Genome-wide patterning in African rice (Oryza glaberrima) landraces helps to explain adaptation to saline landscapes and the historic coevolution between plants and human agroecological practices

African rice (Oryza glaberrima Steud.), domesticated in the Niger river delta, was brought into coastal saline environments where conscious selection for salt tolerance has been reported. West African farmers also minimize salt stress through indigenous technologies. Because high salinity affects 50% of global irrigated land, we chose to trace this evolutionary interaction between agronomic strategy and the genome under selection. The alleles underlying tolerance and adaptation to new environments while undergoing selection to meet human food preferences, were previously unknown.  

102 landraces were phenotyped and whole genome resequenced at >10x nuclear coverage. DNA variants were analyzed for population structure and regions under selection. Phenotypes and sequences were correlated with each other and with both geographic origin and climatic data. We found strong salt tolerance in 20% of the landraces. Genome-wide patterns found relevant to domestication, landscape changes, and salt tolerance, reveal the unique evolution of African rice under human selection.