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241 results for “Brassica; Brassica napus”
Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus)
<p>Supplemental datasets associated with publication: Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (<em>Brassica napus</em>)</p> <p><strong>Abstract</strong></p> <ul> <li>Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species.</li> <li>Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with <em>Brassica napus</em> constitutive QDR to four contrasting fungal pathogens: <em>Alternaria brassicicola</em>, <em>Botrytis cinerea</em>, <em>Pyrenopeziza</em><em> brassicae</em> and <em>Verticillium longisporum. </em>We did not identify any loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen—hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to <em>V. longisporum </em>and potentially broad-spectrum QDR.</li> <li>This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutively expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents and advancement in our understanding if broad-spectrum QDR in <em>B. napus </em>and is a significant resource for the scientific community. </li> </ul> <p><strong>Description of data files</strong></p> <p><strong>Full dataset for input into AT analysis </strong>Full datasets (infection phenotypes for <em>A. brassicicola, B. cinerea, </em>or <em>V.longisporum, </em>ROS measurements for chitin, flg22, or elf18) and link to original <em>P. brassicae </em>dataset. These datasets were used for input into the Associative Transcriptomics pipeline (Nichols, 2022, <a href="https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075">https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075</a>). </p> <p><strong>Table S1 </strong>Mean, normalized phenotype data for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). These data were used for association transcriptomic analysis.<strong> </strong></p> <p><strong>Table S2 </strong>Full list of single nucleotide polymorphism (SNP) markers and significance levels from genome-wide association (GWA) analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. The best fit model for GWA analysis is indicated in the tab title. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates SNP location along the chromosome; the y-axis indicates the -log10(p) (P value). Qqplots are included to demonstrate model fit.</p> <p><strong>Table S3</strong> Full list of gene expression markers (GEMs) and significance levels from GEM analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae and Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates GEM location along the chromosome; the y-axis indicates the -log10(p) (P value). </p> <p><strong>Table S4 </strong>184 gene expression markers (GEMs) associated with chitin-induced ROS compared with GEMs associated with resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and<em> Verticillium longisporum</em>) and ROS response induced by flg22, and elf18. Lists correspond to Venn diagrams in Fig. 2. The first tab includes all 184 GEMs associated with chitin-induced ROS. The subsequent tabs include lists of shared GEMs associated with chitin-induced ROS response and each additional trait (quantitative disease resistance (QDR) to each fungal pathogen or additional PAMP-induced ROS responses). The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S5</strong> Enrichment analyses to determine if the number of gene expression markers (GEMs) shared between different lists is greater than the number of GEMs that would be expected by chance (e.g., lists of quantitative disease resistance (QDR) GEMs for two fungal pathogens). The representation factor is the number of overlapping GEMs divided by the expected number of overlapping GEMs drawn from two independent groups (traits), considering the total number of GEMs sequenced (53884). A representation factor > 1 indicates more overlap than expected of two groups, a representation factor < 1 indicates less overlap than expected, and a representation factor of 1 indicates that the two groups by the number of genes expected for independent groups of genes. </p> <p><strong>Table S6 R</strong>esults from Weighted Co-expression Gene Network Analysis (WGCNA). The first tab indicates significant modules from WGCNA analysis. Black and magenta modules are associated with antagonistic effects on resistance/susceptibility to all four pathogens. The second tab includes a full list of the GEM markers (Table S3), which are in significant WGCNA modules. The third, fourth and, fifth tabs indicate all significant GEMs in the black module, GO terms associated with GEMs in the black module, and all GO terms associated with the black module, respectively. The sixth, seventh and, eighth tabs indicate all significant GEMs in the magenta module, GO terms associated with GEMs in the magenta module, and all GO terms associated with the magenta module, respectively.</p> <p><strong>Table S7 </strong>Shared gene expression markers (GEMs) associated with resistance to different pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>). Lists correspond to matrices and Venn diagrams in Fig. 3. The first tab includes all GEMs associated quantitative disease resistance (QDR) to the fungal pathogens. The subsequent tabs include lists of shared GEMs associated with QDR to two or more fungal pathogens. The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S8 </strong>List of genes in linkage disequilibrium with the top marker for <em>Verticillium longisporum</em> resistance from genome-wide association (GWA) analysis on chromosome A09 (107 genes)(Tab 1) and the homoeologous region on C08 (Tab 2). Their percentage identity and query coverage in <em>Brassica napus</em> reference genotypes Quinta, Tapidor, Westar and Zhongshuang 11 compared to the <em>B. napus</em> pantranscriptome is indicated. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p> </p>
Chromosome-scale assembly of winter oilseed rape Brassica napus
<p>The files correspond to data and results referenced in research article titled "Chromosome-scale assembly of winter oilseed rape Brassica napus".</p> <p>Data files below were used in the scaffolding process of genome assembly:</p> <ol> <li>Genetic maps (csv) <ul> <li>ExR53-DH_60kSNPmap</li> <li>ExV8-DH_60kSNPmap</li> </ul> </li> </ol> <p>Result files below are assembled sequences of the genome and the predicted annotation:</p> <ol> <li>Genome assembly (Express617_v1.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_cds.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_gene.gff3.gz)</li> <li>Predicted protein sequences (Express617_v1_protein.fa.gz)</li> <li>Predicted repetitive elements (Express617_v1_repeats.gff.gz)</li> </ol>
Assembly and comparison of two closely related Brassica napus genomes
<p>Here we present the <em>de novo</em> assembly of the <em>B. napus</em> cultivar Tapidor and comparison with an improved assembly of the <em>B. napus</em> cultivar Darmor<em>-bzh</em>. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor<em>-bzh</em> contains a greater number of genes than the genome of Tapidor.</p>
Fig.2. The phylogenetic tree for 72 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape
Fig.2. The phylogenetic tree for 72 individual of Brassica napus constructed on the basis of RAPD data: M - 'Maskot, S - 'Sw Savan', H -'Heros', U -'Ural', L -'Landmark'
Fig.1 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape
Fig.1. DNA fingerprints from different samples of different oilseed rape cultivars obtained by PCR with primers: OPA-01-S1-S6-'SwSavan'; OPA-04-H1-H6-'Heros'; OPA-04-U1-U6-'Ural'; OPA-09-L1- L5-'Landmark'; OPA11-M1-M6-'Maskot'. M-Gene RulerTM 100 bp DNA Ladder Plus (MBI Fermentas)
Figure 3 in Comparative effectiveness of EDTA and citric acid assisted phytoremediation of Ni contaminated soil by using canola (Brassica napus)
Figure 3. The role of EDTA and citric acid on (a) leaf turgor potential and (b) water use efficiency, (c) potassium and (d) sodium at vegetative stage for phytoremediation of Ni by using canola plant.
Figure 4 in Comparative effectiveness of EDTA and citric acid assisted phytoremediation of Ni contaminated soil by using canola (Brassica napus)
Figure 4. The role of EDTA and citric acid on (a) SOD and (b) CAT, (c) POD, (d) total free amino acid, (e) total soluble proteins, (f) total soluble sugars at vegetative stage for phytoremediation of Ni by using canola plant and the role of EDTA and citric acid on Ni contents (mg/ pot) in above ground biomass (g) at vegetative stage for phytoremediation of Ni by using canola.
Figure 1 in Comparative effectiveness of EDTA and citric acid assisted phytoremediation of Ni contaminated soil by using canola (Brassica napus)
Figure 1. The role of EDTA and CA on (a) plant height and (b) shoot fresh weight at the vegetative stage of two canola cultivars (Con-II and Oscar, respectively) in control and Ni treatment and the role of EDTA and citric acid on (c) dry weight and (d) photosynthetic rate at vegetative stage for phytoremediation of Ni by using canola plant.
Fig. 3 in Effect of Solenopsis invicta (Hymenoptera: Formicidae) on flower-visiting behavior of insects on Brassica napus (Brassicales: Brassicaceae)
Fig. 3. The cumulative probability of visiting frequency and duration of each visit of Pieris rapae on Brassica napus in fire ant–excluded, fire ant–included, and fire-ant-and-aphid-included plots.
Fig. 2 in Effect of Solenopsis invicta (Hymenoptera: Formicidae) on flower-visiting behavior of insects on Brassica napus (Brassicales: Brassicaceae)
Fig. 2. Daily number (mean ± SE, the number of Frankliniella intonsa was calculated per 10 min per 10 flowers) of flower visitors on Brassica napus in fire ant–excluded, fire ant–included, and fire-ant-and-aphid-included plots.
Fig. 1 in Effect of Solenopsis invicta (Hymenoptera: Formicidae) on flower-visiting behavior of insects on Brassica napus (Brassicales: Brassicaceae)
Fig. 1. Means (± SE) of species richness (A) and total number (B) of flower visitors on Brassica napus in fire ant–excluded, fire ant–included, and fire-antand-aphid-included plots.
Fig. 4 in Effect of Solenopsis invicta (Hymenoptera: Formicidae) on flower-visiting behavior of insects on Brassica napus (Brassicales: Brassicaceae)
Fig. 4. GC-EAD responses of Pieris rapae males to volatiles of Solenopsis invicta. GC-EAD active compounds: (1) n-tricosane; (2) 3-methyl tricosane; (3) unknown; (4) n-pentacosane; (5) 13-methyl pentacosane; (6) n-heptacosane; (7) 13,15-dimethyl heptacosane.
Brassica napus L. (BR0000010443330)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000025203349)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000010443286)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000012274604)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000012274710)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000010443705)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000012543816)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Brassica napus L. (BR0000022407160)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
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