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{"title"=>"Reference Genes to Study Herbicide Stress Response in Lolium sp.: Up-Regulation of P450 Genes in Plants Resistant to Acetolactate-Synthase Inhibitors", "type"=>"journal", "authors"=>[{"first_name"=>"Arnaud", "last_name"=>"Duhoux", "scopus_author_id"=>"56633292600"}, {"first_name"=>"Christophe", "last_name"=>"Délye", "scopus_author_id"=>"6701632994"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84877810067", "scopus"=>"2-s2.0-84877810067", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "pui"=>"368926645", "doi"=>"10.1371/journal.pone.0063576", "pmid"=>"23696834"}, "id"=>"17f46876-8ee3-3b82-80bc-8aeb89db4b69", "abstract"=>"<p>Variation in the expression of numerous genes is at the basis of plant response to environmental stresses. Non-target-site-based resistance to herbicides (NTSR), the major threat to grass weed chemical control, is governed by a subset of the genes involved in herbicide stress response. Quantitative PCR assays allowing reliable comparison of gene expression are thus key to identify genes governing NTSR. This work aimed at identifying a set of reference genes with a stable expression to be used as an internal standard for the normalisation of quantitative PCR data in studies investigating NTSR to herbicides inhibiting acetolactate synthase (ALS) in the major grass weed <italic>Lolium</italic> sp. Gene expression stability was assessed in plants resistant or sensitive to two ALS inhibitors, subjected or not to herbicide stress. Using three complementary approaches implemented in the programs BestKeeper, NormFinder and geNorm, cap-binding protein, glyceraldehyde-3-phosphate-dehydrogenase and ubiquitin were identified as the most suitable reference genes. This reference gene set can probably be used to study herbicide response in other weed species. It was used to compare the expression of the genes encoding two herbicide target enzymes (ALS and acetyl-coenzyme A carboxylase) and five cytochromes P450 (CYP) with potential herbicide-degrading activity between plants resistant or sensitive to ALS inhibitors. Overall, herbicide application enhanced <italic>CYP</italic> gene expression. Constitutive up-regulation of all <italic>CYP</italic> genes observed in resistant plants compared to sensitive plants suggested enhanced secondary metabolism in the resistant plants. Comprehensive transcriptome studies associated to gene expression analyses using the reference gene set validated here are required to unravel NTSR genetic determinants.</p>", "link"=>"http://www.mendeley.com/research/reference-genes-study-herbicide-stress-response-lolium-sp-upregulation-p450-genes-plants-resistant-a", "reader_count"=>32, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>5, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>28, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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• {"files"=>["https://ndownloader.figshare.com/files/1062233"], "description"=>"<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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "ranking", "genes", "optimal", "normalisation"], "article_id"=>703990, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_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_/703990", "title"=>"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).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-16 01:06:30"}
• {"files"=>["https://ndownloader.figshare.com/files/1062234"], "description"=>"<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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "genes", "plants", "groups"], "article_id"=>703991, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_of_ALS_ACCase_and_five_CYP_genes_in_individual_Lolium_sp_plants_in_four_groups_of_samples_/703991", "title"=>"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.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-05-16 01:06:31"}
• {"files"=>["https://ndownloader.figshare.com/files/1062236"], "description"=>"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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "genes", "tested", "primer"], "article_id"=>703993, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Candidate_reference_genes_tested_and_primer_information_/703993", "title"=>"Candidate reference genes tested and primer information.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-16 01:06:33"}
• {"files"=>["https://ndownloader.figshare.com/files/1062237"], "description"=>"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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "plants", "samplings", "quantification", "bt", "24hat", "im2"], "article_id"=>703994, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_plants_in_the_samplings_used_for_target_gene_expression_quantification_BT_and_24HAT_samplings_IM2_and_P2_/703994", "title"=>"Number of plants in the samplings used for target gene expression quantification BT and 24HAT (samplings IM2 and P2).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-16 01:06:34"}
• {"files"=>["https://ndownloader.figshare.com/files/1062238"], "description"=>"1<p>BT, before treatment; xHAT, x hours after treatment.</p>2<p>S, sensitive; R, resistant.</p>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "samples", "genes", "im1"], "article_id"=>703995, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RNA_samples_used_to_assess_the_stability_of_candidate_reference_genes_samplings_IM1_and_P1_/703995", "title"=>"RNA samples used to assess the stability of candidate reference genes (samplings IM1 and P1).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-16 01:06:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1062239"], "description"=>"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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "genes", "samplings", "im1", "p1", "computed", "bestkeeper"], "article_id"=>703996, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_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_/703996", "title"=>"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.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-16 01:06:36"}
• {"files"=>["https://ndownloader.figshare.com/files/1062240"], "description"=>"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>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "genes", "primer", "qpcr"], "article_id"=>703997, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Target_genes_investigated_primer_and_qPCR_information_/703997", "title"=>"Target genes investigated, primer and qPCR information.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-05-16 01:06:37"}
• {"files"=>["https://ndownloader.figshare.com/files/1062242", "https://ndownloader.figshare.com/files/1062250", "https://ndownloader.figshare.com/files/1062251"], "description"=>"<div><p>Variation in the expression of numerous genes is at the basis of plant response to environmental stresses. Non-target-site-based resistance to herbicides (NTSR), the major threat to grass weed chemical control, is governed by a subset of the genes involved in herbicide stress response. Quantitative PCR assays allowing reliable comparison of gene expression are thus key to identify genes governing NTSR. This work aimed at identifying a set of reference genes with a stable expression to be used as an internal standard for the normalisation of quantitative PCR data in studies investigating NTSR to herbicides inhibiting acetolactate synthase (ALS) in the major grass weed <i>Lolium</i> sp. Gene expression stability was assessed in plants resistant or sensitive to two ALS inhibitors, subjected or not to herbicide stress. Using three complementary approaches implemented in the programs BestKeeper, NormFinder and geNorm, cap-binding protein, glyceraldehyde-3-phosphate-dehydrogenase and ubiquitin were identified as the most suitable reference genes. This reference gene set can probably be used to study herbicide response in other weed species. It was used to compare the expression of the genes encoding two herbicide target enzymes (ALS and acetyl-coenzyme A carboxylase) and five cytochromes P450 (CYP) with potential herbicide-degrading activity between plants resistant or sensitive to ALS inhibitors. Overall, herbicide application enhanced <i>CYP</i> gene expression. Constitutive up-regulation of all <i>CYP</i> genes observed in resistant plants compared to sensitive plants suggested enhanced secondary metabolism in the resistant plants. Comprehensive transcriptome studies associated to gene expression analyses using the reference gene set validated here are required to unravel NTSR genetic determinants.</p></div>", "links"=>[], "tags"=>["agrochemicals", "herbicides", "Biochemistry", "enzymes", "genetics", "gene expression", "DNA transcription", "Molecular cell biology", "Plant science", "Plant biochemistry", "Secondary metabolism", "Plant genetics", "genes", "herbicide", "up-regulation", "p450", "plants", "resistant", "acetolactate-synthase", "inhibitors"], "article_id"=>703998, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Arnaud Duhoux", "Christophe Délye"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063576.s001", "https://dx.doi.org/10.1371/journal.pone.0063576.s002", "https://dx.doi.org/10.1371/journal.pone.0063576.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Reference_Genes_to_Study_Herbicide_Stress_Response_in_Lolium_sp_Up_Regulation_of_P450_Genes_in_Plants_Resistant_to_Acetolactate_Synthase_Inhibitors/703998", "title"=>"Reference Genes to Study Herbicide Stress Response in <i>Lolium</i> sp.: Up-Regulation of P450 Genes in Plants Resistant to Acetolactate-Synthase Inhibitors", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-05-16 01:06:38"}

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Relative Metric

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F1000Prime