African Rice (Oryza glaberrima) Salinity Tolerance and Genetic Variation Across Coastal West Africa

Introduction- High salinity affects 50% of global irrigated land area. Farmers in the Atlantic Coast region stretching from Senegal to Liberia plant indigenous crops that are tolerant to saline conditions, and this project focuses on one such crop, African rice (Oryza glaberrima Steud.). African rice is irrigated by rivers with a conspicuous salinity gradient. Thus, the agricultural system developed for African rice implies that varieties have been arranged with matched fitness to local saline levels. However, farmers also practice agriculture in unique ways including dyking of mangrove swamps, soil overturning, and sometimes desalination, which spurs questions about the nature of selection on African rice. How has the O. glaberrima genome changed to tolerate salinity? Do tolerant varieties more frequently occur in coastal saline areas?

Methods- We selected 100 African rice landraces from upland and coastal West African environments and screened landraces for salinity tolerant phenotypes. Phenotypes were correlated with each other and with location. We then performed whole genome sequencing on these 100 landraces using Illumina HiSeq aiming for 10x coverage. POPBAM and STRUCTURE were used to conduct population genetic analyses. Candidate genes involved in domestication, diversification, and salinity tolerance in Asian rice were mapped to explore patterns of parallel selection.

Results- Twenty percent of landraces were highly tolerant to saline conditions, although leaf relative [Na+]/[K+] concentrations suggest there are multiple strategies for tolerance. We built a SNP map for O. glaberrima and identified DNA regions that distinguish landraces from different environment types and with different levels of salinity tolerance. Examination of the genome identified several regions with high LD, but without strong decreases in nucleotide diversity. Diversity was high and comparable to Indica rice. Surprisingly few domestication, diversification, or salt tolerance genes underwent parallel selection in African rice, suggesting unique adaptations.