Genomic prediction of vulnerability of African crops to future climate – AfrADAPT

Humanity relies largely on a small number of crops for its subsistence. A major challenge facing agriculture is adaptation to ongoing climatic changes. Using existing crop species varietal diversity and the promotion of crop varietal replacement is viewed as an efficient short-term strategy for rapid adaptation to environmental changes. Recent advances in the field combine genomic diversity with environmental data to identify areas where varieties of a cultivated species are highly vulnerable or maladapted to future climate. These innovative predictions of vulnerabilities improve predictions based on future environmental changes by accounting for the adaptive potential of the crop species, a component barely considered by traditional niche modeling approaches.
The objective of the project is 1) to perform genomic predictions of vulnerabilities of African crops to future climate for a large panel of species, 2) to develop a framework to assess the methods that perform these predictions, and to propose strategies of assisted migration on a broad geographic scale to mitigate climate vulnerabilities. To this end, we will 1) analyze crop diversity, identify outlier markers associated with adaptation to climate, and assess genomic loads; 2) test and assess the methods and variables (climatic, soil related, ethnic and genomic variables related to crops histories) used in genomic prediction, with fitness assessed on a common garden experiment considered as a ground truth; and 3) compute prediction of vulnerabilities for future climate and propose scenarios of assisted migration, including crop replacement and wild contributions
Assessment of African agriculture genomic vulnerability across species would be an invaluable tool to better inform local policy makers and governments. This proposal will also help us to better identify functional variation that could benefit breeding programs, and to increase cultivated genetic diversity to face future environmental challenges.