The detailed information of 46 homoeologous collinear fragments of <i>B. rapa</i> and <i>B. oleracea</i> genomes identified in the <i>B. napus</i> genetic map (the source of the data come from Table S1).

a<p>Linkage group.</p>b<p>The unit of the length is cM.</p>c<p>Chromosome.</p>d<p>Percentage. The percentage refers that the proportion of the physical length of the homoeologous collinear fragment accounts for the whole physical length of the corresponding <i>B. rapa</i> (chromosome_v1.5) or <i>B. oleracea</i> (chromosome_v1.0) chromosome.</p><p>The detailed information of 46 homoeologous collinear fragments of <i>B. rapa</i> and <i>B. oleracea</i> genomes identified in the <i>B. napus</i> genetic map (the source of the data come from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#pone.0109910.s001" target="_blank">Table S1</a>).</p

Comparative genomic analysis of <i>B. napus</i> with <i>B. rapa</i>, <i>B. oleracea</i> and Arabidopsis (the source of the data come from Table S1).

<p>Comparative genomic analysis of <i>B. napus</i> with <i>B. rapa</i>, <i>B. oleracea</i> and Arabidopsis (the source of the data come from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#pone.0109910.s001" target="_blank">Table S1</a>).</p

Overexpression of Three Glucosinolate Biosynthesis Genes in <i>Brassica napus</i> Identifies Enhanced Resistance to <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i>

<div><p><i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i> are notorious plant pathogenic fungi with an extensive host range including Brassica crops. Glucosinolates (GSLs) are an important group of secondary metabolites characteristic of the Brassicales order, whose degradation products are proving to be increasingly important in plant protection. Enhancing the defense effect of GSL and their associated degradation products is an attractive strategy to strengthen the resistance of plants by transgenic approaches. We generated the lines of <i>Brassica napus</i> with three biosynthesis genes involved in GSL metabolic pathway (<i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i>), respectively. We then measured the foliar GSLs of each transgenic lines and inoculated them with <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea</i>. Compared with the wild type control, over-expressing <i>BnUGT74B1</i> in <i>B</i>. <i>napus</i> increased the aliphatic and indolic GSL levels by 1.7 and 1.5 folds in leaves respectively; while over-expressing <i>BnMAM1</i> or <i>BnCYP83A1</i> resulted in an approximate 1.5-fold higher only in the aliphatic GSL level in leaves. The results of plant inoculation demonstrated that <i>BnUGT74B1</i>-overexpressing lines showed less severe disease symptoms and tissue damage compared with the wild type control, but <i>BnMAM1</i> or <i>BnCYP83A1</i>-overexpressing lines showed no significant difference in comparison to the controls. These results suggest that the resistance to <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea</i> in <i>B</i>. <i>napus</i> could be enhanced through tailoring the GSL profiles by transgenic approaches or molecular breeding, which provides useful information to assist plant breeders to design improved breeding strategies.</p></div

Conserved blocks of Brassicaceae Ancestral Karyotype on <i>Brassica napus</i> genetic map.

<p>For each linkage group (LG), the left vertical bar represents the LG with mapped markers (red dashes for single nucleotide polymorphisms (SNPs) and black for simple sequence repeat (SSR)). The conserved Arabidopsis blocks are listed on the right of each LG. The length of LG bars is proportional to their genetic distances. The conserved blocks are identified according to their positions in the Arabidopsis genome (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#s4" target="_blank">Materials and Methods</a>) and depicted with colors based on the Ancestral Karyotype chromosome positions as described by Schranz et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#pone.0109910-Schranz1" target="_blank">[9]</a>. Inverted letters for respective conserved blocks indicate inversions in the LGs relative to Arabidopsis chromosomes. The length of each vertical bar for Ancestral karyotype chromosome is proportional to its physical length.</p

The copy number of the 24 identified conserved blocks and islands in the <i>B. napus</i> genetic map.

a<p> The conserved blocks are defined by Schranz et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#pone.0109910-Schranz1" target="_blank">[9]</a>.</p>b<p> The method for identification of the conserved block and island is described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109910#s4" target="_blank">Materials and Methods</a> section.</p><p>The copy number of the 24 identified conserved blocks and islands in the <i>B. napus</i> genetic map.</p

Resistance of <i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i> overexpressing T₂ plants to <i>S</i>. <i>sclerotiorum</i> and <i>B</i>. <i>cinerea</i>.

<p>(A-D) Disease responses of inoculated plants with <i>S</i>. <i>sclerotiorum</i> at 48 h post-inoculation (hpi). (E) Lesion sizes of leaves inoculated with <i>S</i>. <i>sclerotiorum</i>, which were measured for the first 48 h after inoculation. Means and SE are shown (n ≥ 12). The significant differences is shown as ** (P < 0.05) using t-tests. OE- M-1 and OE-M-2 are transgenic lines for <i>BnMAM1</i>, OE- C-1 and OE-C-2 are transgenic lines for <i>BnCYP83A1</i>, OE- U-1 and OE-U-2 are transgenic lines for <i>BnUGT74B1</i>. WT, untransformed wild-type control. (F-I) Disease responses of inoculated plants with <i>B</i>. <i>cinerea</i> at 96 hpi. (J) Lesion sizes of leaves inoculated with <i>Botrytis cinerea</i>, which were measured at 96 hpi. Means and SE are shown (n ≥ 12). The significant differences is shown as ** (P < 0.05) using t-tests.</p

The relationship of the <i>Brassica napus</i> genetic map to the <i>B. rapa</i> and <i>B. oleracea</i> genomes.

<p>For each <i>B. napus</i> linkage group (LG), the left vertical bar represents the LG with mapped markers (red dashes for single nucleotide polymorphisms (SNPs) and black for simple sequence repeat (SSR)). The length of LG bars is proportional to their genetic distances. The homoeologous collinear fragments of <i>B. rapa</i> and <i>B. oleracea</i> identified in the <i>B. napus</i> genetic map are listed on the right, and colored based on the positions on <i>B. rapa</i> or <i>B. oleracea</i> chromosomes. Inverted letters for respective homoeologous collinear fragments indicate inversions in the LGs relative to <i>B. rapa</i> or <i>B. oleracea</i> chromosomes. The length of each vertical bar for <i>B. rapa</i> and <i>B. oleracea</i> chromosome is proportional to its physical length.</p

GSL contents (nmol/g) in 7-week-old leaves of <i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i> overexpressing T₂ lines.

<p>The data (means ±SE and <i>P</i> value, n = 18) were collected from three independent experiments and were analyzed via ANOVA.</p><p>^aFor GSL abbreviations, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140491#pone.0140491.g001" target="_blank">Fig 1</a>.</p><p>^b<i>P</i> value for GSL differences between the overexpression line and WT as determined by ANOVA.</p><p>^cNot a significant <i>P</i> value (<i>P</i> > 0.05).</p><p>GSL contents (nmol/g) in 7-week-old leaves of <i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i> overexpressing T₂ lines.</p

Response of <i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i> to <i>Sclerotinia sclerotiorum</i> and <i>Botrytis cinerea</i> infection.

<p>Relative expression levels of <i>BnMAM1</i>, <i>BnCYP83A1</i> and <i>BnUGT74B1</i> in <i>Brassica napus</i> were determined by qRT-PCR at 0, 6, 12, 24 and 36 h post <i>S</i>. <i>sclerotiorum</i> inoculation (A) and 0, 12, 24, 48 and 72 h post <i>B</i>. <i>cinerea</i> inoculation (B). The expression levels were relative to no inoculation (0 h) and quantified by qRT-PCR. Values are means of three replicates. Each bar represents means ± SE.</p

Evolutionary relationship between <i>Brassica napus</i> and its progenitor species <i>B. rapa</i> and <i>B. oleracea</i>.

<p>Schematic diagram of the <i>B. napus</i> genome as revealed by a genetic linkage map comprised of simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) markers and comparative analyses with the <i>B. rapa</i>, <i>B. oleracea</i> and Arabidopsis genomes. The colored blocks at the outermost circle represent the Arabidopsis conserved blocks in the <i>B. napus</i> genome identified with the genetic linkage groups of <i>B. napus</i>, which is represented in the second outer circle (all circles were orientated clockwise). The third circle (from the outermost one) represents the <i>B. napus</i> genome that is reconstructed with 46 homoeologous collinear fragments of <i>B. rapa</i> and <i>B. oleracea</i>. Each homoeologous collinear fragment of <i>B. napus</i> (the third circle) is the same color as the corresponding chromosome of <i>B. rapa</i> and <i>B. oleracea</i> in the inner circle. The ribbons between the third and inner circle depict the origins of the homoeologous collinear fragments from <i>B. rapa</i> and <i>B. oleracea</i>. The inverted homoeologous collinear fragments are indicated with twisted ribbons. The gray ribbons represent the skeletons from the <i>B. rapa</i> and <i>B. oleracea</i> genomes retained in <i>B. napus</i> genome; The green ribbons represent the reciprocal translocations between homoeologous chromosomes from the A and C genomes; The purple ribbons represent the reciprocal translocations between non-homologous chromosomes from the A and C genomes; The yellow ribbon represents the repeat fragment from <i>B. rapa</i>/<i>B. oleracea</i> chromosome. The numbers in the inner circle (under each <i>B. rapa</i> or <i>B. oleracea</i> chromosome) are the percentages of all homoeologous collinear fragments of <i>B. rapa</i> or <i>B. oleracea</i> retained in the <i>B. napus</i> genome relative to the physical length of the corresponding <i>B. rapa</i> (chromosome_v1.5) or <i>B. oleracea</i> (chromosome_v1.0) chromosome.</p