Identification of novel seed longevity genes related to oxidative stress and seed coat by genome‐wide association studies and reverse genetics
Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant, Arabidopsis thaliana, for nat...
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| description | Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant, Arabidopsis thaliana, for natural ageing and for three accelerated ageing methods. Genome‐wide analysis, using publicly available single‐nucleotide polymorphisms (SNPs) data sets, identified multiple genomic regions associated with variation in seed longevity. Reverse genetics of 20 candidate genes in Columbia ecotype resulted in seven genes positive for seed longevity (PSAD1, SSLEA, SSTPR, DHAR1, CYP86A8, MYB47 and SPCH) and five negative ones (RBOHD, RBOHE, RBOHF, KNAT7 and SEP3). In this uniform genetic background, natural and accelerated ageing methods provided similar results for seed‐longevity in knock‐out mutants. The NADPH oxidases (RBOHs), the dehydroascorbate reductase (DHAR1) and the photosystem I subunit (PSAD1) highlight the important role of oxidative stress on seed ageing. The cytochrome P‐450 hydroxylase, CYP86A8, and the transcription factors, MYB47, KNAT7 and SEP3, support the protecting role of the seed coat during seed ageing.
A combined strategy of GWAS and reverse genetics in Arabidopsis identify novel genes involved in seed longevity. These new genes highlight the role of oxidative stress and seed coat in seed aging. |
| doi_str_mv | 10.1111/pce.13822 |
| format | Article |
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A combined strategy of GWAS and reverse genetics in Arabidopsis identify novel genes involved in seed longevity. These new genes highlight the role of oxidative stress and seed coat in seed aging.</description><identifier>ISSN: 0140-7791</identifier><identifier>EISSN: 1365-3040</identifier><identifier>DOI: 10.1111/pce.13822</identifier><identifier>PMID: 32519347</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>accelerated ageing ; Aging ; Aging (natural) ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - physiology ; Arabidopsis thaliana ; CYP86A8 ; Cytochromes ; Ecotypes ; Environmental effects ; Genes ; Genes, Plant - genetics ; Genes, Plant - physiology ; Genetics ; Genome-Wide Association Study ; Genomes ; Hydroxylase ; Longevity ; Longevity - genetics ; Microscopy, Confocal ; NAD(P)H oxidase ; NADPH oxidases ; natural variation ; Nucleotides ; Oxidative stress ; Oxidative Stress - genetics ; Phenotypic variations ; Photosystem I ; Plants, Genetically Modified ; Polygenic inheritance ; Polymorphism, Single Nucleotide - genetics ; Quantitative Trait, Heritable ; Reductases ; Reverse Genetics ; seed ageing ; seed coat ; Seed coats ; seed longevity ; Seeds - genetics ; Seeds - physiology ; Seeds - ultrastructure ; Single-nucleotide polymorphism ; Transcription factors ; Transcriptome</subject><ispartof>Plant, cell and environment, 2020-10, Vol.43 (10), p.2523-2539</ispartof><rights>2020 John Wiley & Sons Ltd.</rights><rights>2020 John Wiley & Sons, Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3882-af9321e2fa2db1aa8e746e566e103fd6cefd57d9b0d4a67c3d92777d67bd192f3</citedby><cites>FETCH-LOGICAL-c3882-af9321e2fa2db1aa8e746e566e103fd6cefd57d9b0d4a67c3d92777d67bd192f3</cites><orcidid>0000-0002-3612-7914 ; 0000-0002-1012-7975 ; 0000-0002-7342-3632 ; 0000-0002-5069-1212 ; 0000-0002-4267-0016 ; 0000-0003-4073-6867 ; 0000-0002-0828-121X ; 0000-0003-1797-1578 ; 0000-0002-7862-9509</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%2Fpce.13822$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fpce.13822$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27903,27904,45553,45554,46387,46811</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32519347$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Renard, Joan</creatorcontrib><creatorcontrib>Niñoles, Regina</creatorcontrib><creatorcontrib>Martínez‐Almonacid, Irene</creatorcontrib><creatorcontrib>Gayubas, Beatriz</creatorcontrib><creatorcontrib>Mateos‐Fernández, Rubén</creatorcontrib><creatorcontrib>Bissoli, Gaetano</creatorcontrib><creatorcontrib>Bueso, Eduardo</creatorcontrib><creatorcontrib>Serrano, Ramón</creatorcontrib><creatorcontrib>Gadea, José</creatorcontrib><title>Identification of novel seed longevity genes related to oxidative stress and seed coat by genome‐wide association studies and reverse genetics</title><title>Plant, cell and environment</title><addtitle>Plant Cell Environ</addtitle><description>Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant, Arabidopsis thaliana, for natural ageing and for three accelerated ageing methods. Genome‐wide analysis, using publicly available single‐nucleotide polymorphisms (SNPs) data sets, identified multiple genomic regions associated with variation in seed longevity. Reverse genetics of 20 candidate genes in Columbia ecotype resulted in seven genes positive for seed longevity (PSAD1, SSLEA, SSTPR, DHAR1, CYP86A8, MYB47 and SPCH) and five negative ones (RBOHD, RBOHE, RBOHF, KNAT7 and SEP3). In this uniform genetic background, natural and accelerated ageing methods provided similar results for seed‐longevity in knock‐out mutants. The NADPH oxidases (RBOHs), the dehydroascorbate reductase (DHAR1) and the photosystem I subunit (PSAD1) highlight the important role of oxidative stress on seed ageing. The cytochrome P‐450 hydroxylase, CYP86A8, and the transcription factors, MYB47, KNAT7 and SEP3, support the protecting role of the seed coat during seed ageing.
A combined strategy of GWAS and reverse genetics in Arabidopsis identify novel genes involved in seed longevity. These new genes highlight the role of oxidative stress and seed coat in seed aging.</description><subject>accelerated ageing</subject><subject>Aging</subject><subject>Aging (natural)</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - physiology</subject><subject>Arabidopsis thaliana</subject><subject>CYP86A8</subject><subject>Cytochromes</subject><subject>Ecotypes</subject><subject>Environmental effects</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genes, Plant - physiology</subject><subject>Genetics</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Hydroxylase</subject><subject>Longevity</subject><subject>Longevity - genetics</subject><subject>Microscopy, Confocal</subject><subject>NAD(P)H oxidase</subject><subject>NADPH oxidases</subject><subject>natural variation</subject><subject>Nucleotides</subject><subject>Oxidative stress</subject><subject>Oxidative Stress - genetics</subject><subject>Phenotypic variations</subject><subject>Photosystem I</subject><subject>Plants, Genetically Modified</subject><subject>Polygenic inheritance</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Quantitative Trait, Heritable</subject><subject>Reductases</subject><subject>Reverse Genetics</subject><subject>seed ageing</subject><subject>seed coat</subject><subject>Seed coats</subject><subject>seed longevity</subject><subject>Seeds - genetics</subject><subject>Seeds - physiology</subject><subject>Seeds - ultrastructure</subject><subject>Single-nucleotide polymorphism</subject><subject>Transcription factors</subject><subject>Transcriptome</subject><issn>0140-7791</issn><issn>1365-3040</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc9O3DAQxi3UqmxpD7wAstRLOQT8L_HmWK0oICG1h_YcOfYYGWXjrcdZurc-As_Ik-BugEOlzmWk0e_7ZjQfIcecnfFS5xsLZ1wuhTggCy6bupJMsTdkwbhildYtPyTvEe8YKwPdviOHUtS8lUovyMO1gzEHH6zJIY40ejrGLQwUARwd4ngL25B39BZGQJpgMLnMc6Txd3BFsgWKOQEiNaObRTaaTPu9JK7h8c_DfXBADWK0YV6CeXIBZkmCLSSE_YIcLH4gb70ZED4-9yPy8-vFj9VVdfPt8nr15aaycrkUlfGtFByEN8L13JglaNVA3TTAmfSuseBdrV3bM6dMo610rdBau0b3jrfCyyPyefbdpPhrAszdOqCFYTAjxAk7oTivFatVW9BP_6B3cUpjua5QSglePt8U6nSmbIqICXy3SWFt0q7jrPsbU1di6vYxFfbk2XHq1-BeyZdcCnA-A_dhgN3_nbrvq4vZ8gllcJ--</recordid><startdate>202010</startdate><enddate>202010</enddate><creator>Renard, Joan</creator><creator>Niñoles, Regina</creator><creator>Martínez‐Almonacid, Irene</creator><creator>Gayubas, Beatriz</creator><creator>Mateos‐Fernández, Rubén</creator><creator>Bissoli, Gaetano</creator><creator>Bueso, Eduardo</creator><creator>Serrano, Ramón</creator><creator>Gadea, José</creator><general>John Wiley & Sons, Ltd</general><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>7QP</scope><scope>7ST</scope><scope>C1K</scope><scope>SOI</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3612-7914</orcidid><orcidid>https://orcid.org/0000-0002-1012-7975</orcidid><orcidid>https://orcid.org/0000-0002-7342-3632</orcidid><orcidid>https://orcid.org/0000-0002-5069-1212</orcidid><orcidid>https://orcid.org/0000-0002-4267-0016</orcidid><orcidid>https://orcid.org/0000-0003-4073-6867</orcidid><orcidid>https://orcid.org/0000-0002-0828-121X</orcidid><orcidid>https://orcid.org/0000-0003-1797-1578</orcidid><orcidid>https://orcid.org/0000-0002-7862-9509</orcidid></search><sort><creationdate>202010</creationdate><title>Identification of novel seed longevity genes related to oxidative stress and seed coat by genome‐wide association studies and reverse genetics</title><author>Renard, Joan ; Niñoles, Regina ; Martínez‐Almonacid, Irene ; Gayubas, Beatriz ; Mateos‐Fernández, Rubén ; Bissoli, Gaetano ; Bueso, Eduardo ; Serrano, Ramón ; Gadea, José</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3882-af9321e2fa2db1aa8e746e566e103fd6cefd57d9b0d4a67c3d92777d67bd192f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>accelerated ageing</topic><topic>Aging</topic><topic>Aging (natural)</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis Proteins - genetics</topic><topic>Arabidopsis Proteins - physiology</topic><topic>Arabidopsis thaliana</topic><topic>CYP86A8</topic><topic>Cytochromes</topic><topic>Ecotypes</topic><topic>Environmental effects</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genes, Plant - physiology</topic><topic>Genetics</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Hydroxylase</topic><topic>Longevity</topic><topic>Longevity - genetics</topic><topic>Microscopy, Confocal</topic><topic>NAD(P)H oxidase</topic><topic>NADPH oxidases</topic><topic>natural variation</topic><topic>Nucleotides</topic><topic>Oxidative stress</topic><topic>Oxidative Stress - genetics</topic><topic>Phenotypic variations</topic><topic>Photosystem I</topic><topic>Plants, Genetically Modified</topic><topic>Polygenic inheritance</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Quantitative Trait, Heritable</topic><topic>Reductases</topic><topic>Reverse Genetics</topic><topic>seed ageing</topic><topic>seed coat</topic><topic>Seed coats</topic><topic>seed longevity</topic><topic>Seeds - genetics</topic><topic>Seeds - physiology</topic><topic>Seeds - ultrastructure</topic><topic>Single-nucleotide polymorphism</topic><topic>Transcription factors</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Renard, Joan</creatorcontrib><creatorcontrib>Niñoles, Regina</creatorcontrib><creatorcontrib>Martínez‐Almonacid, Irene</creatorcontrib><creatorcontrib>Gayubas, Beatriz</creatorcontrib><creatorcontrib>Mateos‐Fernández, Rubén</creatorcontrib><creatorcontrib>Bissoli, Gaetano</creatorcontrib><creatorcontrib>Bueso, Eduardo</creatorcontrib><creatorcontrib>Serrano, Ramón</creatorcontrib><creatorcontrib>Gadea, José</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Environment Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Plant, cell and environment</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Renard, Joan</au><au>Niñoles, Regina</au><au>Martínez‐Almonacid, Irene</au><au>Gayubas, Beatriz</au><au>Mateos‐Fernández, Rubén</au><au>Bissoli, Gaetano</au><au>Bueso, Eduardo</au><au>Serrano, Ramón</au><au>Gadea, José</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of novel seed longevity genes related to oxidative stress and seed coat by genome‐wide association studies and reverse genetics</atitle><jtitle>Plant, cell and environment</jtitle><addtitle>Plant Cell Environ</addtitle><date>2020-10</date><risdate>2020</risdate><volume>43</volume><issue>10</issue><spage>2523</spage><epage>2539</epage><pages>2523-2539</pages><issn>0140-7791</issn><eissn>1365-3040</eissn><abstract>Seed longevity is a polygenic trait of relevance for agriculture and for understanding the effect of environment on the ageing of biological systems. In order to identify novel longevity genes, we have phenotyped the natural variation of 270 ecotypes of the model plant, Arabidopsis thaliana, for natural ageing and for three accelerated ageing methods. Genome‐wide analysis, using publicly available single‐nucleotide polymorphisms (SNPs) data sets, identified multiple genomic regions associated with variation in seed longevity. Reverse genetics of 20 candidate genes in Columbia ecotype resulted in seven genes positive for seed longevity (PSAD1, SSLEA, SSTPR, DHAR1, CYP86A8, MYB47 and SPCH) and five negative ones (RBOHD, RBOHE, RBOHF, KNAT7 and SEP3). In this uniform genetic background, natural and accelerated ageing methods provided similar results for seed‐longevity in knock‐out mutants. The NADPH oxidases (RBOHs), the dehydroascorbate reductase (DHAR1) and the photosystem I subunit (PSAD1) highlight the important role of oxidative stress on seed ageing. The cytochrome P‐450 hydroxylase, CYP86A8, and the transcription factors, MYB47, KNAT7 and SEP3, support the protecting role of the seed coat during seed ageing.
A combined strategy of GWAS and reverse genetics in Arabidopsis identify novel genes involved in seed longevity. These new genes highlight the role of oxidative stress and seed coat in seed aging.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>32519347</pmid><doi>10.1111/pce.13822</doi><tpages>17</tpages><orcidid>https://orcid.org/0000-0002-3612-7914</orcidid><orcidid>https://orcid.org/0000-0002-1012-7975</orcidid><orcidid>https://orcid.org/0000-0002-7342-3632</orcidid><orcidid>https://orcid.org/0000-0002-5069-1212</orcidid><orcidid>https://orcid.org/0000-0002-4267-0016</orcidid><orcidid>https://orcid.org/0000-0003-4073-6867</orcidid><orcidid>https://orcid.org/0000-0002-0828-121X</orcidid><orcidid>https://orcid.org/0000-0003-1797-1578</orcidid><orcidid>https://orcid.org/0000-0002-7862-9509</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | accelerated ageing Aging Aging (natural) Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - physiology Arabidopsis thaliana CYP86A8 Cytochromes Ecotypes Environmental effects Genes Genes, Plant - genetics Genes, Plant - physiology Genetics Genome-Wide Association Study Genomes Hydroxylase Longevity Longevity - genetics Microscopy, Confocal NAD(P)H oxidase NADPH oxidases natural variation Nucleotides Oxidative stress Oxidative Stress - genetics Phenotypic variations Photosystem I Plants, Genetically Modified Polygenic inheritance Polymorphism, Single Nucleotide - genetics Quantitative Trait, Heritable Reductases Reverse Genetics seed ageing seed coat Seed coats seed longevity Seeds - genetics Seeds - physiology Seeds - ultrastructure Single-nucleotide polymorphism Transcription factors Transcriptome |
| title | Identification of novel seed longevity genes related to oxidative stress and seed coat by genome‐wide association studies and reverse genetics |
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