Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use
Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in thes...
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| creator | Silva, Daiana Alves da Tsai, Siu Mui Chiorato, Alisson Fernando da Silva Andrade, Sónia Cristina Esteves, José Antonio de Fatima Recchia, Gustavo Henrique Morais Carbonell, Sérgio Augusto |
| description | Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level. |
| doi_str_mv | 10.1371/journal.pone.0210428 |
| format | Article |
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Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0210428</identifier><identifier>PMID: 30657755</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acid phosphatase ; Acids ; Agricultural production ; Analysis ; Analysis of Variance ; Annotations ; Bioinformatics ; Biology ; Biology and life sciences ; Common beans ; Crop growth ; Crops ; Down-Regulation - drug effects ; Down-Regulation - genetics ; Efficiency ; Enrichment ; Farms ; Food production ; Gene expression ; Gene Expression Regulation, Plant - drug effects ; Gene sequencing ; Genes ; Genetic aspects ; Genomes ; Genomics ; Genotype & phenotype ; Genotypes ; Hydroponics ; Metabolism ; Morphology ; Nutrient deficiency ; Phaseolus - drug effects ; Phaseolus - genetics ; Phaseolus - growth & development ; Phaseolus vulgaris ; Phosphates ; Phosphorus ; Phosphorus (Nutrient) ; Phosphorus - pharmacology ; Phosphorylation ; Physical Sciences ; Physiology ; Plant growth ; Plant Roots - drug effects ; Plant Roots - genetics ; Plant Shoots - drug effects ; Plant Shoots - genetics ; Purple acid phosphatase ; Pyrophosphatase ; Quantitative Trait, Heritable ; Ribonucleic acid ; RNA ; RNA sequencing ; Small farms ; Stresses ; Technology ; Transcription factors ; Transcription Factors - metabolism ; Transcriptome - drug effects ; Transcriptome - genetics ; Tropical environment ; Tropical environments ; Up-Regulation - drug effects ; Up-Regulation - genetics</subject><ispartof>PloS one, 2019-01, Vol.14 (1), p.e0210428-e0210428</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Silva et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 Silva et al 2019 Silva et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c659t-95f540991ce60fe7cb358c59ad4167dffbac57fc80772ed491dfac73c40226e13</citedby><cites>FETCH-LOGICAL-c659t-95f540991ce60fe7cb358c59ad4167dffbac57fc80772ed491dfac73c40226e13</cites><orcidid>0000-0002-5054-9806</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338380/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338380/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30657755$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Rouached, Hatem</contributor><creatorcontrib>Silva, Daiana Alves da</creatorcontrib><creatorcontrib>Tsai, Siu Mui</creatorcontrib><creatorcontrib>Chiorato, Alisson Fernando</creatorcontrib><creatorcontrib>da Silva Andrade, Sónia Cristina</creatorcontrib><creatorcontrib>Esteves, José Antonio de Fatima</creatorcontrib><creatorcontrib>Recchia, Gustavo Henrique</creatorcontrib><creatorcontrib>Morais Carbonell, Sérgio Augusto</creatorcontrib><title>Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.</description><subject>Acid phosphatase</subject><subject>Acids</subject><subject>Agricultural production</subject><subject>Analysis</subject><subject>Analysis of Variance</subject><subject>Annotations</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Biology and life sciences</subject><subject>Common beans</subject><subject>Crop growth</subject><subject>Crops</subject><subject>Down-Regulation - drug effects</subject><subject>Down-Regulation - genetics</subject><subject>Efficiency</subject><subject>Enrichment</subject><subject>Farms</subject><subject>Food production</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Hydroponics</subject><subject>Metabolism</subject><subject>Morphology</subject><subject>Nutrient deficiency</subject><subject>Phaseolus - drug effects</subject><subject>Phaseolus - genetics</subject><subject>Phaseolus - growth & development</subject><subject>Phaseolus vulgaris</subject><subject>Phosphates</subject><subject>Phosphorus</subject><subject>Phosphorus (Nutrient)</subject><subject>Phosphorus - pharmacology</subject><subject>Phosphorylation</subject><subject>Physical Sciences</subject><subject>Physiology</subject><subject>Plant growth</subject><subject>Plant Roots - drug effects</subject><subject>Plant Roots - genetics</subject><subject>Plant Shoots - drug effects</subject><subject>Plant Shoots - genetics</subject><subject>Purple acid phosphatase</subject><subject>Pyrophosphatase</subject><subject>Quantitative Trait, Heritable</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>Small farms</subject><subject>Stresses</subject><subject>Technology</subject><subject>Transcription factors</subject><subject>Transcription Factors - metabolism</subject><subject>Transcriptome - drug effects</subject><subject>Transcriptome - genetics</subject><subject>Tropical environment</subject><subject>Tropical environments</subject><subject>Up-Regulation - drug effects</subject><subject>Up-Regulation - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptUluL1DAYLaK46-o_EC34sj5MzaW5vQjD4mVhQB_0OaTpl5kMbTMm7cL8e1Onu-zIEkLC951zvgunKN5iVGEq8Kd9mOJguuoQBqgQwagm8llxiRUlK04Qff7of1G8SmmPEKOS85fFBUWcCcHYZbFbZ41j8qkMrhx3UNrQ92EoGzBDef1zZxKEbkrl3dRtTcywTfWxHKMZko3-MIYeygg50_phW4Jz3noY7HFWO-xCyjdm9pTgdfHCmS7Bm-W9Kn5__fLr5vtq8-Pb7c16s7KcqXGlmGM1Ugpb4MiBsA1l0jJl2hpz0TrXGMuEsxIJQaCtFW6dsYLaGhHCAdOr4v1J99CFpJclJU0wlyyviPGMuD0h2mD2-hB9b-JRB-P1v0CIW23i6G0HWjjFmKwb1SBSS8IaRDE32KomByyaq31eqk1ND62FIe-mOxM9zwx-p7fhTnNKJZUoC1wvAjH8mSCNuvfJQteZAcI09y1UxkksM_TDf9Cnp1tQW5MH8IMLua6dRfWaidyyIoplVPUEKp8Wem-zo5zP8TNCfSLYGFKK4B5mxEjPfrxvRs9-1IsfM-3d4_08kO4NSP8Cagjdaw</recordid><startdate>20190118</startdate><enddate>20190118</enddate><creator>Silva, Daiana Alves da</creator><creator>Tsai, Siu Mui</creator><creator>Chiorato, Alisson Fernando</creator><creator>da Silva Andrade, Sónia Cristina</creator><creator>Esteves, José Antonio de Fatima</creator><creator>Recchia, Gustavo Henrique</creator><creator>Morais Carbonell, Sérgio Augusto</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-5054-9806</orcidid></search><sort><creationdate>20190118</creationdate><title>Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use</title><author>Silva, Daiana Alves da ; Tsai, Siu Mui ; Chiorato, Alisson Fernando ; da Silva Andrade, Sónia Cristina ; Esteves, José Antonio de Fatima ; Recchia, Gustavo Henrique ; Morais Carbonell, Sérgio Augusto</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c659t-95f540991ce60fe7cb358c59ad4167dffbac57fc80772ed491dfac73c40226e13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Acid phosphatase</topic><topic>Acids</topic><topic>Agricultural production</topic><topic>Analysis</topic><topic>Analysis of Variance</topic><topic>Annotations</topic><topic>Bioinformatics</topic><topic>Biology</topic><topic>Biology and life sciences</topic><topic>Common beans</topic><topic>Crop growth</topic><topic>Crops</topic><topic>Down-Regulation - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Silva, Daiana Alves da</au><au>Tsai, Siu Mui</au><au>Chiorato, Alisson Fernando</au><au>da Silva Andrade, Sónia Cristina</au><au>Esteves, José Antonio de Fatima</au><au>Recchia, Gustavo Henrique</au><au>Morais Carbonell, Sérgio Augusto</au><au>Rouached, Hatem</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-01-18</date><risdate>2019</risdate><volume>14</volume><issue>1</issue><spage>e0210428</spage><epage>e0210428</epage><pages>e0210428-e0210428</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Common bean is a highly important food in tropical regions, where most production occurs on small farms with limited use of technology and, consequently, greater vulnerability to abiotic stresses such as nutritional stress. Usually phosphorus (P) is the most limiting nutrient for crop growth in these regions. The aim of this study was to characterize the gene expression profiles of the genotypes of common bean IAC Imperador (P-responsive) and DOR 364 (P-unresponsive) under different P concentrations using RNA-seq transcriptome sequencing technology. Plants were grown hydroponically, with application of two P concentrations (4.00 mg L-1 restrictive level and 8.00 mg L-1 control level). Differential expression analyses, annotation, and functional classification were performed comparing genotypes within each P rate administered and comparing each genotype response to the different P levels. Considering differential expression analyses within genotypes, IAC Imperador exhibited 1538 up-regulated genes under P restriction and 1679 up-regulated genes in the control, while DOR 364 exhibited 13 up-regulated genes in the control and only 2 up-regulated genes under P restriction, strongly corroborating P-unresponsiveness of this genotype. Genes related to phosphorus restriction were identified among the differentially expressed genes, including transcription factors such as WRKY, ERF, and MYB families, phosphatase related genes such as pyrophosphatase, acid phosphatase, and purple acid phosphatase, and phosphate transporters. The enrichment test for the P restriction treatment showed 123 enriched gene ontologies (GO) for IAC Imperador, while DOR 364 enriched only 24. Also, the enriched GO correlated with P metabolism, compound metabolic processes containing phosphate, nucleoside phosphate binding, phosphorylation, and also response to stresses. Thus, this study proved to be informative to phosphorus limitation in common bean showing global changes at transcript level.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30657755</pmid><doi>10.1371/journal.pone.0210428</doi><orcidid>https://orcid.org/0000-0002-5054-9806</orcidid><oa>free_for_read</oa></addata></record> |
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| language | eng |
| recordid | cdi_plos_journals_2168504256 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acid phosphatase Acids Agricultural production Analysis Analysis of Variance Annotations Bioinformatics Biology Biology and life sciences Common beans Crop growth Crops Down-Regulation - drug effects Down-Regulation - genetics Efficiency Enrichment Farms Food production Gene expression Gene Expression Regulation, Plant - drug effects Gene sequencing Genes Genetic aspects Genomes Genomics Genotype & phenotype Genotypes Hydroponics Metabolism Morphology Nutrient deficiency Phaseolus - drug effects Phaseolus - genetics Phaseolus - growth & development Phaseolus vulgaris Phosphates Phosphorus Phosphorus (Nutrient) Phosphorus - pharmacology Phosphorylation Physical Sciences Physiology Plant growth Plant Roots - drug effects Plant Roots - genetics Plant Shoots - drug effects Plant Shoots - genetics Purple acid phosphatase Pyrophosphatase Quantitative Trait, Heritable Ribonucleic acid RNA RNA sequencing Small farms Stresses Technology Transcription factors Transcription Factors - metabolism Transcriptome - drug effects Transcriptome - genetics Tropical environment Tropical environments Up-Regulation - drug effects Up-Regulation - genetics |
| title | Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-06T05%3A05%3A44IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Analysis%20of%20the%20common%20bean%20(Phaseolus%20vulgaris%20L.)%20transcriptome%20regarding%20efficiency%20of%20phosphorus%20use&rft.jtitle=PloS%20one&rft.au=Silva,%20Daiana%20Alves%20da&rft.date=2019-01-18&rft.volume=14&rft.issue=1&rft.spage=e0210428&rft.epage=e0210428&rft.pages=e0210428-e0210428&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0210428&rft_dat=%3Cgale_plos_%3EA570139295%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2168504256&rft_id=info:pmid/30657755&rft_galeid=A570139295&rft_doaj_id=oai_doaj_org_article_7f95584b9b024825b0316a1c9bb02c01&rfr_iscdi=true |