List of QTLs detected on chromosome 3A in the glasshouse study conducted at Pullman, WA.

<p>HD = heading date, PH = plant height, TKW = 1000-kernal weight, KPS = kernels per spike, SB = shoot biomass, TB = total biomass, SWPS = seed weight per spike.</p>*<p>QTLs detected in field data analysis.</p

List of consistent QTLs^* detected on chromosome 3A using data recorded over fourteen different environment years.

**<p>For years 2005 and 2008 data was recorded at Lincoln and Pullman, respectively; SPSM = spike/square meter, PH = plant height, HD = heading date, TKW = 1000-kernel weight, GY = grain yield, KPSM = kernels/square meter, GVWT = grain volume weight, and KPS = kernels per spike.</p>*<p>For the purpose of identifying consistent QTLs, the QTLs detected in overlapping marker intervals with one common marker flanking the region were treated as the same QTL. Among these QTLs the marker interval showing the highest LOD score and R² value was documented in the table (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070526#pone.0070526.s007" target="_blank">table S4</a> for complete list of QTLs).</p

Cytogenetic-ladder map of wheat chromosome 3A showing locations of genes and/or QTLs influencing a number of agronomically important traits.

<p>Markers showing connection between genetic and cytogenetic maps are highlighted in blue on the cytogenetic map. (A) Consensus cytogenetic map of chromosome 3A developed by integrating information for additional markers, genes (underlined) and QTLs on the reference map <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070526#pone.0070526-Dilbirligi1" target="_blank">[11]</a>. (B) Integrated genetic linkage map developed by incorporating SSR, STM and DArT markers on the RFLP skeleton map. The map was used to demarcate locations of consistent QTLs detected in the present study and to depict locations of QTLs detected for a number of agronomical traits in the published literature. (C) List of traits and symbols used to demarcate locations of QTLs published elsewhere. YLD = yield; HD = heading date; GW = grain weight; Yr/Sr/Lr = yellow, stem and leaf rust resistance; FHB = <i>Fusarium</i> head blight resistance; LGSA = leaf glutamine synthetase activity; KPS = kernels per spike; GPC = grain protein content; PH = plant height; GL = grain length; LW = leaf waxiness; DSF = domestication syndrome factor; APT = adult plant type; SWPS = seed weight per spike; LV/BS/DS = loaf volume, bread score and dough score; MGFR = mean grain filling rate; LFW = leaf fresh weight; TE = transpiration efficiency; FN/PHS/GC = falling number, preharvest sprouting tolerance and grain color; GL&GW = grain length and grain width; GVWT = grain volume weight; PGMS = percent greenness at maximum senescence; UTEB = Phosphorus utilization efficiencies based on biomass yield; UTEG = Phosphorus utilization efficiencies based on grain yield; ABAR = ABA responsiveness. (D) List of traits mapped during the present study (see M&M for details). Traits mapped using data recorded in glasshouse are marked with a star.</p