The SP5 sub-project Pangenomic study of diversity was an exploratory project, giving the opportunity to evaluate the potential of NGS for the analysis of pangenomic diversity even in the case of highly heterozygous, unsequenced and/or orphan species.
The program of SP5 sub-project began later than the other ARCAD Sub Projects, since we have modified the objectives from the initial (2009) SP on linkage disequilibrium. The first meeting has been organized in November 2012 in order to launch the project and to decide on the species to be analyzed. In the “ARCAD progress report 2013” a first list of species was given, based on previous expressions of interest.
Due to unavaibility of biological material (leaf samples of accessions or DNA samples of sufficient quality) or of the launching of complementary research projects in the meantime, the list of species effectively studied in the WP1 was reduced and is given in Table SP5-1. This allowed us to increase the sequencing effort on the remaining species.
Four of the species studied in SP5 were also included in the SP1 sub-project (Cotton, Coffea canephora, Olive tree and Grapevine). It will allow comparing the data and results produced by the SP1 sub-project to those obtained using the genomic reduction method. These results will be useful to the entire ARCAD community.
Table SP5-1. List of the crops studied in ARCAD/SP5 and corresponding scientist
|WP1||Coffee (Coffea arabica, C. canepora & C. arabusta)||Thierry Leroy (UMR-AGAP)|
|WP1||Cotton (Gossypium hirsutum & G. herbaceum)||Jean-Marc Lacape (UMR-AGAP)|
|WP1||Coconut (Cocos nucifera)||Luc Baudouin (UMR-AGAP)|
|WP1||Breadfruit (Artocarpus altilis)||Jean-Pierre Labouisse (UMR-AGAP)|
|WP1||Citrus spp.||Patrick Ollitrault (UMR-AGAP)|
|WP2||Grapevine (Vitis vinifera)||Agnès Doligez (UMR-AGAP)|
|WP2||Olive tree (Olea europaea)||Bouchaïd Khadari (UMR-AGAP)|
|WP2||Rubber tree (Hevea brasiliensis & Hevea benthamiana)||Marc Seguin (UMR-AGAP)|