Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat ( Triticum aestivum L.)
The gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In...
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| Veröffentlicht in: | International journal of molecular sciences 2024-12, Vol.26 (1), p.133 |
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| creator | Zhang, Yang Xu, Yanmin Mao, Yulu Tan, Xiaodi Tian, Yuan Ma, Xiaofei Ji, Hutai Zhang, Dingyi |
| description | The
gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the
gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19
genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of
. Furthermore,
-acting elements within the promoters of
were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the
gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify
influencing grain development. Finally, it was found that
had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation. |
| doi_str_mv | 10.3390/ijms26010133 |
| format | Article |
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gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the
gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19
genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of
. Furthermore,
-acting elements within the promoters of
were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the
gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify
influencing grain development. Finally, it was found that
had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms26010133</identifier><identifier>PMID: 39795991</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amino acids ; Binding sites ; CCAAT-Binding Factor - genetics ; CCAAT-Binding Factor - metabolism ; Chromosomes ; Evolution ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes ; Genome, Plant ; Genomes ; Grain ; Haplotypes ; Localization ; Multigene Family ; Phylogenetics ; Phylogeny ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Polymorphism, Single Nucleotide ; Proteins ; Transcription factors ; Triticum - genetics ; Triticum - metabolism</subject><ispartof>International journal of molecular sciences, 2024-12, Vol.26 (1), p.133</ispartof><rights>2024 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><rights>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c300t-e074905c6bb828e74e06b4a9b49e88db27133c46eaa3c980be27d2c1b32c5b223</cites><orcidid>0000-0001-9639-5411</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/PMC11719562/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11719562/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39795991$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Yang</creatorcontrib><creatorcontrib>Xu, Yanmin</creatorcontrib><creatorcontrib>Mao, Yulu</creatorcontrib><creatorcontrib>Tan, Xiaodi</creatorcontrib><creatorcontrib>Tian, Yuan</creatorcontrib><creatorcontrib>Ma, Xiaofei</creatorcontrib><creatorcontrib>Ji, Hutai</creatorcontrib><creatorcontrib>Zhang, Dingyi</creatorcontrib><title>Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat ( Triticum aestivum L.)</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>The
gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the
gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19
genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of
. Furthermore,
-acting elements within the promoters of
were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the
gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify
influencing grain development. Finally, it was found that
had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.</description><subject>Amino acids</subject><subject>Binding sites</subject><subject>CCAAT-Binding Factor - genetics</subject><subject>CCAAT-Binding Factor - metabolism</subject><subject>Chromosomes</subject><subject>Evolution</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>Grain</subject><subject>Haplotypes</subject><subject>Localization</subject><subject>Multigene Family</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Proteins</subject><subject>Transcription factors</subject><subject>Triticum - genetics</subject><subject>Triticum - metabolism</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdkc1vEzEQxS0Eoh9w44wscSkSW_y5uz6hqGpKpQgOFFWcLNs7SRzt2sHercih_zsOLVXgNDPyb57m-SH0hpJzzhX56DdDZjWhhHL-DB1TwVhFSN08P-iP0EnOG0IYZ1K9REdcNUoqRY_R_RWEOEB16zvA1x2E0S-9M6OPAZvQ4ctf2wQ578dZMP0u-4zjEn-ZVz9muOwCnpvB9zvsAx7XZfJ978MKfxvNCvbk7RrMiM_wTfKjd9OADeTR35Vmcf7-FXqxNH2G14_1FH2fX95cfK4WX6-uL2aLynFCxgpIIxSRrra2ZS00AkhthVFWKGjbzrKmeHeiBmO4Uy2xwJqOOWo5c9Iyxk_Rpwfd7WQH6FyxmUyvt8kPJu10NF7_-xL8Wq_inaa0oUrWe4WzR4UUf07Fgh58dtD3JkCcsuZUCkEkFaSg7_5DN3FK5fP-ULyRrJW0UB8eKJdizgmWT9dQovfB6sNgC_720MET_DdJ_hu6jZ4s</recordid><startdate>20241227</startdate><enddate>20241227</enddate><creator>Zhang, Yang</creator><creator>Xu, Yanmin</creator><creator>Mao, Yulu</creator><creator>Tan, Xiaodi</creator><creator>Tian, Yuan</creator><creator>Ma, Xiaofei</creator><creator>Ji, Hutai</creator><creator>Zhang, Dingyi</creator><general>MDPI AG</general><general>MDPI</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>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-9639-5411</orcidid></search><sort><creationdate>20241227</creationdate><title>Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat ( Triticum aestivum L.)</title><author>Zhang, Yang ; 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gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the
gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19
genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of
. Furthermore,
-acting elements within the promoters of
were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the
gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify
influencing grain development. Finally, it was found that
had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39795991</pmid><doi>10.3390/ijms26010133</doi><orcidid>https://orcid.org/0000-0001-9639-5411</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | International journal of molecular sciences, 2024-12, Vol.26 (1), p.133 |
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| source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Amino acids Binding sites CCAAT-Binding Factor - genetics CCAAT-Binding Factor - metabolism Chromosomes Evolution Gene Expression Profiling Gene Expression Regulation, Plant Genes Genome, Plant Genomes Grain Haplotypes Localization Multigene Family Phylogenetics Phylogeny Plant Proteins - genetics Plant Proteins - metabolism Polymorphism, Single Nucleotide Proteins Transcription factors Triticum - genetics Triticum - metabolism |
| title | Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat ( Triticum aestivum L.) |
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