Comparison of genetic distances in <i>Glycine latifolia</i> to physical distances in <i>G. max</i> for linkage groups/chromosomes 1 and 18.

<p><i>Glycine latifolia</i> linkage groups 1 and 18 showed a high degree of collinearity with the corresponding <i>G. max</i> chromosomes. The genetic distances in <i>G. latifolia</i> were plotted against the physical locations of the SNP markers on the <i>G. max</i> chromosomes 1 and 18. As in <i>G. max</i>, the predicted ratios of genetic and physical distances varied along <i>G. latifolia</i> linkage groups. The slopes were steeper near the ends of linkage groups and flatter near the center in regions predicted to correspond to centromeres, where recombination is lower.</p

Comparison of synteny of individual <i>Glycine latifolia</i> linkage groups 7, 10 and 20 with <i>G. max</i> and <i>Phaseolus vulgaris</i> chromosomes.

<p><i>Glycine latifolia</i> linkage groups (A & B) and <i>G. max</i> chromosomes (C) are placed at the top of each circle with colored lines connecting positions of <i>G. latifolia</i> SNP markers (A & B) or <i>G.max</i> gene model (C) sequences to positions in <i>G. max</i> (Gm01 – Gm20) or <i>P. vulgaris</i> (PV01 – PV11) chromosomes, represented by gray boxes. <i>Glycine latifolia</i> linkage groups 7 and 20 appeared to have larger syntenic blocks with single <i>P. vulgaris</i> chromosomes than <i>G. max</i> chromosomes. Both <i>G. latifolia</i> linkage groups 10 and 20 showed large blocks of synteny with <i>P. vulgaris</i> chromosome 7, as did <i>G. max</i> chromosome 10. Synteny maps were constructed using MizBee <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099427#pone.0099427-Meyer2" target="_blank">[42]</a>.</p

Comparison of F₂, F₅ and merged linkage maps for GBS SNP markers for <i>Glycine latifolia</i> linkage groups 1 and 20.

<p>Orders of SNP markers were very similar between the F₂ and F₅ populations. In some cases, markers that segregated in the F₂ population co-localized in the F₅ population, which may have resulted from errors in calling heterozygous loci in the F₂ population. While linkage group 1 showed a high level of collinearity with <i>G. max</i> chromosome 1, linkage group 20 had regions of collinearity with multiple <i>G. max</i> chromosomes. Even so, there was good agreement in marker order between the F₂ and F₅ populations for linkage group 20. Markers were named for the <i>G. max</i> chromosome and the nucleotide position on the chromosome (×10⁻⁶) to which the SNP-containing sequences aligned. Markers that did not align to a <i>G. max</i> chromosome were named for the <i>G. latifolia</i> scaffold containing the SNP.</p

Synteny between <i>Glycine latifolia</i> linkage groups and <i>G. max</i> chromosomes.

<p>Sequences containing mapped <i>G. latifolia</i> SNPs were aligned to the <i>G. max</i> genome sequence. <i>Glycine latifolia</i> linkage groups (top) and physical maps for each <i>G. max</i> chromosome (bottom) are displayed as linear arrays. Vertical and diagonal lines connect genetic and physical locations of SNP markers between the two species.</p

Comparison of the numbers of SNP markers in F₂, F₅, merged and Chang <i>et al</i>. [19] maps.

<p>Comparison of the numbers of SNP markers in F₂, F₅, merged and Chang <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099427#pone.0099427-Chang1" target="_blank">[19]</a> maps.</p