Fig. 1

Determination of soft threshold β The ordinate represents the index of scale free network model in figure A, the red line represents that R2 is equal to 0.85. The ordinate represents the average link degree of each soft threshold in figure B. The abscissa in both figures A and B represent the soft threshold β."

Table 1

SNPs/InDels filter standards"

Fig. 2

Box diagram of 100-seed weight of 12 soybean varieties The abscissa represents 12 soybean varieties, and the ordinate represents the 100-seed weight. One point represents one observation. Soybean varieties with different uppercase letters are significantly different in 100-seed weight at P = 0.01 by Duncan’s new multiple-range test."

Fig. 3

Histogram of the number of genes in modules The abscissa represents the module and the ordinate represents the number of genes in the module."

Fig. 4

Heat map of module-trait relationships (A) and gene expression count of 2904 genes in green module (B) The horizontal axis represents 100-seed weight and seed shape traits, and each column represents the co-expression module in the figure A; red color of each box represents the positive correlation between module and trait, blue color of each box represents the negative relationships between module and trait. B: 2904 genes in the green module are mapped after normalization of the expression levels by row of 12 soybean varieties in three stages. G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively."

Fig. 5

GO enrichment of 2904 genes in green module The abscissa (each column) represents the proportion of enriched genes to input genes, and the ordinate (each row) corresponds to GO Terms. The size of the dot represents the number of enriched genes, and the color of the dot represents the corrected Padjust value by the Fisher exact test."

Fig. 6

Gene expression differences in different stages of seed development between two panels of soybean varieties with extremely significant differences in 100-seed weight (A) and KEGG pathway enrichment map of down-regulated genes in small 100-seed weight varieties (B) G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively. Down-regulated genes represent down-regulated genes in small 100-seed weight varieties, and up-regulated genes represent up-regulated genes in small 100-seed weight varieties."

Fig. 7

Histogram of GS and kME value of hub gene in green module (A) and cluster heat map of differentially expressed genes among soybean varieties with different 100-seed weight (B) 100-SW: 100-seed weight; SA: seed area; SL: seed length; SP: seed perimeter; SW: seed width. G, H, and I represent the early stage, the middle stage, and the later stage of seed development, respectively. Large and Small represent large soybean varieties and small soybean varieties panel at P = 0.01, respectively. Gene in bold represents the first expression pattern in figure B."

Fig. 8

Distribution map of SNPs/InDels and DEGs on soybean chromosomes A: SNPs density; B: InDels density; C: log2 (Fold Change) of DEGs. The inner circle represents significantly up-regulated genes in small 100-seed weight varieties, and the outer circle represents significantly down-regulated genes in small 100-seed weight varieties."

Table 2

SNPs/InDels distributed region"

Table 3

Ten genes with non-synonymous_coding SNP mutants between the large and small 100-seed weight varieties panels in green module"

Table 4

GO annotations of candidate genes Glyma.14G043900 and Glyma.15G217400"

Fig. 9

Co-expression network of candidate genes, hub genes, and differentially expressed genes in the green module Red dots represent candidate genes, yellow dots represent hub genes, green dots represent DEGs, and blue dot represents both DEG and hub gene. The color of the line represents the weight value between genes. Black line represents the weight between genes greater than 0.1, and gray line represents the weight less than 0.1 but greater than 0.01."

Fig. 10

Allele percentage line chart of two non-synonymous_coding SNP mutant of Glyma.14G043900 and Glyma.15G217400 in different soybean types The dots represent the positive effect alleles of 100-seed weight, and the triangles represent the negative effect alleles of 100-seed weight."