Examples of membrane leakage-related (MLR) genes.

<p>A, Four genes: two up-regulated genes, <i>Bra032994</i> (NA) and <i>Bra025083</i> (<i>cytochrome P450</i>; <i>CYP707A3</i>), and two down-regulated genes, <i>Bra006613</i> (<i>FAD</i>/<i>NAD(P)-binding oxidoreductase</i>) and <i>Bra016265</i> (<i>protein kinase superfamily protein</i>). B, Three <i>B</i>. <i>rapa</i> genes for <i>CYP707A3</i>. C, qRT-PCR of three <i>B</i>. <i>rapa</i> cytochrome P450 genes (<i>abscisic acid 8’-hydroxylase</i>). Relative expression was normalized to <i>BrActin</i> and is presented relative to 0 h expression levels. Two biological repeats were performed and error bars represent SD. HS, heat shock.</p

Electrolyte leakage of two DH lines, Chiifu and Kenshin, subjected to treatment at 45°C.

<p>Leakage is expressed as the ratio (%) of the conductivity of the initial (I) and final (F) solution. Error bars represent SD of six replicates.</p

Heat map of orphan genes induced by HS treatment.

<p>Heat map of orphan genes induced by HS treatment.</p

Short Time-series Expression Miner (STEM) clusters of expression profiles with HSR genes in Chiifu.

<p>The number of profiles in each cluster is at the top left corner of each STEM. Profiles are ordered based on the p-value significance of the number (at bottom-left corner) of assigned versus expected genes. Colored frame denotes significant profiles (P-value≤0.01). Each graph displays the mean expression pattern (black lines) of the profile genes.</p

Summary of transcription factor genes represented on the Br135K microarray.

<p>Summary of transcription factor genes represented on the Br135K microarray.</p

qRT-PCR verifications of the expression of several orphan genes.

<p>Relative expression was normalized to <i>BrActin</i> and is presented relative to 0 h expression levels. Two biological repeats were performed, and error bars represent SD. HS, heat shock.</p

GO annotation of intrinsically expressed genes.

<p>One gene can be associated with two or more GO terms. NA, no <i>Arabidopsis</i> homologs.</p

Expression patterns of marker genes for thermotolerance in Chiifu and Kenshin.

<p>PI value indicates probe intensity (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130451#pone.0130451.s022" target="_blank">S20 Table</a>). <b>A</b>, Expression patterns of basal thermotolerance marker genes (BT) and short-term acquired thermotolerance (SAT) in Chiifu and Kenshin. <b>B</b>, Expression patterns of long-term acquired thermotolerance (LAT) marker genes in Chiifu and Kenshin. <b>C</b>, Expression patterns of thermotolerance to moderately high temperatures (TMHT) marker genes in Chiifu and Kenshin.</p

Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in <i>Brassica rapa</i>

<div><p>Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5– 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included ‘response to heat’, ‘response to reactive oxygen species (ROS)’, ‘response to temperature stimulus’, ‘response to abiotic stimulus’, and ‘MAPKKK cascade’. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as <i>HsfB2A</i> (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like <i>glutathione peroxidase 2</i> (<i>BrGPX2</i>, <i>Bra022853</i>), protein kinases, and phosphatases. Among heat stress (HS) marker genes in <i>Arabidopsis</i>, only <i>exportin 1A</i> (<i>XPO1A</i>) (<i>Bra008580</i>, <i>Bra006382</i>) can be applied to <i>B</i>. <i>rapa </i>for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. <i>CYP707A3</i> (<i>Bra025083</i>, <i>Bra021965</i>), which is involved in the dehydration response in <i>Arabidopsis</i>, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including <i>DREB2A</i> (<i>Bra005852</i>), were involved in HS tolerance in both lines, <i>Bra024224 </i>(<i>MYB41</i>) and <i>Bra021735 </i>(a bZIP/<i>AIR1 </i>[<i>Anthocyanin-Impaired-Response-1</i>]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in <i>Brassica rapa</i> reveal a distinct HSR in this species. Our data could also provide a springboard for developing molecular markers of HS and for engineering HS tolerant <i>B</i>. <i>rapa</i>.</p></div

Heat map of genes induced/repressed by HS treatment.

<p>Heat map of genes induced/repressed by HS treatment.</p