Projects

ARCAD (2009-2015) - Funded by Agropolis Fondation

Project coordinator : JL Pham

Other scientists involved from our team : JL Pham, Y Vigouroux, AC Thuillet, G Bezançon, C Mariac, JC Pintaud, N Scarcelli

The ARCAD scientific project aims to contribute to a better conservation and use of Mediterranean and tropical crop genetic resources. It is focused on the study of the relationship between crop diversity and the processes of domestication and adaptation to the agricultural environment. Understanding how genes and genomes have been shaped by history, environment and societies is a key factor to enhance the quality and sustainability of germplasm conservation and use. The scientific project is set on a limited number of priorities :

· The study of the history and patterns of crop domestication and adaptation

· The analysis of the key parameters underpinning adaptation, at various time scales, through studies of evolutionary genomics and population genetics.

The ARCAD scientific project includes several research sub-projects addressing these priorities as well as technological, methodological and capacity building components which aim at supporting these sub-projects, at strengthening the overall consistency and enhancing the attractiveness of the entire ARCAD project.

Associated publications:

Cubry P, Pidon H, Ta KN, Tranchant-Dubreuil C, Thuillet AC, Holzinger M, Adam H, Kam H, Chrestin H, Ghesquière A, François O, Sabot S, Vigouroux Y, Albar L, Jouannic S (2020) Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima. Rice 13:66

Scarcelli N, Cubry P, Akakpo R, Thuillet AC, Obidiegwu J, Baco MN, Otoo E, Sonké B, Dansi A, Djedatin G, Mariac C, Couderc M, Causse S, Alix K, Chaïr H, François O, Vigouroux Y (2019) Yam genomics supports West Africa as a major cradle of crop domestication. Science Advances 5(5):eaaw1947

Assoumane A, Blay C, Sanda AA, Mariac C, Pham JL, Bezançon G, Vigouroux Y (2018) Wild crop relative populations hot-spots of diversity are hot-spots of introgression in the case of pearl millet. Genetic Resources and Crop Evolution 65:1187-1194

Burgarella C, Cubry P, Kane NA, Varshney RK, Mariac C, Liu X, Shi C, Thudi M, Couderc M, Xu X , Chitikineni A, Scarcelli N, Barnaud A, Rhoné B, Dupuy C, François O, Berthouly-Salazar C, Vigouroux Y (2018) A western Sahara origin of African agriculture inferred from pearl millet genomes. Nature Ecology and Evolution 2:1377-1380

Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie MN, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y (2018) The rise and fall of African rice cultivation revealed by analysis of 246 new genomes. Current Biology 28:2274-2282.e6

Magwé-Tindo J, Wieringa JJ, Sonké B, Zapfack L, Vigouroux Y, Couvreur TLP, Scarcelli N (2018) Guinea yam (Dioscorea spp.) wild relatives identified using whole plastome phylogenetic analyses. Taxon 67(5):905-915

Ambrósio Moreira P, Mariac C, Zekraoui L, Couderc M, Garcia Luize B, Picanço DR, Clement CR, Vigouroux Y (2017) Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin. Evolutionary Applications 10(6):577-589

Barnaud A, Vigouroux Y, Diallo MT, Saidou S, Piquet M, Barry MB, Bakasso Y, Zekraoui L, Rivallan R, Kane NA, Billot C (2017) High selfing rate inferred for white fonio [Digitaria exilis (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs. Genet. Res. Crop. Evol 34:1485-1490

Moussouni S , Pintaud JC, Vigouroux Y, Bouguedoura N (2017) Diversity of Algerian oases date palm (Phoenix dactylifera L., Arecaceae): Heterozygote excess and cryptic structure suggest farmer management had a major impact on diversity. PLoS ONE 12(4):e0175232

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M (2016) A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Ressources 17:565-580

Burgarella C, Chantret N, Gay L, Prosperi JM, Bonhomme M, Tiffin P, Young ND, Ronfort J (2016) Adaptation to climate through flowering phenology: a case study in Medicago truncatula. Molecular Ecology 25(14): 3397-3415

Mariac C, Ousseini IS, Alio AK, Judgé H, Pham JL, Bezançon G, Ronfort J, Descroix L, Vigouroux Y (2016) Spatial and temporal variation in selection of genes associated with pearl millet varietal quantitative traits in situ. Frontiers in Genetics 7:130

Ta KN, Sabot F, Adam H, Vigouroux Y, DeMita S, Ghesquiere A, Vinh DN, Gantet P, Jouannic S (2016) miR2118-triggered phased siRNAs are differentially expressed duringthe panicle development of wild and domesticated African rice species. Rice 9(1):10

Saïdou AA,Clotault J, Couderc M, Mariac C, Devos KM, Thuillet AC, Amoukou IA, Vigouroux Y (2014) Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. Theo Appl Genet 127(1):19-32

Saïdou AA, Thuillet AC, Couderc M, Mariac C, Vigouroux Y (2014) Association studies including genotype by environment interactions: prospects and limits. BMC Genetics 15(3)

De Mita S, Thuillet AC, Gay L, Ahmadi N, Manel S, Ronfort J, Vigouroux Y (2013) Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations. Mol Ecol. 22:1383-1399

Vigouroux Y, Barnaud A, Scarcelli N, Thuillet AC (2011) Biodiversity, evolution and adaptation of cultivated crops. CR Biol 334(5-6):450-457

Mariac C, Jehin L, Saïdou AA, Thuillet AC, Couderc M, Sire S, Jugdé H, Adam H, Bezançon G, Pham JL, Vigouroux Y (2011) Genetic basis of pearl millet population adaptation along an environmental gradient investigated by a combination of genome scan and association mapping. Mol Ecol 20:81-91