Cocoa pods, Venezuela. Photo: C.Lanaud ©CIRAD
Arabica coffee, Ethiopia. Photo: ©Jean-Pierre Labouisse
Yams in Benin. Photo: J-L Pham ©IRD
Rice harvest, Guinea. Photo: J-L Pham ©IRD
Maize corn. Photo: ©Brigitte Gouesnard

Objectives and general methodology

Main objectives

First, we conducted comparative analyses of the effect of domestication on genome evolution in different crop species to:

  • quantify the loss/recovery of diversity associated with domestication;
  • identify the genes selectively involved in the domestication process;
  • investigate variations in domestication patterns among crop species based on their life history, domestication depth, or phylogenetic position.

Second, we  investigated the genomic selective patterns among angiosperm species and possible causes of variation using a comparative approach, taking into account the life-history traits and the genomic environment (GC-content, BGC) of the species to:

  • quantify the whole genome level of selective constraints and the proportion of adaptive substitutions;
  • test the predictions of the effects of life-history traits (breeding systems, life span) on polymorphism within species and divergence among species;
  • investigate the phylogenetic distribution of the BGC process in angiosperms, and how it affects selective patterns.

Third, we investigated in more detail how genes functionally evolve in the different species to:

  • identify general tendencies, in terms of gene or gene family content, along the angiosperm phylogeny and lineage-specific families, subfamilies or clades;
  • compare selective constraints between genes from different functional categories, and genes belonging to subfamilies with different expansion dynamics;
  • quantify selective constraints in gene families involved in specific metabolic networks.

This project also demonstrated that such investigation can be made on orphan species as well as on model species. The Montpellier community, enlarged to Avignon, has acknowledged competences on tropical and Mediterranean crops and the management of their genetic resources. Using these resources, network and knowledge, the project proposes a joint action: 13 crops were finally recruited and funded by ARCAD : coffee, vine grape, diploid wheat (einkorn), yam, banana, palm tree, African rice (O. glaberrima), fonio, sorghum, cocoa, alfalfa, pearl millet and tomato. Two other species joined the project on their own funding for data production and benefited from the project’s infrastructure: cotton and olive tree. As two outgroup species are used for phylogenetic purposes, 45 species are finally involved in the study.

General approach

For each crop, genetic diversity was first investigated in 10 cultivated and 10 wild individuals and phylogenetic patterns were established using 2 outgroups species, whose genomes are somewhat divergent from the crop. Each out of the 15 crops is thus represented by a quadruplet (figure 1).


Figure 1: Species sampling design

We will compare 11 quadruplets of diploid species with contrasted life-history traits, across the angiosperm phylogeny (Table 1). 

Table 1. List of studied crops

Crop Family Domestication Cultivated taxon Life span Mating system Life form Outgroups
African rice Poaceae Old Oryza glaberrima Annual selfing herb O. sativa, O. meridionalis
Banana Musaceae Old Musa acuminata perennial outcrossing herb M.balbisiana, M. becarii
Cocoa Malvaceae Old Theobroma cacao perennial mixed tree T. speciosa, Herrania nitida
Coffee Rubiaceae recent Coffea canephora perennial outcrossing tree Empogona ruandensis, Bertiera laxa
Einkorn wheat Poaceae Old Triticum monococcum Annual selfing herb Eremopyrum bonaepartis, Taeniatherum caput-medusae
Grapevine Vitaceae Old Vitis vinifera ssp. sativa perennial outcrossing vine V. romaneti, V. riparia
Medicago Fabaceae Old Medicago sativa perennial outcrossing herb M. truncatula ,M. marina
Oil palm Arecaceae ? Elaeis guineensis perennial outcrossing tree Phoenix dactylifera, Mauritia flexuosa
Pearl millet Poaceae Old Pennisetum glaucum Annual outcrossing herb P. polystachyion, P. alopecuroides
Sorghum Poaceae Old Sorghum bicolor ssp bicolor Annual selfing herb S. brachypodium, Zea mays
Tomato Solanaceae Old Solanum lycopersicum Annual selfing herb Capsicum annuum, Solanum melongena
Yam Dioscoreaceae Old Dioscorea rotundata perennial outcrossing herb D. trifida, D. alata
Fonio Poaceae Old ? Digitaria exilis Annual selfing herb D. longiflora, D. sanguinalis
Cotton Malvaceae Old Gossypium hirsutum Annual selfing shrub G. barbadense, G. mustelinum, G. raymondii;G. herbaceum
Olive tree Oleaceae Old Olea europea perennial outcrossing tree Phillyrea latifolia

For each quadruplet, the domestication process will be investigated by comparing gene polymorphism patterns between the wild and the domesticated species. Selective constraints, adaptive evolution, and GC-content evolution will be investigated using classical frameworks, and both polymorphism and divergence data and recent tools developed by the ISEM partner. It is worth noting that model species that still have numerous genomic resources will also be used in the comparison. Data are about several thousands of genes in each quadruplet. The SP1 project also aimed at using local resources and at developing up to date skills and capacity in NGS pre and post-processing.

To address these questions it is still neither possible nor reasonable to sequence full genomes. Instead, we propose to focus on the expressed portion of the genome to obtain information on the maximum possible number of genes and hence to draw a general and comparable picture between different species. We thus aim to gather large amounts of polymorphism and divergence data by sequencing the transcriptome of each species, using 454 Roche GsFlex technology.

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