Dynamic transcriptome landscape of maize pericarp development
SUMMARY As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we develop...
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| Veröffentlicht in: | The Plant journal : for cell and molecular biology 2024-03, Vol.117 (5), p.1574-1591 |
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| container_title | The Plant journal : for cell and molecular biology |
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| creator | Zhang, Jihong Yue, Yang Hu, Mingjian Yi, Fei Chen, Jian Lai, Jinsheng Xin, Beibei |
| description | SUMMARY
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
Significance Statement
This study provides a high temporal resolution transcriptome atlas for unraveling the genetic control of maize pericarp development. |
| doi_str_mv | 10.1111/tpj.16548 |
| format | Article |
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As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
Significance Statement
This study provides a high temporal resolution transcriptome atlas for unraveling the genetic control of maize pericarp development.</description><identifier>ISSN: 0960-7412</identifier><identifier>EISSN: 1365-313X</identifier><identifier>DOI: 10.1111/tpj.16548</identifier><identifier>PMID: 37970738</identifier><language>eng</language><publisher>England: Blackwell Publishing Ltd</publisher><subject>Apoptosis ; Cell death ; cell wall ; Cell walls ; Clustering ; coexpression ; Corn ; Developmental stages ; Embryos ; Endosperm ; Endosperm - metabolism ; Fertilization ; Gene expression ; Gene Expression Regulation, Plant - genetics ; gene regulatory network ; Genes ; Genetic control ; Genomes ; Jasmonic acid ; maize (Zea mays) ; Pericarp ; pericarp development ; pericarp‐specific ; programmed cell death ; RNA‐seq ; Seeds - metabolism ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcriptome - genetics ; Transcriptomes ; Zea mays - metabolism</subject><ispartof>The Plant journal : for cell and molecular biology, 2024-03, Vol.117 (5), p.1574-1591</ispartof><rights>2023 Society for Experimental Biology and John Wiley & Sons Ltd.</rights><rights>Copyright © 2024 Society for Experimental Biology and John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3888-158c147177cbbf0693ecf1e091fcf8193c19e2b736fbdb98deae41421a83e253</citedby><cites>FETCH-LOGICAL-c3888-158c147177cbbf0693ecf1e091fcf8193c19e2b736fbdb98deae41421a83e253</cites><orcidid>0000-0002-1764-8394 ; 0000-0003-0448-2417</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Ftpj.16548$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Ftpj.16548$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37970738$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Jihong</creatorcontrib><creatorcontrib>Yue, Yang</creatorcontrib><creatorcontrib>Hu, Mingjian</creatorcontrib><creatorcontrib>Yi, Fei</creatorcontrib><creatorcontrib>Chen, Jian</creatorcontrib><creatorcontrib>Lai, Jinsheng</creatorcontrib><creatorcontrib>Xin, Beibei</creatorcontrib><title>Dynamic transcriptome landscape of maize pericarp development</title><title>The Plant journal : for cell and molecular biology</title><addtitle>Plant J</addtitle><description>SUMMARY
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
Significance Statement
This study provides a high temporal resolution transcriptome atlas for unraveling the genetic control of maize pericarp development.</description><subject>Apoptosis</subject><subject>Cell death</subject><subject>cell wall</subject><subject>Cell walls</subject><subject>Clustering</subject><subject>coexpression</subject><subject>Corn</subject><subject>Developmental stages</subject><subject>Embryos</subject><subject>Endosperm</subject><subject>Endosperm - metabolism</subject><subject>Fertilization</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>gene regulatory network</subject><subject>Genes</subject><subject>Genetic control</subject><subject>Genomes</subject><subject>Jasmonic acid</subject><subject>maize (Zea mays)</subject><subject>Pericarp</subject><subject>pericarp development</subject><subject>pericarp‐specific</subject><subject>programmed cell death</subject><subject>RNA‐seq</subject><subject>Seeds - metabolism</subject><subject>Transcription factors</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcriptome - genetics</subject><subject>Transcriptomes</subject><subject>Zea mays - metabolism</subject><issn>0960-7412</issn><issn>1365-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kDtPwzAURi0EoqUw8AdQJBYYQn3jJLYHBlTeqgRDBzbLcW6kVHlhJ6Dy6zGkMCBxl7scHX06hBwDvQB_875bX0CaxGKHTIGlSciAveySKZUpDXkM0YQcOLemFDhL430yYVxyypmYksvrTaPr0gS91Y0ztuz6tsag0k3ujO4waIug1uUHBh3a0mjbBTm-YdV2NTb9IdkrdOXwaPtnZHV7s1rch8unu4fF1TI0TAgRQiIMxBw4N1lW0FQyNAUglVCYQoBkBiRGmR9XZHkmRY4aY4gj0IJhlLAZORu1nW1fB3S9qktnsPIrsR2cioSkPEmjFDx6-gddt4Nt_DgVSQYi4XEqPHU-Usa2zlksVGfLWtuNAqq-kiqfVH0n9ezJ1jhkNea_5E9DD8xH4L2scPO_Sa2eH0flJxK2f7w</recordid><startdate>202403</startdate><enddate>202403</enddate><creator>Zhang, Jihong</creator><creator>Yue, Yang</creator><creator>Hu, Mingjian</creator><creator>Yi, Fei</creator><creator>Chen, Jian</creator><creator>Lai, Jinsheng</creator><creator>Xin, Beibei</creator><general>Blackwell Publishing Ltd</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>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1764-8394</orcidid><orcidid>https://orcid.org/0000-0003-0448-2417</orcidid></search><sort><creationdate>202403</creationdate><title>Dynamic transcriptome landscape of maize pericarp development</title><author>Zhang, Jihong ; Yue, Yang ; Hu, Mingjian ; Yi, Fei ; Chen, Jian ; Lai, Jinsheng ; Xin, Beibei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3888-158c147177cbbf0693ecf1e091fcf8193c19e2b736fbdb98deae41421a83e253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Apoptosis</topic><topic>Cell death</topic><topic>cell wall</topic><topic>Cell walls</topic><topic>Clustering</topic><topic>coexpression</topic><topic>Corn</topic><topic>Developmental stages</topic><topic>Embryos</topic><topic>Endosperm</topic><topic>Endosperm - metabolism</topic><topic>Fertilization</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant - genetics</topic><topic>gene regulatory network</topic><topic>Genes</topic><topic>Genetic control</topic><topic>Genomes</topic><topic>Jasmonic acid</topic><topic>maize (Zea mays)</topic><topic>Pericarp</topic><topic>pericarp development</topic><topic>pericarp‐specific</topic><topic>programmed cell death</topic><topic>RNA‐seq</topic><topic>Seeds - metabolism</topic><topic>Transcription factors</topic><topic>Transcription Factors - genetics</topic><topic>Transcription Factors - metabolism</topic><topic>Transcriptome - genetics</topic><topic>Transcriptomes</topic><topic>Zea mays - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Jihong</creatorcontrib><creatorcontrib>Yue, Yang</creatorcontrib><creatorcontrib>Hu, Mingjian</creatorcontrib><creatorcontrib>Yi, Fei</creatorcontrib><creatorcontrib>Chen, Jian</creatorcontrib><creatorcontrib>Lai, Jinsheng</creatorcontrib><creatorcontrib>Xin, Beibei</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The Plant journal : for cell and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Jihong</au><au>Yue, Yang</au><au>Hu, Mingjian</au><au>Yi, Fei</au><au>Chen, Jian</au><au>Lai, Jinsheng</au><au>Xin, Beibei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dynamic transcriptome landscape of maize pericarp development</atitle><jtitle>The Plant journal : for cell and molecular biology</jtitle><addtitle>Plant J</addtitle><date>2024-03</date><risdate>2024</risdate><volume>117</volume><issue>5</issue><spage>1574</spage><epage>1591</epage><pages>1574-1591</pages><issn>0960-7412</issn><eissn>1365-313X</eissn><abstract>SUMMARY
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome‐wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA‐seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non‐seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp‐specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene‐related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
Significance Statement
This study provides a high temporal resolution transcriptome atlas for unraveling the genetic control of maize pericarp development.</abstract><cop>England</cop><pub>Blackwell Publishing Ltd</pub><pmid>37970738</pmid><doi>10.1111/tpj.16548</doi><tpages>1591</tpages><orcidid>https://orcid.org/0000-0002-1764-8394</orcidid><orcidid>https://orcid.org/0000-0003-0448-2417</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | The Plant journal : for cell and molecular biology, 2024-03, Vol.117 (5), p.1574-1591 |
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| subjects | Apoptosis Cell death cell wall Cell walls Clustering coexpression Corn Developmental stages Embryos Endosperm Endosperm - metabolism Fertilization Gene expression Gene Expression Regulation, Plant - genetics gene regulatory network Genes Genetic control Genomes Jasmonic acid maize (Zea mays) Pericarp pericarp development pericarp‐specific programmed cell death RNA‐seq Seeds - metabolism Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcriptome - genetics Transcriptomes Zea mays - metabolism |
| title | Dynamic transcriptome landscape of maize pericarp development |
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