Fig. 1: GWAS of seed width and haplotype analysis of GmSW17 in soybean.
From: Natural variation in GmSW17 controls seed size in soybean
a Manhattan plot of GWAS results for seed width using 2 years of best linear unbiased prediction (BLUP) data from the 1853 accessions. b Quantile-quantile plot of the seed width. For the quantile-quantile plot, -Log10-transformed observed P values are plotted against -Log10-transformed expected P values. c Genome-wide Manhattan plot of the 8.3-8.7 Mb region on chromosome 17. The red dashed lines indicate the candidate region for the peak. The red plot indicates the nucleotide variation in GmSW17. d Linkage disequilibrium plot for SNPs in the 8.495-8.589 Mb region from a continuous association block. Candidate genes are depicted at the top of the panel, and GmSW17 are shown in red. The color key (white to red) represents the linkage disequilibrium value (r2) of the accessions. e An expression heatmap of candidate genes located in the candidate region. The color key (blue to red) represents gene expression (Transcripts per kilobase million, TPM). f Gene structure of GmSW17. The nonsynonymous locus (+988th C/T) in the second exon (UCH domain) is labeled on the gene sketch. Two domains (ZF-UBP and ubiquitin carboxyl-terminal hydrolase namely, the UCH domain) are depicted at the top of the panel. g Haplotype analysis of GmSW17H1 (n = 295 accessions) and GmSW17H2 (n = 731 accessions). The edges of the box plot represent the first and third quartiles, the center line represents the median, and the whiskers extend to the smallest and largest data points within 1.5 interquartile ranges from the edges. Statistical significance is determined using a two-sided t-test. Source data are provided as a Source Data file.
