Abstract
BackgroundClimate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited.MethodologyA panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.ConclusionsThe genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.
Highlights
According to the Food and Agriculture Organization of the UN, maize (Zea mays ssp. mays) is the most important food crop in Africa with an annual production of more than 63 million metric tons in 2010
The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions
Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season
Summary
According to the Food and Agriculture Organization of the UN, maize (Zea mays ssp. mays) is the most important food crop in Africa with an annual production of more than 63 million metric tons in 2010 (http://faostat.fao.org/default.aspx). The intraspecific diversity of maize reflects both the historical introductions of the crop on the continent as well as the local adaptations to a variety of biotic and abiotic conditions. This diversity represents the biological foundation for a substantial part of the food production in Africa and exploring it contributes to research efforts aimed at reducing food insecurity. Unless effective adaptation measures are taken, climate change is predicted to have critical impacts on maize productivity in sub-Saharan Africa [2,3] For this reason plant breeding efforts and international development assistance are increasingly focusing on developing and disseminating maize varieties adapted to abiotic stress [4,5]. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited
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