Table S1

List of fresh corn varieties used in this study"

Fig. 1

Characteristics of 5067 SNPs in 385 fresh corn hybrids A: the Minor Allele Frequency (MAF); B: heterozygosity of all groups of corn; C-F: box plots of missing rate (C), gene diversity (D), polymorphism information content (PIC) (E), and heterozygosity of individual corn varieties (F), respectively."

Fig. 2

Principal component analysis (PCA) and population structure of the 385 fresh corn hybrids A: PCA plot of the first two components (PC1 and PC2) of the 385 corn varieties. Four varieties, Wannuo 2000, Jingkenuo 928, Cupola and Guangliangtian 27, which represent the typical waxy, sweet-waxy, temperate sweet, and tropic sweet corn respectively are highlighted with red dots. B: estimated ΔK over five repeats of STRUCTURE analysis. C: population structure analysis using 5067 SNPs. Each individual is represented by a vertical bar, partitioned into colored segments with the length of each segment representing the proportion of the individual's genome from K = 2 and 3 groups. The genetic groups, namely groups 1, 2, and 3, roughly correspond to the non-sweet, sweet-temp, and sweet-tropic groups."

Table S2

Genetic relationship among 385 lines inferred by STRUCTURE analysis (K=3)"

Fig. 3

Genetic relationships among 385 fresh corn hybrids A: the heatmap of IBS values among all corn lines. Blue represents a low IBS value, showing a close distance between two lines. Red represents a high IBS value, showing a greater distance between two lines. B: IBS values for four groups."

Table 1

Closest pairs with IBS < 0.15"

Fig. 4

Neighbor-Joining tree for 385 fresh corn varieties based on IBS matrix calculated from 5067 SNP markers The groups are represented as follows: red for sweet-temp; blue for sweet-tropic; green for sweet-waxy; purple for waxy. Four main cultivars are highlighted with filled triangles. The lines under the black line came from the Guangdong Academy of Agricultural Sciences."

Fig. 5

Selective-sweep signals among the four fresh corn groups A genome-wide distribution of selective-sweep signals identified through comparisons between two different corn groups (except the comparison between sweet-waxy and waxy groups). The blue dashed lines represent the thresholds (top 1% of FST values). Five known genes are identified and shown with vertical dashed lines. S-Temp, S-Tropic, SW, and W represent the sweet-temp group, the sweet-tropic group, the sweet-waxy group, and the waxy group, respectively."

Table S3

160 selected sweep regions with top 1% of FST values among four groups in fresh corn"

Fig. 6

Selection patterns of two known genes among four fresh corn groups A-B: FST profiles for the identified genes among four corn groups. The vertical dashed lines indicate the position of two genes. The gene structure and position of the markers used here are shown with red arrows. The functional site of DGAT1-2 is shown with a green arrow. C-D: frequency changes for markers of sh2 (C) and DGAT1-2 (D) among four fresh corn groups."

Fig. S1

The density distribution of SNPs in whole genome The x-axis represents the physical distance in each chromosome. The y-axis represents numbers of SNPs in 1 Mb window."

Fig. S2

Selective-sweep signals between sweet-waxy and waxy groups Genome-wide distribution of selective-sweep signals identified through the comparison between sweet-waxy and waxy groups. SW represents sweet-waxy group, W represents waxy group."