Publicação
Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics
| Resumo: | Citrus tristeza virus (CTV) affects citrus crops with differing severity, depending on the viral strain, the citrus cultivar and the scion/rootstock combinations. In this study we address the problem of identifying asymptomatic infected plants using reflectance spectra of the leaves in the visible/near infrared region. Sixteen young citrus plants (8 Citrus x clementina hort. ex Tanaka ‘Fina’ and 8 Citrus sinensis (L.) Osbeck ‘Valencia Late’) were split into control and T318A isolate infected groups. Measurements of reflectance in the 400-1100 nm range, in two leaves per plant, were performed monthly over 6 months and the presence of the virus was confirmed by IC/RT-PCR and real-time PCR. The spectra acquired in a single day of measurements was inconsistent for inoculated and control plants. However, by monitoring the same leaves over 6 months it was possible to identify infected plants on the basis of the spectra time evolution. In order to achieve this a simple unfolding implementation of 3-way PCA was applied such that group separation in the scores plot was spontaneous and not forced by any a priori assumption. The model was tested through leave-one-out cross validation with a good rate of correct classification for the left out sample. A real situation was simulated by applying the NPCA algorithm to healthy plants only and checking if the infected ones would be projected on the model scores plot as outliers. Again, a good rate of classification was obtained. Finally, we discuss the spectral features that may be associated with the clustering obtained through NPCA and their physiological significance. Reflectance measurements between infected and healthy samples of two citrus cultivars and their correlation with real-time PCR results for the presence of CTV suggest reflectance spectra of the leaves in the visible/near infrared region is a promising tool for plant stress monitoring linked to the presence of CTV infection prior to symptom expression. |
|---|---|
| Autores principais: | Afonso, Andreia |
| Outros Autores: | Guerra, Rui Manuel Farinha das Neves; Cavaco, A. M.; Pinto, Patricia IS; Andrade, André; Duarte, Amílcar; Power, Deborah; Marques, N T. |
| Assunto: | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| Ano: | 2017 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Universidade do Algarve |
| Idioma: | inglês |
| Origem: | Sapientia - Universidade do Algarve |
| _version_ | 1867050897618501632 |
|---|---|
| author | Afonso, Andreia |
| author2 | Guerra, Rui Manuel Farinha das Neves Cavaco, A. M. Pinto, Patricia IS Andrade, André Duarte, Amílcar Power, Deborah Marques, N T. |
| author2_role | author author author author author author author |
| author_facet | Afonso, Andreia Guerra, Rui Manuel Farinha das Neves Cavaco, A. M. Pinto, Patricia IS Andrade, André Duarte, Amílcar Power, Deborah Marques, N T. |
| author_role | author |
| contributor_name_str_mv | Sapientia |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Afonso, Andreia\",\"Person.identifier.orcid\":\"0000-0003-4906-0082\"},{\"Person.name\":\"Guerra, Rui Manuel Farinha das Neves\",\"Person.identifier.orcid\":\"0000-0002-8642-5792\"},{\"Person.name\":\"Cavaco, A. M.\",\"Person.identifier.orcid\":\"0000-0003-2708-5991\"},{\"Person.name\":\"Pinto, Patricia IS\",\"Person.identifier.orcid\":\"0000-0001-7854-3898\"},{\"Person.name\":\"Andrade, André\",\"Person.identifier.orcid\":\"0000-0002-5900-8782\"},{\"Person.name\":\"Duarte, Amílcar\",\"Person.identifier.orcid\":\"0000-0002-2763-1916\"},{\"Person.name\":\"Power, Deborah\",\"Person.identifier.orcid\":\"0000-0003-1366-0246\"},{\"Person.name\":\"Marques, N T.\",\"Person.identifier.orcid\":\"0000-0002-0222-621X\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Sapientia |
| datacite.creators.creator.creatorName.fl_str_mv | Afonso, Andreia Guerra, Rui Manuel Farinha das Neves Cavaco, A. M. Pinto, Patricia IS Andrade, André Duarte, Amílcar Power, Deborah Marques, N T. |
| datacite.date.Accepted.fl_str_mv | 2017-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2017-09-14T10:18:56Z |
| datacite.date.embargoed.fl_str_mv | 2017-09-14T10:18:56Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| datacite.subjects.subject.fl_str_mv | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| datacite.titles.title.fl_str_mv | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| dc.contributor.none.fl_str_mv | Sapientia |
| dc.creator.none.fl_str_mv | Afonso, Andreia Guerra, Rui Manuel Farinha das Neves Cavaco, A. M. Pinto, Patricia IS Andrade, André Duarte, Amílcar Power, Deborah Marques, N T. |
| dc.date.Accepted.fl_str_mv | 2017-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2017-09-14T10:18:56Z |
| dc.date.embargoed.fl_str_mv | 2017-09-14T10:18:56Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10400.1/9939 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Elsevier |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| dc.subject.none.fl_str_mv | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| dc.title.fl_str_mv | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | Citrus tristeza virus (CTV) affects citrus crops with differing severity, depending on the viral strain, the citrus cultivar and the scion/rootstock combinations. In this study we address the problem of identifying asymptomatic infected plants using reflectance spectra of the leaves in the visible/near infrared region. Sixteen young citrus plants (8 Citrus x clementina hort. ex Tanaka ‘Fina’ and 8 Citrus sinensis (L.) Osbeck ‘Valencia Late’) were split into control and T318A isolate infected groups. Measurements of reflectance in the 400-1100 nm range, in two leaves per plant, were performed monthly over 6 months and the presence of the virus was confirmed by IC/RT-PCR and real-time PCR. The spectra acquired in a single day of measurements was inconsistent for inoculated and control plants. However, by monitoring the same leaves over 6 months it was possible to identify infected plants on the basis of the spectra time evolution. In order to achieve this a simple unfolding implementation of 3-way PCA was applied such that group separation in the scores plot was spontaneous and not forced by any a priori assumption. The model was tested through leave-one-out cross validation with a good rate of correct classification for the left out sample. A real situation was simulated by applying the NPCA algorithm to healthy plants only and checking if the infected ones would be projected on the model scores plot as outliers. Again, a good rate of classification was obtained. Finally, we discuss the spectral features that may be associated with the clustering obtained through NPCA and their physiological significance. Reflectance measurements between infected and healthy samples of two citrus cultivars and their correlation with real-time PCR results for the presence of CTV suggest reflectance spectra of the leaves in the visible/near infrared region is a promising tool for plant stress monitoring linked to the presence of CTV infection prior to symptom expression. |
| dirty | 0 |
| eu_rights_str_mv | restrictedAccess |
| format | article |
| fulltext.url.fl_str_mv | https://sapientia.ualg.pt/bitstreams/0729a353-6960-4588-b89b-35425cdcd432/download |
| id | sapientia_684e3fbf117794de1b747c27e50436bb |
| identifier.url.fl_str_mv | http://hdl.handle.net/10400.1/9939 |
| instacron_str | ualg |
| institution | Universidade do Algarve |
| instname_str | Universidade do Algarve |
| language | eng |
| network_acronym_str | sapientia |
| network_name_str | Sapientia - Universidade do Algarve |
| oai_identifier_str | oai:sapientia.ualg.pt:10400.1/9939 |
| organization_str_mv | urn:organizationAcronym:ualg |
| person_str_mv | Afonso, Andreia Afonso, Andreia https://www.ciencia-id.pt/BB11-9B39-F095 BB11-9B39-F095 http://orcid.org/0000-0003-4906-0082 0000-0003-4906-0082 Guerra, Rui Manuel Farinha das Neves Guerra, Rui Manuel Farinha das Neves https://www.ciencia-id.pt/3D16-5067-D6BB 3D16-5067-D6BB http://orcid.org/0000-0002-8642-5792 0000-0002-8642-5792 Cavaco, A. M. Cavaco, A. M. https://www.ciencia-id.pt/C91E-B434-E327 C91E-B434-E327 http://orcid.org/0000-0003-2708-5991 0000-0003-2708-5991 Pinto, Patricia IS Pinto, Patricia IS https://www.ciencia-id.pt/E51D-5CCB-B1C6 E51D-5CCB-B1C6 http://orcid.org/0000-0001-7854-3898 0000-0001-7854-3898 Andrade, André Andrade, André https://www.ciencia-id.pt/F513-56ED-7088 F513-56ED-7088 http://orcid.org/0000-0002-5900-8782 0000-0002-5900-8782 Duarte, Amílcar Duarte, Amílcar https://www.ciencia-id.pt/081B-5FD8-0E51 081B-5FD8-0E51 http://orcid.org/0000-0002-2763-1916 0000-0002-2763-1916 Power, Deborah Power, Deborah https://www.ciencia-id.pt/891A-8A44-3CAE 891A-8A44-3CAE http://orcid.org/0000-0003-1366-0246 0000-0003-1366-0246 Marques, N T. Marques, N T. https://www.ciencia-id.pt/1510-CD2F-81CE 1510-CD2F-81CE http://orcid.org/0000-0002-0222-621X 0000-0002-0222-621X |
| publishDate | 2017 |
| publisher.none.fl_str_mv | Elsevier |
| reponame_str | Sapientia - Universidade do Algarve |
| repository_id_str | urn:repositoryAcronym:sapientia |
| service_str_mv | urn:repositoryAcronym:sapientia |
| spelling | engElsevierpt_PTCitrus tristeza virus (CTV) affects citrus crops with differing severity, depending on the viral strain, the citrus cultivar and the scion/rootstock combinations. In this study we address the problem of identifying asymptomatic infected plants using reflectance spectra of the leaves in the visible/near infrared region. Sixteen young citrus plants (8 Citrus x clementina hort. ex Tanaka ‘Fina’ and 8 Citrus sinensis (L.) Osbeck ‘Valencia Late’) were split into control and T318A isolate infected groups. Measurements of reflectance in the 400-1100 nm range, in two leaves per plant, were performed monthly over 6 months and the presence of the virus was confirmed by IC/RT-PCR and real-time PCR. The spectra acquired in a single day of measurements was inconsistent for inoculated and control plants. However, by monitoring the same leaves over 6 months it was possible to identify infected plants on the basis of the spectra time evolution. In order to achieve this a simple unfolding implementation of 3-way PCA was applied such that group separation in the scores plot was spontaneous and not forced by any a priori assumption. The model was tested through leave-one-out cross validation with a good rate of correct classification for the left out sample. A real situation was simulated by applying the NPCA algorithm to healthy plants only and checking if the infected ones would be projected on the model scores plot as outliers. Again, a good rate of classification was obtained. Finally, we discuss the spectral features that may be associated with the clustering obtained through NPCA and their physiological significance. Reflectance measurements between infected and healthy samples of two citrus cultivars and their correlation with real-time PCR results for the presence of CTV suggest reflectance spectra of the leaves in the visible/near infrared region is a promising tool for plant stress monitoring linked to the presence of CTV infection prior to symptom expression.application/pdfpt_PTIdentification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristicsPersonalAfonso, AndreiaDSpacehttp://dspace.org/items/14a734d1-dcb4-4dde-b24d-76f244e55fedDSpacehttp://dspace.org/items/14a734d1-dcb4-4dde-b24d-76f244e55fedAfonsoAndreiaCiência IDhttps://www.ciencia-id.ptBB11-9B39-F095ORCIDhttp://orcid.org0000-0003-4906-0082PersonalGuerra, Rui Manuel Farinha das NevesDSpacehttp://dspace.org/items/eff7071e-e676-465b-bae3-983f522acd98DSpacehttp://dspace.org/items/eff7071e-e676-465b-bae3-983f522acd98GuerraRuiCiência IDhttps://www.ciencia-id.pt3D16-5067-D6BBORCIDhttp://orcid.org0000-0002-8642-5792PersonalCavaco, A. M.DSpacehttp://dspace.org/items/18ad736f-b1f3-4a19-9636-e7a80248cf94DSpacehttp://dspace.org/items/18ad736f-b1f3-4a19-9636-e7a80248cf94Cavaco GuerraAna MargaridaCiência IDhttps://www.ciencia-id.ptC91E-B434-E327ORCIDhttp://orcid.org0000-0003-2708-5991Scopus Author IDhttps://www.scopus.com6602899707PersonalPinto, Patricia ISDSpacehttp://dspace.org/items/64bc526e-5281-44e5-91eb-5743436109f9DSpacehttp://dspace.org/items/64bc526e-5281-44e5-91eb-5743436109f9PintoPatricia ISCiência IDhttps://www.ciencia-id.ptE51D-5CCB-B1C6ORCIDhttp://orcid.org0000-0001-7854-3898Researcher IDhttps://www.researcherid.comM-3817-2013Scopus Author IDhttps://www.scopus.com10240774300PersonalAndrade, AndréDSpacehttp://dspace.org/items/44cc56db-1879-412b-86eb-8ce5465a427aDSpacehttp://dspace.org/items/44cc56db-1879-412b-86eb-8ce5465a427aAlçada Baptista Rebelo de AndradeAndréCiência IDhttps://www.ciencia-id.ptF513-56ED-7088ORCIDhttp://orcid.org0000-0002-5900-8782PersonalDuarte, AmílcarDSpacehttp://dspace.org/items/88280e66-023a-49f6-8081-c827a15900ceDSpacehttp://dspace.org/items/88280e66-023a-49f6-8081-c827a15900ceDuarteAmilcarCiência IDhttps://www.ciencia-id.pt081B-5FD8-0E51ORCIDhttp://orcid.org0000-0002-2763-1916Researcher IDhttps://www.researcherid.comF-1472-2010Scopus Author IDhttps://www.scopus.com7102602102PersonalPower, DeborahDSpacehttp://dspace.org/items/c68f5ffb-63f6-4c70-8957-29e464fb59c0DSpacehttp://dspace.org/items/c68f5ffb-63f6-4c70-8957-29e464fb59c0PowerDeborah MaryCiência IDhttps://www.ciencia-id.pt891A-8A44-3CAEORCIDhttp://orcid.org0000-0003-1366-0246Scopus Author IDhttps://www.scopus.com7101806760PersonalMarques, N T.DSpacehttp://dspace.org/items/4b1751aa-958b-4d68-ae97-ea628673ba00DSpacehttp://dspace.org/items/4b1751aa-958b-4d68-ae97-ea628673ba00Tomás MarquesNatáliaCiência IDhttps://www.ciencia-id.pt1510-CD2F-81CEORCIDhttp://orcid.org0000-0002-0222-621XHostingInstitutionOrganizationalSapientiae-mailmailto:repositorio@ualg.ptrepositorio@ualg.ptISSNIsPartOf0168-1699URNIsPartOfAUT: RGU01166; ACA01304; ADU00268; DPO00386; NMA00640;DOIIsPartOfhttp://dx.doi.org/10.1016/j.compag.2017.08.0012017-09-14T10:18:56Z20172017-01-01T00:00:00ZHandlehttp://hdl.handle.net/10400.1/9939http://purl.org/coar/access_right/c_16ecrestricted accessSpectroscopyN-way PCACTVClosterovirusCitrus sinensisCitrus clementina2997329 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal articlehttp://purl.org/coar/access_right/c_16ecapplication/pdffulltexthttps://sapientia.ualg.pt/bitstreams/0729a353-6960-4588-b89b-35425cdcd432/downloadComputers and Electronics in Agriculture141340350 |
| spellingShingle | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics Afonso, Andreia Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| status | SINGLETON |
| subject.fl_str_mv | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| title | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| title_full | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| title_fullStr | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| title_full_unstemmed | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| title_short | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| title_sort | Identification of asymptomatic plants infected with Citrus tristeza virus from a time series of leaf spectral characteristics |
| topic | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| topic_facet | Spectroscopy N-way PCA CTV Closterovirus Citrus sinensis Citrus clementina |
| url | http://hdl.handle.net/10400.1/9939 |
| visible | 1 |