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A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems
Summary Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis of its early development is lacking. Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice inflorescence cells and construc...
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| Published in: | The New phytologist 2022-04, Vol.234 (2), p.494-512 |
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| Main Authors: | , , , , , , , , , , , , , |
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| Language: | English |
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| cites | cdi_FETCH-LOGICAL-c3538-c8fb9d19c246ab9d7b162a738f19c7d6fc319b41193ea9ead27b57452e2534ad3 |
| container_end_page | 512 |
| container_issue | 2 |
| container_start_page | 494 |
| container_title | The New phytologist |
| container_volume | 234 |
| creator | Zong, Jie Wang, Li Zhu, Lu Bian, Lianle Zhang, Bo Chen, Xiaofei Huang, Guoqiang Zhang, Xuelian Fan, Junyi Cao, Liming Coupland, George Liang, Wanqi Zhang, Dabing Yuan, Zheng |
| description | Summary
Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis of its early development is lacking.
Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome‐scale gene expression resource covering the inflorescence‐to‐floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.
Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.
Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single‐cell‐level insights into AM differentiation and floret development. |
| doi_str_mv | 10.1111/nph.18008 |
| format | article |
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Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis of its early development is lacking.
Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome‐scale gene expression resource covering the inflorescence‐to‐floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.
Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.
Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single‐cell‐level insights into AM differentiation and floret development.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/nph.18008</identifier><identifier>PMID: 35118670</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Auxins ; axillary meristem ; Cell differentiation ; Differentiation ; differentiation trajectory ; Fluorescent indicators ; Gene expression ; Gene Expression Regulation, Plant ; Gene sequencing ; Genomes ; Hybridization ; Inflorescence ; Meristem - metabolism ; Meristems ; Oryza - metabolism ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Rice ; rice inflorescence ; RNA sequencing ; scRNA‐seq ; spikelet ; Transcription ; Transcriptome - genetics ; Transcriptomics</subject><ispartof>The New phytologist, 2022-04, Vol.234 (2), p.494-512</ispartof><rights>2022 The Authors. © 2022 New Phytologist Foundation</rights><rights>2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.</rights><rights>Copyright © 2022 New Phytologist Trust</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3538-c8fb9d19c246ab9d7b162a738f19c7d6fc319b41193ea9ead27b57452e2534ad3</citedby><cites>FETCH-LOGICAL-c3538-c8fb9d19c246ab9d7b162a738f19c7d6fc319b41193ea9ead27b57452e2534ad3</cites><orcidid>0000-0001-5315-9224 ; 0000-0002-3237-319X ; 0000-0001-8797-2811 ; 0000-0002-9938-5793 ; 0000-0001-6107-3228 ; 0000-0002-6103-5704 ; 0000-0003-1254-0410 ; 0000-0001-9702-1147 ; 0000-0002-0003-2147 ; 0000-0003-3181-9812 ; 0000-0003-4716-4857 ; 0000-0001-6988-4172</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35118670$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zong, Jie</creatorcontrib><creatorcontrib>Wang, Li</creatorcontrib><creatorcontrib>Zhu, Lu</creatorcontrib><creatorcontrib>Bian, Lianle</creatorcontrib><creatorcontrib>Zhang, Bo</creatorcontrib><creatorcontrib>Chen, Xiaofei</creatorcontrib><creatorcontrib>Huang, Guoqiang</creatorcontrib><creatorcontrib>Zhang, Xuelian</creatorcontrib><creatorcontrib>Fan, Junyi</creatorcontrib><creatorcontrib>Cao, Liming</creatorcontrib><creatorcontrib>Coupland, George</creatorcontrib><creatorcontrib>Liang, Wanqi</creatorcontrib><creatorcontrib>Zhang, Dabing</creatorcontrib><creatorcontrib>Yuan, Zheng</creatorcontrib><title>A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>Summary
Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis of its early development is lacking.
Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome‐scale gene expression resource covering the inflorescence‐to‐floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.
Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.
Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single‐cell‐level insights into AM differentiation and floret development.</description><subject>Auxins</subject><subject>axillary meristem</subject><subject>Cell differentiation</subject><subject>Differentiation</subject><subject>differentiation trajectory</subject><subject>Fluorescent indicators</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene sequencing</subject><subject>Genomes</subject><subject>Hybridization</subject><subject>Inflorescence</subject><subject>Meristem - metabolism</subject><subject>Meristems</subject><subject>Oryza - metabolism</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Rice</subject><subject>rice inflorescence</subject><subject>RNA sequencing</subject><subject>scRNA‐seq</subject><subject>spikelet</subject><subject>Transcription</subject><subject>Transcriptome - genetics</subject><subject>Transcriptomics</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp1kctOxCAUhonR6HhZ-AKGxI0uqlxaSpfGeEuMutDEXUPpqTJpoQKjmbcXp-rCRBZw4Hz5AvwI7VNyQtM4tePrCZWEyDU0o7moMkl5uY5mhDCZiVw8b6HtEOaEkKoQbBNt8YJSKUoyQ8sz7I0GHIx96QFr6HscvbJBezNGNxiNVexVwC10xkLA8RVS_Q69GwewUa3wOejovElt102-rnceIla2xcauNkGDTY0BvAkRhrCLNjrVB9j7XnfQ0-XF4_l1dnt_dXN-dptpXnCZadk1VUsrzXKhUlU2VDBVctmls7IVnea0anJKKw6qAtWysinKvGDACp6rlu-go8k7eve2gBDrwYSvdyoLbhFqJpgg6TcqmdDDP-jcLbxNt0tUTliayjxRxxOlvQvBQ1eP3gzKL2tK6q886pRHvcojsQffxkUzQPtL_gSQgNMJ-DA9LP831XcP15PyE_ZVljI</recordid><startdate>202204</startdate><enddate>202204</enddate><creator>Zong, Jie</creator><creator>Wang, Li</creator><creator>Zhu, Lu</creator><creator>Bian, Lianle</creator><creator>Zhang, Bo</creator><creator>Chen, Xiaofei</creator><creator>Huang, Guoqiang</creator><creator>Zhang, Xuelian</creator><creator>Fan, Junyi</creator><creator>Cao, Liming</creator><creator>Coupland, George</creator><creator>Liang, Wanqi</creator><creator>Zhang, Dabing</creator><creator>Yuan, Zheng</creator><general>Wiley Subscription Services, Inc</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>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-5315-9224</orcidid><orcidid>https://orcid.org/0000-0002-3237-319X</orcidid><orcidid>https://orcid.org/0000-0001-8797-2811</orcidid><orcidid>https://orcid.org/0000-0002-9938-5793</orcidid><orcidid>https://orcid.org/0000-0001-6107-3228</orcidid><orcidid>https://orcid.org/0000-0002-6103-5704</orcidid><orcidid>https://orcid.org/0000-0003-1254-0410</orcidid><orcidid>https://orcid.org/0000-0001-9702-1147</orcidid><orcidid>https://orcid.org/0000-0002-0003-2147</orcidid><orcidid>https://orcid.org/0000-0003-3181-9812</orcidid><orcidid>https://orcid.org/0000-0003-4716-4857</orcidid><orcidid>https://orcid.org/0000-0001-6988-4172</orcidid></search><sort><creationdate>202204</creationdate><title>A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems</title><author>Zong, Jie ; Wang, Li ; Zhu, Lu ; Bian, Lianle ; Zhang, Bo ; Chen, Xiaofei ; Huang, Guoqiang ; Zhang, Xuelian ; Fan, Junyi ; Cao, Liming ; Coupland, George ; Liang, Wanqi ; Zhang, Dabing ; Yuan, Zheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3538-c8fb9d19c246ab9d7b162a738f19c7d6fc319b41193ea9ead27b57452e2534ad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Auxins</topic><topic>axillary meristem</topic><topic>Cell differentiation</topic><topic>Differentiation</topic><topic>differentiation trajectory</topic><topic>Fluorescent indicators</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene sequencing</topic><topic>Genomes</topic><topic>Hybridization</topic><topic>Inflorescence</topic><topic>Meristem - metabolism</topic><topic>Meristems</topic><topic>Oryza - metabolism</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Rice</topic><topic>rice inflorescence</topic><topic>RNA sequencing</topic><topic>scRNA‐seq</topic><topic>spikelet</topic><topic>Transcription</topic><topic>Transcriptome - genetics</topic><topic>Transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zong, Jie</creatorcontrib><creatorcontrib>Wang, Li</creatorcontrib><creatorcontrib>Zhu, Lu</creatorcontrib><creatorcontrib>Bian, Lianle</creatorcontrib><creatorcontrib>Zhang, Bo</creatorcontrib><creatorcontrib>Chen, Xiaofei</creatorcontrib><creatorcontrib>Huang, Guoqiang</creatorcontrib><creatorcontrib>Zhang, Xuelian</creatorcontrib><creatorcontrib>Fan, Junyi</creatorcontrib><creatorcontrib>Cao, Liming</creatorcontrib><creatorcontrib>Coupland, George</creatorcontrib><creatorcontrib>Liang, Wanqi</creatorcontrib><creatorcontrib>Zhang, Dabing</creatorcontrib><creatorcontrib>Yuan, Zheng</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>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</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 New phytologist</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zong, Jie</au><au>Wang, Li</au><au>Zhu, Lu</au><au>Bian, Lianle</au><au>Zhang, Bo</au><au>Chen, Xiaofei</au><au>Huang, Guoqiang</au><au>Zhang, Xuelian</au><au>Fan, Junyi</au><au>Cao, Liming</au><au>Coupland, George</au><au>Liang, Wanqi</au><au>Zhang, Dabing</au><au>Yuan, Zheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems</atitle><jtitle>The New phytologist</jtitle><addtitle>New Phytol</addtitle><date>2022-04</date><risdate>2022</risdate><volume>234</volume><issue>2</issue><spage>494</spage><epage>512</epage><pages>494-512</pages><issn>0028-646X</issn><eissn>1469-8137</eissn><abstract>Summary
Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high‐resolution analysis of its early development is lacking.
Here, we have used high‐throughput single‐cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome‐scale gene expression resource covering the inflorescence‐to‐floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.
Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.
Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single‐cell‐level insights into AM differentiation and floret development.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>35118670</pmid><doi>10.1111/nph.18008</doi><tpages>19</tpages><orcidid>https://orcid.org/0000-0001-5315-9224</orcidid><orcidid>https://orcid.org/0000-0002-3237-319X</orcidid><orcidid>https://orcid.org/0000-0001-8797-2811</orcidid><orcidid>https://orcid.org/0000-0002-9938-5793</orcidid><orcidid>https://orcid.org/0000-0001-6107-3228</orcidid><orcidid>https://orcid.org/0000-0002-6103-5704</orcidid><orcidid>https://orcid.org/0000-0003-1254-0410</orcidid><orcidid>https://orcid.org/0000-0001-9702-1147</orcidid><orcidid>https://orcid.org/0000-0002-0003-2147</orcidid><orcidid>https://orcid.org/0000-0003-3181-9812</orcidid><orcidid>https://orcid.org/0000-0003-4716-4857</orcidid><orcidid>https://orcid.org/0000-0001-6988-4172</orcidid></addata></record> |
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| ispartof | The New phytologist, 2022-04, Vol.234 (2), p.494-512 |
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| subjects | Auxins axillary meristem Cell differentiation Differentiation differentiation trajectory Fluorescent indicators Gene expression Gene Expression Regulation, Plant Gene sequencing Genomes Hybridization Inflorescence Meristem - metabolism Meristems Oryza - metabolism Plant Proteins - genetics Plant Proteins - metabolism Rice rice inflorescence RNA sequencing scRNA‐seq spikelet Transcription Transcriptome - genetics Transcriptomics |
| title | A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems |
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