(A) The GENESPACE syntenic map (‘riparian plot’) of orthologous regions among eight grass genomes. Chromosomes are ordered horizontally to maximize synteny with rice and ribbons are color coded by synteny to rice chromosomes. Genomes are ordered vertically by general phylogenetic positions. (B) The upper bars display the proportion of maize gene models without syntenic orthologs (‘absent’) in each genome, split by the full background (dark colors) and 86 C3/C4 genes (light colors). (C) The proportion of absent genes is higher in the C3 genomes (green bars), even when controlling for more global gene absences (lower odds ratios). (D) Syntenic orthologs, excluding homeologs among the 26 maize nested association mapping (NAM) founder genomes, with two quantitative trait loci (QTL) intervals highlighted on chromosome 3 (‘Chr3’) and chromosome 6 (’Chr6’). (E) Focal QTL regions that affect productivity in drought where only the genome that drives the QTL effect (middle), the top (B73) and bottom (Tzi8) genomes are presented and the region plotted is restricted to the physical B73 QTL interval and a 25 M bp buffer on either side. Note that the Chr3 QTL disarticulates into two intervals. Due to a larger number of potential candidate genes, the larger Chr3 region, flagged with **, is explored separately in Figure 3—figure supplement 1. (F) Presence–absence and copy number variation are presented for two of the three intervals as heatmaps where each row is a genome (order following panel D), each column is a pan-genome entry (see Figure 1), and the color of each tile indicates absence (gray), single copy (light blue), and multicopy (dark blue). PAV/CNV of the focal genome is outlined. For each interval, the estimated QTL allelic effect relative to B73 of each genome is plotted as bars to the right of the heatmap.