Additional file 1: of An efficient and improved method for virus-induced gene silencing in sorghum

Figure S1. BMV capsid protein quantification. BMV level was analyzed by western blot using an antibody against BMV coat protein. The capsid protein was normalized with Actin protein of the plants. In N. benthamiana, the BMV level was more in the BMV:: Ubiq infected plant compared to BMV:: anti-Ubiq infected plant. In sorghum, BMV level is similar in both BMV:: anti-Ubiq and BMV:: Ubiq infected plants. (PDF 63 kb

Additional file 2: of An efficient and improved method for virus-induced gene silencing in sorghum

Table S1. List of sorghum genotypes/varieties showing BMV infection. (XLSX 11 kb

Additional file 3: of An efficient and improved method for virus-induced gene silencing in sorghum

Table S2. List of primers used in this study. (XLSX 12 kb

Příspěvek k problematice extramatrimoniálních vztahů

Basic parameters showing soil properties at two N levels across years. (xls 22.0 kb

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

Phenotypic changes over MSH1 F2, F3 and F4 generations.

<p>(A) Selection had varying results, with response for yield into the F₃ generation, but not into the F₄ generation. For each lineage, the mean generation performance is represented as a point. (B) Boxplots of F₂, F₃, and F₄ line means for various traits, giving a population-wide view of line performance. Dashed lines indicate the 95% confidence interval for wild type Tx430 mean.</p

Enhanced growth phenotype of MSH1 lines in sorghum.

<p>The transgene and crossing procedure used to derive sorghum populations is indicated. (A) The phenotype of the F₁ progeny derived from crossing Tx430×MSH1-dr. (B) Field grown F₂, F₃ and F₄ sorghum lines show variation in plant architecture and height. (C) Panicles from Tx430 (on left, 66 g, 8 mm stem) versus a larger F₂ individual (on right, 112 g, 11 mm stem), and (D) seed yield after threshing. (E) The MSH1-dr sorghum phenotype under field conditions. (F) Sorghum MSH1 F₂, F₃ and F₄ populations grown in progeny rows in a 2011 field experiment. Wild type inbred Tx430 is indicated. Variation in plant height, flowering time and plant architecture is apparent; all plants shown are non-transgenic and Tx430 genotype.</p

<i>MSH1</i>-Induced Non-Genetic Variation Provides a Source of Phenotypic Diversity in <i>Sorghum bicolor</i>

<div><p><i>MutS Homolog 1</i> (<i>MSH1</i>) encodes a plant-specific protein that functions in mitochondria and chloroplasts. We showed previously that disruption or suppression of the <i>MSH1</i> gene results in a process of developmental reprogramming that is heritable and non-genetic in subsequent generations. In Arabidopsis, this developmental reprogramming process is accompanied by striking changes in gene expression of organellar and stress response genes. This developmentally reprogrammed state, when used in crossing, results in a range of variation for plant growth potential. Here we investigate the implications of <i>MSH1</i> modulation in a crop species. We found that <i>MSH1</i>-mediated phenotypic variation in <i>Sorghum bicolor</i> is heritable and potentially valuable for crop breeding. We observed phenotypic variation for grain yield, plant height, flowering time, panicle architecture, and above-ground biomass. Focusing on grain yield and plant height, we found some lines that appeared to respond to selection. Based on amenability of this system to implementation in a range of crops, and the scope of phenotypic variation that is derived, our results suggest that <i>MSH1</i> suppression provides a novel approach for breeding in crops.</p></div

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

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