Giovanni Giuliano (ENEA, Italy), Emmanuel Couturon, Serge Hamon,
& Alexandre de Kochko (IRD, DIADE), Romain Guyot (IRD, IPME), Victor A. Albert (University at Buffalo, USA), Dominique Crouzillat (Nestlé R & D, Tours), Robert J Henry (University of Queensland, Australia).
Partners from the South : Douglas S. Domingues (FUT, Brazil), Luiz Filipe Pereira (EMBRAPA, Brazil), Selastique Akaffou (UJLoG, Ivory Coast), Hosahalli Sreenath (CBI, India), Sylvain Razafimandimbison (SMNH, Sweden), Jean-Jacques Rakotomalala and Nathalie Raharimalala (FOFIFA, Madagascar).
Key words: coffee trees, comparative genomics, genomes evolution
The overall objective of the project aim to a better understanding of the evolutionary history of the coffee trees permitting a better preservation and use of the available genetic resources based on whole genome sequencing of small (Illumina,) and long reads (PacBio) of currently 65 and seven species respectively.
More specifically, the goals are i) - to establish the maternal phylogeny of the genus, ii) - to analyze the dynamics of transposable elements and to compare gene contents, iii) - to study the genetic and functional basis of traits of interest for varietal improvement; and (iv) ultimately fostering the preservation and enhancement of genetic resources in a context of sustainable development.
ACGC Arabica Coffee Genome Consortium
Sequencing the Coffea arabica genome
Coordinators: Alexandre de Kochko & Dominique Crouzillat (Nestlé R&D, France)
Partners: 14 countries, 26 Institutions, 65 members
Keywords: Whole Genome Sequencing, Polyploidy, C. arabica, C. canephora, C. eugenioides, genetic mapping, genome evolution, gene loss
Produce a high quality C. arabica genome from a di-haploid.
Produce a version 2 of the C. canephora genome and a version 1 of that of C. eugenoides.
Differentiate the two sub genomes of C. arabica.
Realize a fine gene annotation using RNASeq from Illumina and full length cDNA sequences (Iso-Seq from PacBio).
Assess structural effects of polyploidization.
Catalog genetic diversity in C. arabica through re-sequencing of multiple wild and cultivated accessions.
Realize a population genomics analysis.
Make data easily accessible to breeders and researchers through a web interface by establishing a devoted website and using the existing Sol genomics and MoccaDB websites.
Drought and temperature stress adaptation in Coffea canephora: from candidate genes to drought tolerant variants
Responsibles: Valérie Poncet (UMR DIADE, DYNADIV) & Alan Andrade (EMBRAPA café, Brazil)
Partners from the North: Alexandre de Kochko (UMR DIADE, EVOGEC), Christine Tranchant-Dubreuil (UMR DIADE, RICE), Pierre Marraccini (CIRAD), Dominique Crouzillat, Olivier Daracq (Nestlé R&D), Anten Niels, Aad van Ast (Univ. Wageningen, The Netherlands)
Partners from the South: Luciano V Paiva, (Univ. Lavras, Brazil), Gustavo C Rodrigues, Milene A Carvalho, Antônio F Guerra, Gabriel F Bartholo (EMBRAPA, Brazil), Andrew Kiggundu, Pascal Musoli, Catherine Kiwuka (NARO, Uganda
Keywords: Coffea, drought tolerance traits, candidate genes, Next Generation sequencing (NGS), natural habitats, wild crop relatives (WCR), climate resilient varieties.
Objectives: The aim of this project is to explore the natural genetic variability of C. canephora (the second most widely cultivated Coffee tree species) in response to changing climate conditions.
Three main addressed issues are: i) to assess the diversity of drought-tolerance traits in C. canephora in a large set of both cultivated and wild accessions from Brazil and Uganda; already characterized drought tolerant and drought sensitive clones of the conilon variety from Brazil will be used as controls as well as a representative subset of each of the diversity groups for the whole Robusta diversity; ii) to identify and characterize the allelic diversity (SNPs) at both drought- tolerant candidate genes and genome wide level using last generation sequencing techniques, and iii) to conduct a detailed analysis of the relationship between climate variation and C. canephora genetic variation at drought-tolerance candidate genes using the geographic distribution of wild populations with contrasted habitats.