General guidelines for CRISPR/Cas-based genome editing in plants
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding me...
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| Veröffentlicht in: | Molecular biology reports 2022-12, Vol.49 (12), p.12151-12164 |
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| creator | Aksoy, Emre Yildirim, Kubilay Kavas, Musa Kayihan, Ceyhun Yerlikaya, Bayram Ali Çalik, Irmak Sevgen, İlkay Demirel, Ufuk |
| description | CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T
2
generation. |
| doi_str_mv | 10.1007/s11033-022-07773-8 |
| format | Article |
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generation.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-022-07773-8</identifier><identifier>PMID: 36107373</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Bioinformatics ; Biomedical and Life Sciences ; Cell culture ; Climate change ; CRISPR ; CRISPR-Cas systems ; CRISPR-Cas Systems - genetics ; crops ; Gene Editing - methods ; Genetic Engineering ; Genetic transformation ; genome ; Genome editing ; Genome, Plant - genetics ; Genomes ; guidelines ; Histology ; Life Sciences ; Morphology ; Plant Breeding ; Plants - genetics ; prediction ; Progress in genomics ; Promoters ; Review ; RNA ; RNA, Small Untranslated - genetics ; Tissue culture ; transcriptomics and breeding of crops</subject><ispartof>Molecular biology reports, 2022-12, Vol.49 (12), p.12151-12164</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2022. Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2022. The Author(s), under exclusive licence to Springer Nature B.V.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c338t-ab63c83f9df9a1b25397af4e94169a54cd7540ae70dabc75ce068055f67f91ae3</citedby><cites>FETCH-LOGICAL-c338t-ab63c83f9df9a1b25397af4e94169a54cd7540ae70dabc75ce068055f67f91ae3</cites><orcidid>0000-0002-9410-2715 ; 0000-0003-1684-4147 ; 0000-0002-2864-7709 ; 0000-0002-8185-2453 ; 0000-0002-3457-5086 ; 0000-0002-1495-5866 ; 0000-0003-1254-3515 ; 0000-0001-5903-2873</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/s11033-022-07773-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-022-07773-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36107373$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Aksoy, Emre</creatorcontrib><creatorcontrib>Yildirim, Kubilay</creatorcontrib><creatorcontrib>Kavas, Musa</creatorcontrib><creatorcontrib>Kayihan, Ceyhun</creatorcontrib><creatorcontrib>Yerlikaya, Bayram Ali</creatorcontrib><creatorcontrib>Çalik, Irmak</creatorcontrib><creatorcontrib>Sevgen, İlkay</creatorcontrib><creatorcontrib>Demirel, Ufuk</creatorcontrib><title>General guidelines for CRISPR/Cas-based genome editing in plants</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T
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generation.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Cell culture</subject><subject>Climate change</subject><subject>CRISPR</subject><subject>CRISPR-Cas systems</subject><subject>CRISPR-Cas Systems - genetics</subject><subject>crops</subject><subject>Gene Editing - methods</subject><subject>Genetic Engineering</subject><subject>Genetic transformation</subject><subject>genome</subject><subject>Genome editing</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>guidelines</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Morphology</subject><subject>Plant Breeding</subject><subject>Plants - genetics</subject><subject>prediction</subject><subject>Progress in genomics</subject><subject>Promoters</subject><subject>Review</subject><subject>RNA</subject><subject>RNA, Small Untranslated - genetics</subject><subject>Tissue culture</subject><subject>transcriptomics and breeding of crops</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kMFKxDAQhoMo7rr6Ah6k4MVL3UmTNMlNKboKC8qq55C209Kl265Je_Dt7dpVwYOnGZhv_hk-Qs4pXFMAOfeUAmMhRFEIUkoWqgMypWJouJbqkEyBAQ25EnRCTrxfAwCnUhyTCYspSCbZlNwssEFn66DsqxzrqkEfFK0LktXjy_NqnlgfptZjHpTYtBsMMK-6qimDqgm2tW06f0qOClt7PNvXGXm7v3tNHsLl0-IxuV2GGWOqC20as0yxQueFtjSNBNPSFhw1p7G2gme5FBwsSshtmkmRIcQKhChiWWhqkc3I1Zi7de17j74zm8pnWA9PYNt7EymuleKxVAN6-Qddt71rhu9MJHmkNBcxHahopDLXeu-wMFtXbaz7MBTMzq8Z_ZrBr_nya3bRF_voPt1g_rPyLXQA2Aj4YdSU6H5v_xP7Cfr8g70</recordid><startdate>20221201</startdate><enddate>20221201</enddate><creator>Aksoy, Emre</creator><creator>Yildirim, Kubilay</creator><creator>Kavas, Musa</creator><creator>Kayihan, Ceyhun</creator><creator>Yerlikaya, Bayram Ali</creator><creator>Çalik, Irmak</creator><creator>Sevgen, İlkay</creator><creator>Demirel, Ufuk</creator><general>Springer Netherlands</general><general>Springer Nature B.V</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>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0002-9410-2715</orcidid><orcidid>https://orcid.org/0000-0003-1684-4147</orcidid><orcidid>https://orcid.org/0000-0002-2864-7709</orcidid><orcidid>https://orcid.org/0000-0002-8185-2453</orcidid><orcidid>https://orcid.org/0000-0002-3457-5086</orcidid><orcidid>https://orcid.org/0000-0002-1495-5866</orcidid><orcidid>https://orcid.org/0000-0003-1254-3515</orcidid><orcidid>https://orcid.org/0000-0001-5903-2873</orcidid></search><sort><creationdate>20221201</creationdate><title>General guidelines for CRISPR/Cas-based genome editing in plants</title><author>Aksoy, Emre ; Yildirim, Kubilay ; Kavas, Musa ; Kayihan, Ceyhun ; Yerlikaya, Bayram Ali ; Çalik, Irmak ; Sevgen, İlkay ; Demirel, Ufuk</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c338t-ab63c83f9df9a1b25397af4e94169a54cd7540ae70dabc75ce068055f67f91ae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Cell culture</topic><topic>Climate change</topic><topic>CRISPR</topic><topic>CRISPR-Cas systems</topic><topic>CRISPR-Cas Systems - 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Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Aksoy, Emre</au><au>Yildirim, Kubilay</au><au>Kavas, Musa</au><au>Kayihan, Ceyhun</au><au>Yerlikaya, Bayram Ali</au><au>Çalik, Irmak</au><au>Sevgen, İlkay</au><au>Demirel, Ufuk</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>General guidelines for CRISPR/Cas-based genome editing in plants</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2022-12-01</date><risdate>2022</risdate><volume>49</volume><issue>12</issue><spage>12151</spage><epage>12164</epage><pages>12151-12164</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) technology is a versatile genome editing tool that has been used to improve agriculturally important plant traits. Due to its precision, CRISPR/Cas9 is more effective than either conventional plant breeding methods or standard genetic engineering approaches for the rapid development of new varieties resilient to climate change. In addition to knowledge in tissue culture-based plant transformation, effective gene-specific single guide RNA (sgRNA) design, prediction of its off-target effect and utilization of vectors, promoters, Cas proteins and terminators is required for CRISPR/Cas9. Various bioinformatics tools are available for the best sgRNA design and screening of the off-targets. Various tools are used in the delivery of CRISPR/Cas components into cells and the genome. Moreover, some recent studies proved the simultaneous silencing of different paralogs in the same family or several genes working in the same pathway by using multiple-target sgRNA designs. This review summarizes the type of promoters, Cas proteins, recognition sequences, and terminators available for the development of knock-out and overexpression plant lines. It also provides a general guideline for the development of genome-edited plants from the design of sgRNAs to the selection of non-transgenic genome-edited T
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| subjects | Animal Anatomy Animal Biochemistry Bioinformatics Biomedical and Life Sciences Cell culture Climate change CRISPR CRISPR-Cas systems CRISPR-Cas Systems - genetics crops Gene Editing - methods Genetic Engineering Genetic transformation genome Genome editing Genome, Plant - genetics Genomes guidelines Histology Life Sciences Morphology Plant Breeding Plants - genetics prediction Progress in genomics Promoters Review RNA RNA, Small Untranslated - genetics Tissue culture transcriptomics and breeding of crops |
| title | General guidelines for CRISPR/Cas-based genome editing in plants |
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