Fig. 4

Characteristics of the phenotype associated QTLs, genes, and causal variants. A Distribution of the associated QTLs, genes, and causal variations (example with chromosome 1, see Additional file 1: Fig. S14 for the whole genome). The heatmap represents the QTL density within each 1-Mb window, while the histograms indicate the density of the candidate causal variants that were normalized with the number of all variants within the 1-Mb window. B Proportions of QTL types (QTLs lead with different variant types). C Proportions of INDEL/SV-specific QTLs (QTLs that cannot be detected by SNPs). D Proportions of associated gPAVs for the reference genome genes (Ref-Genes) and non-reference genome genes (NonRef Genes). E Manhattan plot of the association result of the Ga1 locus related to the ratio of seed sets, with gPAVs highlighted in red. F The proportion of different levels of seed set ratio related to the absence/presence of PZ00001a032490; the larger the number, the higher the seed set ratio. G The genome alignment indicates the anchoring of the NRS (PanRep_01830195) on the AGPv4 genome, and the schematic plot illustrates the differences between the three PME genes (PZ00001a032490, SDGa25, and Zm00001d048936). Solid rectangles indicate the gene coding sequence, while the dashed rectangles indicate the missing coding part related to SDGa25. Gray ribbons indicate the matched blocks. Pink ribbons indicate the matched CDS blocks. H Distribution of the PAV patterns (track 2) of the six PME genes and the ratio of seed sets (track 3) according to the structure tree of pan-Zea individuals (track 1). I Distribution of the number of presented PME genes (# PMEs) related to the levels of the seed set ratio. The gray histogram is the distribution of total sample numbers (count) according to the X-axis, while the colored histogram indicates the proportions. The P-value was calculated from 10,000 permutations of the Wilcoxon-Mann-Whitney test