Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors
Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and...
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| Veröffentlicht in: | International journal of molecular sciences 2023-12, Vol.24 (23), p.17107 |
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| creator | Lu, Jianyu Wang, Zhenhui Li, Jinxi Zhao, Qian Qi, Fan Wang, Fu Xiaoyang, Chunxiao Tan, Guofei Wu, Hanlu Deyholos, Michael K Wang, Ningning Liu, Yingnan Zhang, Jian |
| description | Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17
genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17
(88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades;
genes were found in four clades. Most
gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of
genes were also analyzed. The three-dimensional structure of
proteins was predicted using homology modeling. The transcript expression data indicated that most
family members were highly expressed in flax fruit and embryos, whereas
,
and
were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both
and
were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense.
was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of
gene function and obtaining improved flax breeding lines. |
| doi_str_mv | 10.3390/ijms242317107 |
| format | Article |
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genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17
(88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades;
genes were found in four clades. Most
gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of
genes were also analyzed. The three-dimensional structure of
proteins was predicted using homology modeling. The transcript expression data indicated that most
family members were highly expressed in flax fruit and embryos, whereas
,
and
were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both
and
were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense.
was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of
gene function and obtaining improved flax breeding lines.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms242317107</identifier><identifier>PMID: 38069430</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amino acids ; Cell growth ; Chromosomes ; Flax - genetics ; Flax - metabolism ; Gene Expression Regulation, Plant ; Genes ; Genomes ; Localization ; MicroRNAs - genetics ; Phylogenetics ; Phylogeny ; Plant Breeding ; Plants, Genetically Modified - genetics ; Proteins ; Rice ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - metabolism</subject><ispartof>International journal of molecular sciences, 2023-12, Vol.24 (23), p.17107</ispartof><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c360t-237462f9af4808090fc72fb193b6b6b5ed8aaf5ee51a40789655801be557b4243</citedby><cites>FETCH-LOGICAL-c360t-237462f9af4808090fc72fb193b6b6b5ed8aaf5ee51a40789655801be557b4243</cites><orcidid>0000-0003-4205-3891 ; 0000-0002-8947-7619 ; 0000-0003-1507-4718 ; 0000-0002-1332-4480 ; 0000-0002-1308-3357</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38069430$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lu, Jianyu</creatorcontrib><creatorcontrib>Wang, Zhenhui</creatorcontrib><creatorcontrib>Li, Jinxi</creatorcontrib><creatorcontrib>Zhao, Qian</creatorcontrib><creatorcontrib>Qi, Fan</creatorcontrib><creatorcontrib>Wang, Fu</creatorcontrib><creatorcontrib>Xiaoyang, Chunxiao</creatorcontrib><creatorcontrib>Tan, Guofei</creatorcontrib><creatorcontrib>Wu, Hanlu</creatorcontrib><creatorcontrib>Deyholos, Michael K</creatorcontrib><creatorcontrib>Wang, Ningning</creatorcontrib><creatorcontrib>Liu, Yingnan</creatorcontrib><creatorcontrib>Zhang, Jian</creatorcontrib><title>Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17
genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17
(88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades;
genes were found in four clades. Most
gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of
genes were also analyzed. The three-dimensional structure of
proteins was predicted using homology modeling. The transcript expression data indicated that most
family members were highly expressed in flax fruit and embryos, whereas
,
and
were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both
and
were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense.
was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of
gene function and obtaining improved flax breeding lines.</description><subject>Amino acids</subject><subject>Cell growth</subject><subject>Chromosomes</subject><subject>Flax - genetics</subject><subject>Flax - metabolism</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genomes</subject><subject>Localization</subject><subject>MicroRNAs - genetics</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Breeding</subject><subject>Plants, Genetically Modified - genetics</subject><subject>Proteins</subject><subject>Rice</subject><subject>Transcription factors</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdkc1Lw0AQxRdRbK0evcqCl_YQnexHdvdYiq1CQSgVj2GTburWJFt3E7T_vZFWUZnDzPB-vMN7CF3GcEOpglu7qQJhhMYiBnGE-jEjJAJIxPGvu4fOQtgAEEq4OkU9KiFRjEIfvc5M7SoTPduVweNal7tgA3YFnpb6Aw_x3NZthdtgG93YEGzVffObEZ559968RAuzbstOqdd4qvPGeTycLaYjvPS6Drm328a6-iCFc3RS6DKYi8MeoKfp3XJyH80fZw-T8TzKaQJNRKhgCSmULpgECQqKXJAiixXNkm64WUmtC24MjzUDIVXCuYQ4M5yLjBFGB2i4991699aa0KSVDbkpS10b14aUKCAqIUKoDr3-h25c67sYOkoqxZjkSnZUtKdy70Lwpki33lba79IY0q8W0j8tdPzVwbXNKrP6ob9jp5-MzoD-</recordid><startdate>20231204</startdate><enddate>20231204</enddate><creator>Lu, Jianyu</creator><creator>Wang, Zhenhui</creator><creator>Li, Jinxi</creator><creator>Zhao, Qian</creator><creator>Qi, Fan</creator><creator>Wang, Fu</creator><creator>Xiaoyang, Chunxiao</creator><creator>Tan, Guofei</creator><creator>Wu, Hanlu</creator><creator>Deyholos, Michael K</creator><creator>Wang, Ningning</creator><creator>Liu, Yingnan</creator><creator>Zhang, Jian</creator><general>MDPI AG</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>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-4205-3891</orcidid><orcidid>https://orcid.org/0000-0002-8947-7619</orcidid><orcidid>https://orcid.org/0000-0003-1507-4718</orcidid><orcidid>https://orcid.org/0000-0002-1332-4480</orcidid><orcidid>https://orcid.org/0000-0002-1308-3357</orcidid></search><sort><creationdate>20231204</creationdate><title>Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors</title><author>Lu, Jianyu ; Wang, Zhenhui ; Li, Jinxi ; Zhao, Qian ; Qi, Fan ; Wang, Fu ; Xiaoyang, Chunxiao ; Tan, Guofei ; Wu, Hanlu ; Deyholos, Michael K ; Wang, Ningning ; Liu, Yingnan ; Zhang, Jian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c360t-237462f9af4808090fc72fb193b6b6b5ed8aaf5ee51a40789655801be557b4243</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Amino acids</topic><topic>Cell growth</topic><topic>Chromosomes</topic><topic>Flax - genetics</topic><topic>Flax - metabolism</topic><topic>Gene Expression Regulation, Plant</topic><topic>Genes</topic><topic>Genomes</topic><topic>Localization</topic><topic>MicroRNAs - genetics</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant Breeding</topic><topic>Plants, Genetically Modified - genetics</topic><topic>Proteins</topic><topic>Rice</topic><topic>Transcription factors</topic><topic>Transcription Factors - genetics</topic><topic>Transcription Factors - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lu, Jianyu</creatorcontrib><creatorcontrib>Wang, Zhenhui</creatorcontrib><creatorcontrib>Li, Jinxi</creatorcontrib><creatorcontrib>Zhao, Qian</creatorcontrib><creatorcontrib>Qi, Fan</creatorcontrib><creatorcontrib>Wang, Fu</creatorcontrib><creatorcontrib>Xiaoyang, Chunxiao</creatorcontrib><creatorcontrib>Tan, Guofei</creatorcontrib><creatorcontrib>Wu, Hanlu</creatorcontrib><creatorcontrib>Deyholos, Michael K</creatorcontrib><creatorcontrib>Wang, Ningning</creatorcontrib><creatorcontrib>Liu, Yingnan</creatorcontrib><creatorcontrib>Zhang, Jian</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lu, Jianyu</au><au>Wang, Zhenhui</au><au>Li, Jinxi</au><au>Zhao, Qian</au><au>Qi, Fan</au><au>Wang, Fu</au><au>Xiaoyang, Chunxiao</au><au>Tan, Guofei</au><au>Wu, Hanlu</au><au>Deyholos, Michael K</au><au>Wang, Ningning</au><au>Liu, Yingnan</au><au>Zhang, Jian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors</atitle><jtitle>International journal of molecular sciences</jtitle><addtitle>Int J Mol Sci</addtitle><date>2023-12-04</date><risdate>2023</risdate><volume>24</volume><issue>23</issue><spage>17107</spage><pages>17107-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17
genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17
(88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades;
genes were found in four clades. Most
gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of
genes were also analyzed. The three-dimensional structure of
proteins was predicted using homology modeling. The transcript expression data indicated that most
family members were highly expressed in flax fruit and embryos, whereas
,
and
were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both
and
were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense.
was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of
gene function and obtaining improved flax breeding lines.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38069430</pmid><doi>10.3390/ijms242317107</doi><orcidid>https://orcid.org/0000-0003-4205-3891</orcidid><orcidid>https://orcid.org/0000-0002-8947-7619</orcidid><orcidid>https://orcid.org/0000-0003-1507-4718</orcidid><orcidid>https://orcid.org/0000-0002-1332-4480</orcidid><orcidid>https://orcid.org/0000-0002-1308-3357</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Amino acids Cell growth Chromosomes Flax - genetics Flax - metabolism Gene Expression Regulation, Plant Genes Genomes Localization MicroRNAs - genetics Phylogenetics Phylogeny Plant Breeding Plants, Genetically Modified - genetics Proteins Rice Transcription factors Transcription Factors - genetics Transcription Factors - metabolism |
| title | Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors |
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