Distribution of <i>Dw1</i> Coding Sequence Variants in Sorghum Genotypes.

<p>The polymorphism number corresponds to the number in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151271#pone.0151271.t004" target="_blank">Table 4</a>.</p

Relative expression of <i>Dw1</i> in stem internodes.

<p>RNA was extracted from a full length internode (Mature), the lower half of an elongating internode, and the upper half of an elongating internode for each parental genotype (n = 3 each). Relative expression was determined by qRT-PCR using the ΔΔCt method with 18S rRNA as the normalizer and the sample from 80M mature tissue as the calibrator.</p

A schematic of the region of SBI-09 encoding <i>Dw1</i>.

<p>The top bar shows the <i>Dw1</i> locus delimited by QTL mapping in the F₂. The region was refined in the F₃ population (n = 75 for each of six families) using the DG markers labeled in the diagram. The numbers below the bar are the number of recombinants (both bars). Note that all members of one of the families (237) had a breakpoint in between Fse5 and the end of the region shown. The lower bar represents the delimited <i>Dw1</i> locus defined by mapping in the F₃ generation with SNP markers labeled. Dark purple shows the location of <i>Dw1</i> based on fine mapping. SNP markers are named with the last six digits of the gene name of the gene the SNP is in or near. Fse4 is included for perspective though it was not scored in the F₄.</p

QTL for Average Internode Length Identified in the Entire Population of Hegari x 80M F₂.

<p>QTL for Average Internode Length Identified in the Entire Population of Hegari x 80M F₂.</p

Polymorphisms Distinguishing 80M and Hegari in Genes in the Delimited <i>Dw1</i> Locus.

<p>Polymorphisms Distinguishing 80M and Hegari in Genes in the Delimited <i>Dw1</i> Locus.</p

Sequence Variants in Exons of Sobic.009G229800 in Diverse Sorghum Genotypes.

<p>Sequence Variants in Exons of Sobic.009G229800 in Diverse Sorghum Genotypes.</p

Stem internode length QTL identified in a population from Hegari x 80M.

<p>F₂ plants from a cross of Hegari and 80M (n = 218) were grown in the greenhouse and the length of each internode was measured. The average internode length was used to map QTL. (A) The resulting graph shows four QTL, including <i>Dw1</i> and <i>Dw2</i>. The x-axis is the genetic map and the y-axis is the LOD score. The boxes above each trait identify the <i>Dw</i> loci, if any, the percentage of the variation explained by the QTL, and the location of the peak LOD value. (B) Photograph of Hegari (left) and 80M. (C) Photograph of F₅ plants that are <i>Dw1Dw1</i> (left), <i>Dw1dw1</i> (center), and <i>dw1dw1</i> (right) in otherwise uniform genetic backgrounds at the other loci that affect internode length.</p

Genes in the Delimited <i>Dw1</i> Locus.

<p>Genes in the Delimited <i>Dw1</i> Locus.</p

SNP density distribution on sorghum chromosome 2.

<p>Average density of SNP/Kbp within genic DNA (red) and intergenic DNA (grey) on SBI-02 in the pericentromeric region (24–44 Mbp) well as DNA flanking this region from 14–24 Mbp and 44–60 Mbp. Bins are 10 Mbp.</p

Variation in gene density, DNA methylation, recombination frequency, and SNP density across sorghum chromosome 2.

<p>(A) Gene density (blue line), percentage <i>Ngo</i>MIV site methylation (red line), and recombination (cM/Mbp, black diamonds) of SBI-02 are shown. Approximate location of the centromere (white), distribution of euchromatin (maroon), and heterochromatin (grey) are indicated at the top of the graph. Centromere location and distribution of euchromatin, and heterochromatin were obtained from Kim et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079192#pone.0079192-Kim1" target="_blank">[19]</a>. SNP density between Tx7000 and BTx623 on sorghum chromosome 2 is shown within (B) genic DNA and (C) intergenic DNA on a SNP/100 Kbp basis. Gene density is represented as a bar graph at the top of Fig. 5C.</p