Genome Anchored QTLs for Biomass Productivity in Hybrid <em>Populus</em> Grown under Contrasting Environments

<div><p>Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in a <em>Populus trichocarpa</em> × <em>P. deltoides</em> F₂ population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which <em>BM-1</em>, <em>BM-2</em>, and <em>BM-7</em> were identified in all three years for both height and diameter. One putative QTL, <em>BM-7,</em> and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs <em>BM-4</em> and <em>BM-6</em> exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the <em>P. trichocarpa</em> genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in <em>Populus</em>.</p> </div

QTLs associated with height and diameter identified in <i>Populus</i> family 331 F₂ pedigree based on linkage-group- (LG) and genome-wise LOD significance thresholds (GW).

<p>%PVE = percent phenotypic variance explained;</p>†<p>Mean associated with heterozygous genotypes ‘ac’ and ‘bd’ where alleles are derived from the same species;</p>‡<p>Mean associated with heterozygous genotypes ‘ad’ and ‘bc’ where alleles are derived from different species, a = additive; d = dominance; d/|a| = QTL mode of action.</p

Synteny between (A) Family 331 genetic map LG II, (B) <i>Populus</i> consensus genetic map LG II, and (C) Scaffold 2 of the <i>Populus</i> genome assembly illustrating the genome anchoring of QTL <i>BM-2</i> using flanking markers.

<p>Map distance units in A and B represent cM distances and distance units in C represent genomic sequence length (x1OKb).</p

Genome anchored QTL positions on the <i>Populus</i> V2.2 assembly.

<p>Blue bars represent SSR marker coverage for each scaffold, red bars indicate scaffold intervals between flanking SSR markers used for genome anchoring, vertical green lines represent QTL intervals and estimated peak position. Scaffold intervals are represented in Mb.</p

AMMI analysis results for location specificity in QTL detection between the Clatskanie and Boardman sites.

<p>AMMI analysis results for location specificity in QTL detection between the Clatskanie and Boardman sites.</p

LOD traces for QTL B<i>M-2</i> on LG II based on 4-year height (red) and 4-year diameter (green) measured in Clatskanie and 4-year height measured in Boardman (purple).

<p>Broken horizontal line represents linkage groupwise LOD significance threshold calculated based on 1,000 permutations at the 0.05 significance level.</p

Suggestive QTLs associated with height and diameter identified in <i>Populus</i> family 331 F₂ pedigree.

†<p>LG = Linkage groupwise significance; GW = Genomewise significance.</p

Top 20 unique retention times ranked by antimicrobial significance against MRSA using random forests.

<p>Top 20 unique retention times ranked by antimicrobial significance against MRSA using random forests.</p

Overlay of initial yerba mate extract fraction chromatograms.

<p>A) The black chromatogram corresponds to a yerba mate extract fraction that demonstrated antibacterial activity against methicillin-resistant <i>Staphylococcus aureus</i> (MRSA); the red chromatogram corresponds to a yerba mate fraction that had no antibacterial activity against MRSA. B) Retention times of identified compounds and quantification in sorbitol equivalents were reported.</p

Classification accuracy of a single major mz peak for each of the 3 identified compounds of interest.

<p>Classification accuracy of a single major mz peak for each of the 3 identified compounds of interest.</p