Projects

AfriCrop (2013-2018) - Documenting African Crop Domestication - Funded by ANR (France)

Project leader: Y Vigouroux

Scientists involved from our team : Y Vigouroux, N Scarcelli, C Mariac, M Couderc, AC Thuillet, A Barnaud, Y Vigouroux

The development of sedentary societies is tightly linked to the development of agriculture. Several scenarios about the time and speed of the settlement of agricultural societies in the different continents are still under debate. The study of the origin, domestication process and spread of different co-existing crops significantly improves our knowledge about how, when and where such societies developed. In this project, we will address the study of the least studied domestication center: Africa. We will document the evolutionary history of several African crops. We plan to study the geographic origin, the spread dynamics and timing of their domestication. We will address long standing biological and social hypotheses about agriculture origin in order to cross-validate multidisciplinary scenarios of crop domestication in Africa.

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

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

Akakpo R, Scarcelli N, Chair H, Dansi A, Djedatin G, Thuillet AC, Rhone B, Francois O, Alix K, Vigouroux Y (2017) Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. BMC Genomics 18:782

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

Cubry P, Vigouroux Y, François O (2017) The Empirical Distribution of Singletons for Geographic Samples of DNA Sequences. Frontiers in Genetics 8:139

Scarcelli N, Chaïr H, Causse S, Vesta R, Couvreur T, Vigouroux Y (2017) Crop wild relative conservation: wild yams are not that wild. Biological Conservation 210:325-333

Varshney R, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava R, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta S, Wang H, Jiang Y, Couderc M, Katta M, Paudel D, Mungra K, Chen W, Harris-Shultz K, Garg MV, Desai N, Doddamani D, Kane N, Conner J, Ghatak A, Chaturvedi P, Subramaniam S, Yadav O, Berthouly-Salazar C, Falalou H, Wang J, Liang X, Clotault J, Upadhyaya H, Cubry P, Rhoné B, Gueye M, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala R, Singh B, Yadav R, Lyons E, Datta S, Hash C, Devos K, Buckler E, Bennetzen J, Paterson A, Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif J, Liu X, Vigouroux Y, Xu X (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology 35:969-984

Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc'h JB, Vigouroux Y (2016) Genotyping-by-sequencing SNP identification for crops without a reference genome: using transcriptome based mapping as an alternative strategy. Frontiers in Plant Science 7:777

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y (2016) Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?. Molecular Eciology Resources 16(2):434-445