High density mapping and haplotype analysis of the major stem-solidness locus <i>SSt1</i> in durum and common wheat

<div><p>Breeding for solid-stemmed durum <i>(Triticum turgidum</i> L. var <i>durum</i>) and common wheat (<i>Triticum aestivum</i> L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (<i>Cephus cinctus</i> Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94–127, <i>R</i>^<i>2</i> = 78–92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate <i>SSt1</i>. We further examined the <i>SSt1</i> interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the <i>SSt1</i> interval spans a physical distance of 1.6 Mb in WEW (positions 833.4–835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of <i>SSt1</i> to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining <i>SSt1</i> with favorable alleles at minor loci within both wheat species.</p></div

Haplotypes of 103 durum cultivars within the Kofa/W9262-260D3 <i>SSt1</i> QTL interval.

<p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. The matrix consists of 90K genotypic data where cells shaded in blue denote expression of the W9262-260D3 (solid-stem) allele, whereas cells shaded in red denote expression of the Kofa (hollow-stem) allele. The name and position of each 90K probe, the anchored physical position on WEW chromosome 3B, and the corresponding position on the common wheat consensus map are shown. Two dimensional (row and column) hierarchical cluster analysis was performed to group lines into haplotypes as indicated by the colorized dendogram along the top X-axis, whereas similarly marker order is shown along the left Y-axis. *Lines showing identical haplotypes (n = 45) were collapsed into a single haplotype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175285#pone.0175285.s002" target="_blank">S2A Table</a>).</p

Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.

<p>Synergistic two-way interactions between <i>SSt1</i> and minor QTL identified in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.</p

Summary of composite interval mapping (CIM) results.

<p>QTL were localized in the Kofa/W9262-260D3 (durum) and Lillian/Vesper (common wheat) mapping populations.</p

Frequency histograms displaying least-square means for stem-solidness.

<p>Scores are averaged across testing environments for DH lines in a) Kofa/W9262-260D3 (durum), and b) Lillian/Vesper (common wheat) mapping populations.</p

High confidence annotated genes within the <i>SSt1</i> interval in WEW chromosome 3B.

<p>High confidence annotated genes within the <i>SSt1</i> interval in WEW chromosome 3B.</p

Haplotypes of 98 common cultivars within the Lillian/Vesper <i>SSt1</i> QTL interval.

<p>Stem-solidness LS means for each line are shown in the bar chart along the top X-axis. The matrix consists of 90K genotypic data where cells shaded in blue denote expression of the Lillian (solid-stem) allele, whereas cells shaded in red denote expression of the Vesper (hollow-stem) allele. The name and position of each 90K probe, the anchored physical position on WEW chromosome 3B, and the corresponding position on the common wheat consensus map are shown. Two dimensional (row and column) hierarchical cluster analysis was performed to group lines into groups as indicated by the colorized dendogram along the top X-axis, whereas markers were grouped along the Y-axis. *Lines showing identical haplotypes (n = 45) were collapsed into a single haplotype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175285#pone.0175285.s002" target="_blank">S2B Table</a>). ¹ Winter wheat, stem-solidness was evaluated on plants grown in a growth chamber.</p

Genetic map interval of <i>SSt1</i>.

<p>a) Kofa/W9262-260D3 DH population genetic map, b) durum wheat consensus map, c) common wheat consensus map, d) Lillian/Vesper DH population. The position of each QTL is indicated by green shading for each mapping population, and estimated in the consensus map. The markers associated with each QTL peak are highlighted in green text. Common markers between consensus maps are highlighted in blue text.</p