Target genes investigated, primer and qPCR information.

1<p>Organism from which the gene of interest had originally been isolated.</p>2<p><i>Lolium</i> sp. genes investigated in this work. <i>ALS</i>, Acetolactate synthase; <i>ACCase</i>, Acetyl-coenzyme A carboxylase; <i>CYP</i>: cytochrome P450. Accession numbers are given for the <i>Lolium CYP</i> genes available in GenBank/EMBL that display the highest amino-acid identity with the <i>CYP</i> gene of interest. % identity, % of amino-acid identity between the <i>CYP</i> gene of interest and the <i>Lolium CYP</i> gene studied.</p>3<p>F, forward primer; R, reverse primer.</p

Ranking of the eight candidate reference genes according to the stability of their expression in samplings IM1 (top) and P1 (bottom) computed using BestKeeper and NormFinder.

1<p>Sampling composition given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063576#pone-0063576-t001" target="_blank">Table 1</a>.</p>2<p>The three reference genes selected are in bold. <i>TUB</i>, beta tubulin; <i>CAP</i>, Capsine phosphatase; <i>EF1</i>, Elongation factor 1; <i>GADPH</i>, Glyceraldehyde 3-phosphate dehydrogenase; <i>RUB</i>, Ribulose-1,5-bisphosphate carboxylase oxygenase; <i>UBQ</i>, Ubiquitin; <i>18S</i>, ribosomal RNA 18S; <i>25S</i>, ribosomal RNA 25S.</p>3<p>Standard deviation of Cq values. SD values higher than the threshold value (1.00) are underlined.</p>4<p>Pearson’s coefficient of correlation.</p>5<p>Stability value.</p>*<p>associated p-value <0.001.</p

Candidate reference genes tested and primer information.

1<p><i>TUB</i>, beta tubulin; <i>CAP</i>, Capsine phosphatase; <i>EF1</i>, Elongation factor 1; <i>GADPH</i>, Glyceraldehyde 3-phosphate dehydrogenase; <i>RUB</i>, Ribulose-1,5-bisphosphate carboxylase oxygenase; <i>UBQ</i>, Ubiquitin; <i>18S</i>, ribosomal RNA 18S; <i>25S</i>, ribosomal RNA 25S.</p>2<p>F, forward primer; R, reverse primer.</p>3<p>Values obtained using samplings IM1 or P1 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063576#pone-0063576-t001" target="_blank">Table 1</a>).</p>4<p>Average Cq value computed over all samples in samplings IM1 and P1.</p

Expression of <i>ALS</i>, <i>ACCase</i> and five <i>CYP</i> genes in individual <i>Lolium</i> sp. plants in four groups of samples.

<p>A group of samples consists of the plants from the same population that have been used to assess the effect of the same herbicide in sampling IM2 or P2 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063576#pone-0063576-t002" target="_blank">Table 2</a>). For every individual plant, the relative expression levels of each gene measured in the absence of herbicide (BT) and 24 hours after herbicide application (24HAT) are connected by a solid line for herbicide-resistant plants, a dotted line for herbicide-sensitive plants or a dashed-and-dotted line for plants with a moderately resistant phenotype. A given colour in all panels in a column (i.e., in a given group of samples) indicates the same individual plant. Panels on lanes A to G, relative expression levels for <i>ALS</i>, <i>ACCase</i>, <i>CYP71R4</i>, <i>CYP72A</i>, <i>CYP81B1</i>, <i>CYP81A</i> and <i>CYP92A</i>, respectively. The herbicide considered is indicated below the population code using the sampling code (IM2, iodosulfuron+mesosulfuron; P2, pyroxsulam, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063576#pone-0063576-t002" target="_blank">Table 2</a>). Identical letters in a given panel and in a given experimental modality (BT or 24HAT) indicate relative expression levels that are not significantly different.</p

geNorm ranking of the eight candidate reference genes according to their average expression stability value M (A) and determination of the optimal number of reference genes for accurate normalisation (B).

<p>A, ranking was performed for all RNA samples in samplings IM1 (top) and P1 (bottom). M-values of the remaining genes at each step during stepwise exclusion of the least stable gene are shown. The genes are ranked according to increasing expression stability (i.e., decreasing M-value). B, pairwise variation analysis to determine the optimal number of reference genes for accurate normalisation in samplings IM1 (open boxes) and P1 (solid boxes). The pairwise variation between consecutive normalisation factors (Vi/i+1) indicating the optimal number of reference genes is arrowed.</p

Number of plants in the samplings used for target gene expression quantification BT and 24HAT (samplings IM2 and P2).

1<p>IM2, sprayed with iodosulfuron+mesosulfuron; P2, sprayed with pyroxsulam.</p>2<p>S, sensitive; R, resistant, r, moderately resistant. All plants were analysed before treatment (BT) and 24 hours after treatment (24HAT).</p

RNA samples used to assess the stability of candidate reference genes (samplings IM1 and P1).

1<p>BT, before treatment; xHAT, x hours after treatment.</p>2<p>S, sensitive; R, resistant.</p

<i>A</i>. <i>myosuroides</i> herbarium specimen.

<p>Specimen collected in May 1876 in a vineyard in Russin (Switzerland), and kept at the conservatory and botanical gardens of Geneva (Switzerland). This specimen is denominated <i>Alopecurus </i><i>agrestis</i>, a former synonym for <i>A</i>. <i>myosuroides</i>. Reprinted with permission of the copyright holder: Conservatory and Botanical Gardens of Geneva (Switzerland), 2013.</p

A Social Democratic Response to Market-led Education Policies: Concession or Rejection?

RT-qPCR expression patterns of the 21 contigs used for RNA-Seq expression data validation. The expression values were measured in each of the three resistant F2 plants (R1, R2, R3; red bars) and each of the three sensitive F2 plants (S1, S2, S3; green bars) used for RNA-Seq in each experimental modality. RT-qPCR expression data is normalised using three reference genes. (PPTX 876 kb

Darmency ID-14-0256-R2-Field

Darmency ID-14-0256-R2-Fiel