BSR-Seq.

<p>A. A flowchart of BSR-Seq experimental design. B. The physical position of each SNP marker (x-axis) was plotted versus the probability of each SNP marker being in complete linkage disequilibrium with the causal gene (y-axis). C. <i>gl3</i> mutants (the <i>gl3-ref</i> allele) express a glossy phenotype due to altered accumulation of epicuticular waxes. Water is sprayed on seedlings to distinguish mutant (<i>gl3-ref</i>/<i>gl3-ref</i>) from non-mutant (<i>gl3-ref</i>/+ or +/+). D. Chromosome 4 was scanned by using a window containing 50 SNPs with a step size of 5 SNPs. Within each window, the median linkage probability obtained from a Bayesian BSA analysis across all the 50 SNPs was determined and was plotted against the middle physical position of the window.</p

Gene structure of the <i>gl3</i> gene and lesions of its mutant alleles.

<p>A. RNA-Seq reads shown in the Integrative Genomics Viewer. Blue indicates reads that have a forward orientation relative to the reference genome; red indicates reverse orientation. B. Based on the supporting ESTs and the annotation from the gene models, the <i>gl3</i> gene contains only a single exon. All six lesions associated with <i>gl3</i> mutant alleles are located in the coding region. They include <i>Mu</i> insertion alleles (a: <i>gl3-93-4700-5</i>; b: <i>gl3-93-4700-6</i>; c: <i>gl3-93B111</i>), EMS alleles (1: <i>gl3-AEW-A632-363-EMS</i>, premature stop at position 171 nt in coding region (G->A); 2: <i>gl3-94-1001-326-EMS</i>, premature stop at position 358 nt in coding region (C–T)) and the reference allele (3: <i>gl3-ref</i>, insertion or rearrangement at 430–758 nt of the coding region).</p

Lipidome of US and Chinese sorghum accessions

Seedling lipid profile of US (BTx623 and RTx430) and Chinese (Niu Shenz Zui, Kaoliang, Hong Ke Zi, and Shan Qui Red) accessions subjected to optimal and chilling temperature

The ISSR profiles of 54 isolates of <i>Rathayibacter toxicus</i>.

<p>(A) Primer P15 produced an unique locus of 1.2 kb to differentiate population RT-I (locus absent) from RT-II and RT-III populations (locus present); (B) primer P16 produced an unique locus of 1.7 kb only with population RT-II; (C) primer UBC 810 produced an unique locus of 3.5 kb only with population RT-III of <i>R</i>. <i>toxicus</i>. The numbers above the gel images correspond to the individual isolates listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156182#pone.0156182.t001" target="_blank">Table 1</a>.</p

MapMan Analysis - Chilling Stress Pathways

MapMan analysis of BTx623 and NSZ seedling transcriptome subjected to chilling and optimal temperature

A phylogenetic tree of 54 isolates of <i>Rathayibacter toxicus</i> was generated using concatenated consensus partial gene sequences six genes.

<p>A total of 5,182 nucleotides from vancomycin resistant protein <i>vanA</i>, CRISPR-associated protein <i>cse4</i>, <i>secA</i> ATPase, chromosome partition protein SMC, tRNA dihydrouridine synthase, and cysteine desulfurase genes, were analyzed to generate this tree. Three distinct groups RT-I, RT-II and RT-II were formed. The tree was constructed using neighbor-joining and Tamura-Nei genetic distance model. A consensus tree was generated through bootstrap analysis using Geneious Tree Builder program with 1000 cycles; the obtained values labeled at the forks indicate the confidence limits for the grouping. The scale bar at the bottom indicates the substitution rate. Detail for all isolates and gene accession numbers submitted to NCBI GenBank are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156182#pone.0156182.t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0156182#pone.0156182.s007" target="_blank">S1 Table</a>.</p

ISSR loci data for the three <i>Rathayibacter toxicus</i> populations: RT-I, RT-II and RT-III.

<p>ISSR loci data for the three <i>Rathayibacter toxicus</i> populations: RT-I, RT-II and RT-III.</p

Primer sequences and results for ISSR analysis of 54 isolates of <i>Rathayibacter toxicus</i> collected from South and Western Australia.

<p>Primer sequences and results for ISSR analysis of 54 isolates of <i>Rathayibacter toxicus</i> collected from South and Western Australia.</p

Nucleotide differences in the partial gene sequences used for multi-locus sequence typing (MLST) analyses of <i>Rathayibacter toxicus</i> populations RT-I, RT-II, and RT-III.

<p>Nucleotide differences in the partial gene sequences used for multi-locus sequence typing (MLST) analyses of <i>Rathayibacter toxicus</i> populations RT-I, RT-II, and RT-III.</p

Primers designed and used to amplify MLST genes for <i>Rathayibacter toxicus</i>.

<p>Primers designed and used to amplify MLST genes for <i>Rathayibacter toxicus</i>.</p