Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis
Indole-3-butyric acid (IBA) is widely used to encourage root development in cuttings of general field crops, vegetables, forest trees, fruit trees, and flowers. However, previous studies reported that IBA inhibited the germination of citrus buds via an unknown molecular mechanism. This study aimed t...
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| Veröffentlicht in: | Functional & integrative genomics 2021-11, Vol.21 (5-6), p.619-631 |
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| description | Indole-3-butyric acid (IBA) is widely used to encourage root development in cuttings of general field crops, vegetables, forest trees, fruit trees, and flowers. However, previous studies reported that IBA inhibited the germination of citrus buds via an unknown molecular mechanism. This study aimed to unravel the regulatory mechanisms underlying this inhibition. Citrus apical buds were sprayed with 100 mg ⋅ L
−1
IBA. Subsequently, the plant hormone levels were analyzed, and transcriptomic analysis was performed. The results identified 3325 upregulated genes and 2926 downregulated genes in the citrus apical buds. The gene set enrichment analysis method was used to determine the Gene Ontology related to the treatment. Genes were enriched into 157 sets, including 17 upregulated sets and 140 downregulated sets, after indole butyric acid treatment. The upregulated gene sets were related to glucose import, sugar transmembrane transporter activity, and photosynthesis. The downregulated genes were mainly related to the ribosomal subunit and cell cycle process under butyric acid treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the enrichment of 11 pathways. Of note, genes related to the ribosome and proteasome pathways were significantly downregulated. Only one pathway was significantly upregulated: the autophagy pathway. Overall, these results provided insights into the molecular mechanisms underpinning the IBA-mediated inhibition of citrus bud germination inhibition. Also, the study provided a large transcriptomics dataset that could be used for further research. |
| doi_str_mv | 10.1007/s10142-021-00802-y |
| format | Article |
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−1
IBA. Subsequently, the plant hormone levels were analyzed, and transcriptomic analysis was performed. The results identified 3325 upregulated genes and 2926 downregulated genes in the citrus apical buds. The gene set enrichment analysis method was used to determine the Gene Ontology related to the treatment. Genes were enriched into 157 sets, including 17 upregulated sets and 140 downregulated sets, after indole butyric acid treatment. The upregulated gene sets were related to glucose import, sugar transmembrane transporter activity, and photosynthesis. The downregulated genes were mainly related to the ribosomal subunit and cell cycle process under butyric acid treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the enrichment of 11 pathways. Of note, genes related to the ribosome and proteasome pathways were significantly downregulated. Only one pathway was significantly upregulated: the autophagy pathway. Overall, these results provided insights into the molecular mechanisms underpinning the IBA-mediated inhibition of citrus bud germination inhibition. Also, the study provided a large transcriptomics dataset that could be used for further research.</description><identifier>ISSN: 1438-793X</identifier><identifier>EISSN: 1438-7948</identifier><identifier>DOI: 10.1007/s10142-021-00802-y</identifier><identifier>PMID: 34476672</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Acids ; Animal Genetics and Genomics ; Autophagy ; Biochemistry ; Bioinformatics ; Biomedical and Life Sciences ; Buds ; Cell Biology ; Cell cycle ; Citrus - genetics ; Citrus - metabolism ; Flowers ; Fruit trees ; Gene Expression Regulation, Plant ; Gene set enrichment analysis ; Genes ; Genetics & Heredity ; Genomes ; Germination ; Glucose transporter ; Indole-3-butyric acid ; Indoles - metabolism ; Life Sciences ; Life Sciences & Biomedicine ; Microbial Genetics and Genomics ; Molecular modelling ; Original Article ; Phagocytosis ; Photosynthesis ; Plant Genetics and Genomics ; Proteasomes ; Science & Technology ; Transcriptome ; Trees</subject><ispartof>Functional & integrative genomics, 2021-11, Vol.21 (5-6), p.619-631</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021</rights><rights>2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.</rights><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>2</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000692061000001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c375t-4aa9fc449a220f6e4bb2dea13eaaee7592e72276ed5144a0ec0b3149ea7b21413</citedby><cites>FETCH-LOGICAL-c375t-4aa9fc449a220f6e4bb2dea13eaaee7592e72276ed5144a0ec0b3149ea7b21413</cites><orcidid>0000-0002-0792-9539</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10142-021-00802-y$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10142-021-00802-y$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>315,782,786,27931,27932,39265,41495,42564,51326</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34476672$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jiao, Yun</creatorcontrib><creatorcontrib>Xie, Rangjin</creatorcontrib><creatorcontrib>Zhang, Hongjin</creatorcontrib><title>Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis</title><title>Functional & integrative genomics</title><addtitle>Funct Integr Genomics</addtitle><addtitle>FUNCT INTEGR GENOMIC</addtitle><addtitle>Funct Integr Genomics</addtitle><description>Indole-3-butyric acid (IBA) is widely used to encourage root development in cuttings of general field crops, vegetables, forest trees, fruit trees, and flowers. However, previous studies reported that IBA inhibited the germination of citrus buds via an unknown molecular mechanism. This study aimed to unravel the regulatory mechanisms underlying this inhibition. Citrus apical buds were sprayed with 100 mg ⋅ L
−1
IBA. Subsequently, the plant hormone levels were analyzed, and transcriptomic analysis was performed. The results identified 3325 upregulated genes and 2926 downregulated genes in the citrus apical buds. The gene set enrichment analysis method was used to determine the Gene Ontology related to the treatment. Genes were enriched into 157 sets, including 17 upregulated sets and 140 downregulated sets, after indole butyric acid treatment. The upregulated gene sets were related to glucose import, sugar transmembrane transporter activity, and photosynthesis. The downregulated genes were mainly related to the ribosomal subunit and cell cycle process under butyric acid treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the enrichment of 11 pathways. Of note, genes related to the ribosome and proteasome pathways were significantly downregulated. Only one pathway was significantly upregulated: the autophagy pathway. Overall, these results provided insights into the molecular mechanisms underpinning the IBA-mediated inhibition of citrus bud germination inhibition. Also, the study provided a large transcriptomics dataset that could be used for further research.</description><subject>Acids</subject><subject>Animal Genetics and Genomics</subject><subject>Autophagy</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Buds</subject><subject>Cell Biology</subject><subject>Cell cycle</subject><subject>Citrus - genetics</subject><subject>Citrus - metabolism</subject><subject>Flowers</subject><subject>Fruit trees</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genetics & Heredity</subject><subject>Genomes</subject><subject>Germination</subject><subject>Glucose transporter</subject><subject>Indole-3-butyric acid</subject><subject>Indoles - metabolism</subject><subject>Life Sciences</subject><subject>Life Sciences & Biomedicine</subject><subject>Microbial Genetics and Genomics</subject><subject>Molecular modelling</subject><subject>Original Article</subject><subject>Phagocytosis</subject><subject>Photosynthesis</subject><subject>Plant Genetics and Genomics</subject><subject>Proteasomes</subject><subject>Science & Technology</subject><subject>Transcriptome</subject><subject>Trees</subject><issn>1438-793X</issn><issn>1438-7948</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>HGBXW</sourceid><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqNkU2L1TAUhosozjj6B1xIwI0g1Xw1aZdy8WNgwI2Cu3KanjoZ2qQm6Vy686ebTscruBCzSQjP-3IOT1E8Z_QNo1S_jYwyyUvKWUlpTXm5PijOmRR1qRtZPzy9xbez4kmMN5TSijbicXEmpNRKaX5e_Lzs0SU7WAPJekf8QGafti8YyQzp-ghrJBCjNxYS9uRo0zWxrvcjlqLslrQGawgY2-dfYmwKSyTd0pPvGCbr9tZbCyQFcNEEOyc_bQkH4xptfFo8GmCM-Oz-vii-fnj_5fCpvPr88fLw7qo0QleplADNYKRsgHM6KJRdx3sEJhAAUVcNR825VthXTEqgaGgnmGwQdMeZZOKieLX3zsH_WDCmdrLR4DiCQ7_ElleqEbWoK5nRl3-hN34Jed6NqpWqNNcbxXfKBB9jwKGdg50grC2j7ean3f202U9756ddc-jFffXSTdifIr-FZOD1Dhyx80M0Fp3BE5YNqoZTlevz2Zaq_58-2HRn4-AXl3JU7NGYcZdl_VnyH_P_AsdDvxI</recordid><startdate>20211101</startdate><enddate>20211101</enddate><creator>Jiao, Yun</creator><creator>Xie, Rangjin</creator><creator>Zhang, Hongjin</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature</general><general>Springer Nature B.V</general><scope>BLEPL</scope><scope>DTL</scope><scope>HGBXW</scope><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>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PADUT</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-0792-9539</orcidid></search><sort><creationdate>20211101</creationdate><title>Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis</title><author>Jiao, Yun ; Xie, Rangjin ; Zhang, Hongjin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-4aa9fc449a220f6e4bb2dea13eaaee7592e72276ed5144a0ec0b3149ea7b21413</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Acids</topic><topic>Animal Genetics and Genomics</topic><topic>Autophagy</topic><topic>Biochemistry</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Buds</topic><topic>Cell Biology</topic><topic>Cell cycle</topic><topic>Citrus - genetics</topic><topic>Citrus - metabolism</topic><topic>Flowers</topic><topic>Fruit trees</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene set enrichment analysis</topic><topic>Genes</topic><topic>Genetics & Heredity</topic><topic>Genomes</topic><topic>Germination</topic><topic>Glucose transporter</topic><topic>Indole-3-butyric acid</topic><topic>Indoles - metabolism</topic><topic>Life Sciences</topic><topic>Life Sciences & Biomedicine</topic><topic>Microbial Genetics and Genomics</topic><topic>Molecular modelling</topic><topic>Original Article</topic><topic>Phagocytosis</topic><topic>Photosynthesis</topic><topic>Plant Genetics and Genomics</topic><topic>Proteasomes</topic><topic>Science & Technology</topic><topic>Transcriptome</topic><topic>Trees</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jiao, Yun</creatorcontrib><creatorcontrib>Xie, Rangjin</creatorcontrib><creatorcontrib>Zhang, Hongjin</creatorcontrib><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>Web of Science - 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Academic</collection><jtitle>Functional & integrative genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jiao, Yun</au><au>Xie, Rangjin</au><au>Zhang, Hongjin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis</atitle><jtitle>Functional & integrative genomics</jtitle><stitle>Funct Integr Genomics</stitle><stitle>FUNCT INTEGR GENOMIC</stitle><addtitle>Funct Integr Genomics</addtitle><date>2021-11-01</date><risdate>2021</risdate><volume>21</volume><issue>5-6</issue><spage>619</spage><epage>631</epage><pages>619-631</pages><issn>1438-793X</issn><eissn>1438-7948</eissn><abstract>Indole-3-butyric acid (IBA) is widely used to encourage root development in cuttings of general field crops, vegetables, forest trees, fruit trees, and flowers. However, previous studies reported that IBA inhibited the germination of citrus buds via an unknown molecular mechanism. This study aimed to unravel the regulatory mechanisms underlying this inhibition. Citrus apical buds were sprayed with 100 mg ⋅ L
−1
IBA. Subsequently, the plant hormone levels were analyzed, and transcriptomic analysis was performed. The results identified 3325 upregulated genes and 2926 downregulated genes in the citrus apical buds. The gene set enrichment analysis method was used to determine the Gene Ontology related to the treatment. Genes were enriched into 157 sets, including 17 upregulated sets and 140 downregulated sets, after indole butyric acid treatment. The upregulated gene sets were related to glucose import, sugar transmembrane transporter activity, and photosynthesis. The downregulated genes were mainly related to the ribosomal subunit and cell cycle process under butyric acid treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the enrichment of 11 pathways. Of note, genes related to the ribosome and proteasome pathways were significantly downregulated. Only one pathway was significantly upregulated: the autophagy pathway. Overall, these results provided insights into the molecular mechanisms underpinning the IBA-mediated inhibition of citrus bud germination inhibition. Also, the study provided a large transcriptomics dataset that could be used for further research.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>34476672</pmid><doi>10.1007/s10142-021-00802-y</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-0792-9539</orcidid></addata></record> |
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| subjects | Acids Animal Genetics and Genomics Autophagy Biochemistry Bioinformatics Biomedical and Life Sciences Buds Cell Biology Cell cycle Citrus - genetics Citrus - metabolism Flowers Fruit trees Gene Expression Regulation, Plant Gene set enrichment analysis Genes Genetics & Heredity Genomes Germination Glucose transporter Indole-3-butyric acid Indoles - metabolism Life Sciences Life Sciences & Biomedicine Microbial Genetics and Genomics Molecular modelling Original Article Phagocytosis Photosynthesis Plant Genetics and Genomics Proteasomes Science & Technology Transcriptome Trees |
| title | Identification of potential pathways associated with indole-3-butyric acid in citrus bud germination via transcriptomic analysis |
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