A pan-Zea genome map for enhancing maize improvement

Abstract

AbstractBackgroundMaize (Zea maysL.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for theZeagenus and a comprehensive genetic variation map for maize breeding are still lacking.ResultsHere, we construct an approximately 6.71-Gb pan-Zeagenome that contains around 4.57-Gb non-B73 reference sequences from fragmented de novo assemblies of 721 pan-Zeaindividuals. We annotate a total of 58,944 pan-Zeagenes and find around 44.34% of them are dispensable in the pan-Zeapopulation. Moreover, 255,821 common structural variations are identified and genotyped in a maize association mapping panel. Further analyses reveal gene presence/absence variants and their potential roles during domestication of maize. Combining genetic analyses with multi-omics data, we demonstrate how structural variants are associated with complex agronomic traits.ConclusionsOur results highlight the underexplored role of the pan-Zeagenome and structural variations to further understand domestication of maize and explore their potential utilization in crop improvement.