Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions
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{"title"=>"Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions", "type"=>"journal", "authors"=>[{"first_name"=>"Dung Tien", "last_name"=>"Le", "scopus_author_id"=>"7005205625"}, {"first_name"=>"Donavan L.", "last_name"=>"Aldrich", "scopus_author_id"=>"26221555200"}, {"first_name"=>"Babu", "last_name"=>"Valliyodan", "scopus_author_id"=>"12647034600"}, {"first_name"=>"Yasuko", "last_name"=>"Watanabe", "scopus_author_id"=>"55497634000"}, {"first_name"=>"Chien", "last_name"=>"van Ha", "scopus_author_id"=>"55372157800"}, {"first_name"=>"Rie", "last_name"=>"Nishiyama", "scopus_author_id"=>"7005685871"}, {"first_name"=>"Satish K.", "last_name"=>"Guttikonda", "scopus_author_id"=>"26221711600"}, {"first_name"=>"Truyen N.", "last_name"=>"Quach", "scopus_author_id"=>"26221938600"}, {"first_name"=>"Juan J.", "last_name"=>"Gutierrez-Gonzalez", "scopus_author_id"=>"27867763300"}, {"first_name"=>"Lam Son Phan", "last_name"=>"Tran", "scopus_author_id"=>"7102277565"}, {"first_name"=>"Henry T.", "last_name"=>"Nguyen", "scopus_author_id"=>"7403322495"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84867012974", "sgr"=>"84867012974", "pui"=>"365766162", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"23029532", "doi"=>"10.1371/journal.pone.0046487"}, "id"=>"71565ba6-027d-3947-9ffc-b14ac5966a05", "abstract"=>"Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid) treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the Fbox/ABC, Fbox/60s gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. Fbox and 60s genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the ELF1b/IDE and Fbox/ELF1b are the most stably expressed gene pairs in roots and shoots, respectively, while 60s/Fbox is the best gene pair in both tissues. For studying cold stress in roots or shoots, IDE/60s and Fbox/Act27 are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, 60s/ELF1b, ELF1b/Fbox and 60s/ELF1b are the most suitable reference genes, respectively. The expression of ELF1b/60s, 60s/Fbox and 60s/Fbox genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, 60s was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.", "link"=>"http://www.mendeley.com/research/evaluation-candidate-reference-genes-normalization-quantitative-rtpcr-soybean-tissues-under-various", "reader_count"=>63, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>6, "Researcher"=>17, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>6, "Researcher"=>17, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>51, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Japan"=>1, "Brazil"=>1, "India"=>1}, "group_count"=>1}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/567572"], "description"=>"<p>Differential expression of known dehydration-inducible genes normalized with <i>60S</i>, <i>Fbox</i> or <i>SUBI2</i> reference genes.</p>", "links"=>[], "tags"=>["dehydration-inducible", "genes", "normalized"], "article_id"=>238057, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.t004", "stats"=>{"downloads"=>6, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_of_known_dehydration_inducible_genes_normalized_with_60S_Fbox_or_SUBI2_reference_genes_/238057", "title"=>"Differential expression of known dehydration-inducible genes normalized with <i>60S</i>, <i>Fbox</i> or <i>SUBI2</i> reference genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-28 02:14:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/300281", "https://ndownloader.figshare.com/files/300326", "https://ndownloader.figshare.com/files/300353"], "description"=>"<div><p>Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid) treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the <em>Fbox</em>/<em>ABC</em>, <em>Fbox</em>/<em>60s</em> gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. <em>Fbox</em> and <em>60s</em> genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the <em>ELF1b</em>/<em>IDE</em> and <em>Fbox</em>/<em>ELF1b</em> are the most stably expressed gene pairs in roots and shoots, respectively, while <em>60s</em>/<em>Fbox</em> is the best gene pair in both tissues. For studying cold stress in roots or shoots, <em>IDE</em>/<em>60s</em> and <em>Fbox</em>/<em>Act27</em> are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, <em>60s</em>/<em>ELF1b</em>, <em>ELF1b</em>/<em>Fbox</em> and <em>60s</em>/<em>ELF1b</em> are the most suitable reference genes, respectively. The expression of <em>ELF1b</em>/<em>60s</em>, <em>60s</em>/<em>Fbox</em> and <em>60s</em>/<em>Fbox</em> genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, <em>60s</em> was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.</p> </div>", "links"=>[], "tags"=>["genes", "normalization", "quantitative", "rt-pcr", "soybean", "tissues", "abiotic", "conditions"], "article_id"=>119207, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046487.s001", "https://dx.doi.org/10.1371/journal.pone.0046487.s002", "https://dx.doi.org/10.1371/journal.pone.0046487.s003"], "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evaluation_of_Candidate_Reference_Genes_for_Normalization_of_Quantitative_RT_PCR_in_Soybean_Tissues_under_Various_Abiotic_Stress_Conditions/119207", "title"=>"Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-28 02:33:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/567139"], "description"=>"<p>(A) Dehydration treatment. (B) Salt stress treatment. (C) Cold stress treatment. (D) ABA treatment.</p>", "links"=>[], "tags"=>["ranking", "genes", "genorm", "tissues", "hormonal"], "article_id"=>237621, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_stability_and_ranking_for_the_candidate_reference_genes_as_determined_by_geNorm_in_the_root_tissues_under_individual_stress_or_hormonal_treatment_/237621", "title"=>"Expression stability and ranking for the candidate reference genes as determined by geNorm in the root tissues under individual stress or hormonal treatment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-28 02:07:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/567241"], "description"=>"<p>(A) Dehydration treatment. (B) Salt stress treatment. (C) Cold stress treatment. (D) ABA treatment.</p>", "links"=>[], "tags"=>["ranking", "genes", "genorm", "tissues", "hormonal"], "article_id"=>237716, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_stability_and_ranking_for_the_candidate_reference_genes_as_determined_by_geNorm_in_the_shoot_tissues_under_individual_stress_or_hormonal_treatment_/237716", "title"=>"Expression stability and ranking for the candidate reference genes as determined by geNorm in the shoot tissues under individual stress or hormonal treatment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-28 02:08:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/567042"], "description"=>"<p>Soybean seedlings were subjected to dehydration, cold stress, salt stress and ABA treatments, and geNorm was used to assess expression stability in (A) treated roots and shoots; (B) treated roots; (C) treated shoots.</p>", "links"=>[], "tags"=>["genes", "tissues", "soybean", "seedlings", "abiotic", "hormonal"], "article_id"=>237519, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_stability_of_the_candidate_reference_genes_in_root_and_shoot_tissues_of_soybean_seedlings_under_various_abiotic_stress_and_hormonal_treatments_/237519", "title"=>"Expression stability of the candidate reference genes in root and shoot tissues of soybean seedlings under various abiotic stress and hormonal treatments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-28 02:05:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/567324"], "description"=>"<p>(A) Dehydration treatment. (B) Salt stress treatment. (C) Cold stress treatment. (D) ABA treatment.</p>", "links"=>[], "tags"=>["ranking", "genes", "genorm", "tissues", "hormonal"], "article_id"=>237806, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_stability_and_ranking_for_the_candidate_reference_genes_as_determined_by_geNorm_in_both_root_and_shoot_tissues_under_individual_stress_or_hormonal_treatment_/237806", "title"=>"Expression stability and ranking for the candidate reference genes as determined by geNorm in both root and shoot tissues under individual stress or hormonal treatment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-28 02:10:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/567404"], "description"=>"<p>Data obtained for the top five genes are shown in bold letters, while those for the top two genes are in italic and bold letters.</p>", "links"=>[], "tags"=>["deviations", "delta", "ct", "tissues"], "article_id"=>237884, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_of_standard_deviations_of_delta_CT_obtained_from_tissues_under_individual_stress_/237884", "title"=>"Average of standard deviations of delta CT obtained from tissues under individual stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-28 02:11:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/567490"], "description"=>"a<p>The exact locations of primers on the transcripts are shown in the data set S1.</p>b<p>As calculated by LinRegPCR software.</p>", "links"=>[], "tags"=>["primer"], "article_id"=>237976, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_primer_sequence_and_related_information_for_each_candidate_reference_gene_/237976", "title"=>"List of primer sequence and related information for each candidate reference gene.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-28 02:12:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/567447"], "description"=>"<p>Data obtained for the top five genes are shown in bold letters, while those for the top two genes are in italic and bold letters.</p>", "links"=>[], "tags"=>["thresholds", "deviations", "delta", "ct", "tissues"], "article_id"=>237925, "categories"=>["Molecular Biology", "Biological Sciences", "Cell Biology", "Genetics", "Plant Biology"], "users"=>["Dung Tien Le", "Donavan L. Aldrich", "Babu Valliyodan", "Yasuko Watanabe", "Chien Van Ha", "Rie Nishiyama", "Satish K. Guttikonda", "Truyen N. Quach", "Juan J. Gutierrez-Gonzalez", "Lam-Son Phan Tran", "Henry T. Nguyen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046487.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cycle_thresholds_and_average_of_standard_deviations_STDEVP_of_delta_CT_obtained_from_tissues_under_all_stress_combinations_/237925", "title"=>"Cycle thresholds and average of standard deviations (STDEVP) of delta CT obtained from tissues under all stress combinations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-28 02:12:05"}

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Relative Metric

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