Supplemental Figures and Tables
Table S1 Genotype calls and association analysis results across the 19 accessions for 1,519 SNPs
(between 11,672,572 and 12,499,932 bp on chromosome 2) identified from a ~1 Mb region containing
the Rsv4 locus. The accessions are grouped by species and Rsv4 genotypes, and SNP statistics are as
described in the Materials and Methods section “Association analysis”.
Table S2 Genotype calls and association analysis results for the 88 SNPs located in a ~94 kb haplotype
block from 12,071,517 to 12,165,890 bp on soybean chromosome 2 (Fig. 1f; Fig. 2). Accessions with
identical genotypes are grouped in the same column and listed in the row labeled “Accessions”. The
numbers in the “Haplotype ID” row correspond to haplotype identifiers from Fig. 2b and Fig3a. The
four SNPs perfectly associated with Rsv4 are highlighted in red. The two SNPs distinguishing the two
Rsv4-associated haplotypes are highlighted in yellow.
Fig. S3 Scatter plot of association results from a Firth’s logistic regression (FLR) analysis testing for an
association between SNPs and Rsv4 genotypes (Rsv4Rsv4 vs. rsv4rsv4) and linkage disequilibrium
(LD) estimates (r2) across a chromosome 2 region of the Wm82.a2.v1 soybean reference genome. The
peak SNP from the original association analysis (at 12,121,100 bp) was included as a covariate in the
FLR model. Negative log10-transformed P-values (left y-axis) from FLR and r2 values (right y-axis) are
plotted against physical position (Wm82.a2.v1) for a ~1 Mb region on chromosome 2. The gray
vertical lines are –log10 P-values for SNPs that are non-significant at 5% FDR. Triangles are the r2
values of each SNP relative to the peak SNP indicated in red at 12,121,100 bp. The red vertical dashed
lines indicate the boundaries of the ~120 kb region identified in the genetic mapping analysis of the SV
population. The physical position of molecular markers from the genetic linkage map is indicated by
orange boxes on the x-axis, and each molecular marker is labeled below its respective box. The
position of the four SNPs perfectly associated with Rsv4 are demarcated with a red arrow below, with
the most centrally positioned SNP designated as the peak marker with a solid red arrow.
Fig. S4 Smoothed, averaged genotype difference from the reference genome (G. max accession
Williams 82) for rsv4 G. max accessions (dark grey), Rsv4 G. max accessions (red) and rsv4 G. soja
accessions (purple) across an ~1 Mb region of the genome containing the Rsv4 locus. The difference is
represented as the percentage of genotype calls in each group that differ from the reference genome.
For the rsv4 G. max group, the accessions most closely related to the reference genome (Pureun and
Williams82K) were removed from the analysis. Genotypes are smoothed using an 8th order polynomial
regression fit (a) and a moving average smoothing function with a range of 51 SNPs (b). The Rsv4
region identified by genetic mapping is indicated by the vertical solid orange bars, and the haplotype
block containing the four peak associated markers is indicated by the vertical dotted grey lines. In a, R2
values indicate regression curve fit to the data.
Fig. S5 Structural variants and sequencing coverage within the haplotype block containing the four
peak SNPs. Depth of coverage in each sample is indicated by the line plot, with orange representing
rsv4 accessions of G. max, blue representing Rsv4 accessions of G. max, and grey representing G. soja
accessions. Gene models are indicated below the line plots by blue bars, with exons highlighted by
darker blue colors. Repetitive elements are indicated below the line plots by grey bars, and
retrotransposon-related motifs and repeats are highlighted by purple bars. Inferred structural variants
are indicated above the line plots by green (deletion) and yellow (duplication) bars. The positions of the
four SNP markers perfectly correlated with Rsv4 are indicated by red vertical dashed lines.
Fig. S6 Haploview plot of the haplotype block containing the four peak SNPs. The light grey bar above
indicates the position of the SNP markers on the physical map of chromosome 2 between coordinates
12,071,517 and 12,165,890, with the four SNP markers having a perfect association with Rsv4
indicated by solid black arrows, and the approximate position of the molecular marker S6ac indicated
by the open white arrow. The corresponding marker order positions in the linkage plot are indicated by
black circles (SNP markers) and a white circle (molecular marker).