Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery
Centro de Investigación Forestal (CIFOR)
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Other Authors: | |
| Format: | artículo biblioteca |
| Language: | English |
| Published: |
John Wiley & Sons
2021-02
|
| Subjects: | Pinus halepensis, SNPs, Genome-wide association studies, Genomics, Remote sensing; unmanned aerial vehicle (UAV), |
| Online Access: | http://hdl.handle.net/10261/272161 http://dx.doi.org/10.13039/501100003329 https://api.elsevier.com/content/abstract/scopus_id/85090199299 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| id |
dig-inia-es-10261-272161 |
|---|---|
| record_format |
koha |
| spelling |
dig-inia-es-10261-2721612024-05-15T20:37:18Z Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery Santini, Filippo Kefauver, Shawn C. Araus, José Luis Resco de Dios, Víctor Martín García, Saray Grivet, Delphine Voltas, Jordi Ministerio de Ciencia, Innovación y Universidades (España) Ministerio de Economía y Competitividad (España) Santini, Filippo [0000-0002-5681-6039] Kefauver, Shawn Carlisle [0000-0002-1687-1965] Araus, José Luis [0000-0002-8866-2388] Resco de Dios, Víctor [0000-0002-5721-1656] Martín García, Saray [0000-0003-3472-400X] Grivet, Delphine [0000-0001-8168-4456] Voltas, Jordi [0000-0003-4051-1158] Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) Centro de Investigación Forestal (CIFOR) Progress in high-throughput phenotyping and genomics provides the potential to understand the genetic basis of plant functional differentiation. We developed a semi-automatic methodology based on unmanned aerial vehicle (UAV) imagery for deriving tree-level phenotypes followed by genome-wide association study (GWAS). An RGB-based point cloud was used for tree crown identification in a common garden of Pinus halepensis in Spain. Crowns were combined with multispectral and thermal orthomosaics to retrieve growth traits, vegetation indices and canopy temperature. Thereafter, GWAS was performed to analyse the association between phenotypes and genomic variation at 235 single nucleotide polymorphisms (SNPs). Growth traits were associated with 12 SNPs involved in cellulose and carbohydrate metabolism. Indices related to transpiration and leaf water content were associated with six SNPs involved in stomata dynamics. Indices related to leaf pigments and leaf area were associated with 11 SNPs involved in signalling and peroxisome metabolism. About 16-20% of trait variance was explained by combinations of several SNPs, indicating polygenic control of morpho-physiological traits. Despite a limited availability of markers and individuals, this study is provides a successful proof-of-concept for the combination of high-throughput UAV-based phenotyping with cost-effective genotyping to disentangle the genetic architecture of phenotypic variation in a widespread conifer. This work was supported by the Spanish Government, grant number RTI2018-094691-B-C31 (MCIU/AEI/FEDER, EU). We thank Ricardo Alía (CIFOR-INIA) for providing the genotypic data. We thank three anonymous reviewers whose insightful comments and suggestions helped to improve the manuscript. The authors declare no conflicts of interest.AGL2015-68274-C3-3-R Peer reviewed 14 Pág. 2022-06-10T08:08:31Z 2022-06-10T08:08:31Z 2021-02 artículo http://purl.org/coar/resource_type/c_6501 New Phytologist 229 (1): 245–258 (2021) 0028-646X http://hdl.handle.net/10261/272161 10.1111/nph.16862 http://dx.doi.org/10.13039/501100003329 32893885 2-s2.0-85090199299 https://api.elsevier.com/content/abstract/scopus_id/85090199299 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-094691-B-C31/ES/PAPEL DE LA EVOLUCION DE LOS FENOTIPOS INTEGRADOS EN LA RESILIENCIA DE LOS PINOS MEDITERRANEOS EN UN AMBIENTE CAMBIANTE/ info:eu-repo/grantAgreement/MINECO//AGL2015-68274-C3-3-R/ES/APROXIMACIONES ECOFISIOLOGICAS Y RESPUESTA AL CLIMA EN PINOS MEDITERRANEOS: RELEVANCIA PARA LA GESTION FUTURA DE SUS RECURSOS GENETICOS/ The New phytologist Publisher's version https://doi.org/10.1111/nph.16862 Sí open John Wiley & Sons |
| institution |
INIA ES |
| collection |
DSpace |
| country |
España |
| countrycode |
ES |
| component |
Bibliográfico |
| access |
En linea |
| databasecode |
dig-inia-es |
| tag |
biblioteca |
| region |
Europa del Sur |
| libraryname |
Biblioteca del INIA España |
| language |
English |
| topic |
Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) |
| spellingShingle |
Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) Santini, Filippo Kefauver, Shawn C. Araus, José Luis Resco de Dios, Víctor Martín García, Saray Grivet, Delphine Voltas, Jordi Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| description |
Centro de Investigación Forestal (CIFOR) |
| author2 |
Ministerio de Ciencia, Innovación y Universidades (España) |
| author_facet |
Ministerio de Ciencia, Innovación y Universidades (España) Santini, Filippo Kefauver, Shawn C. Araus, José Luis Resco de Dios, Víctor Martín García, Saray Grivet, Delphine Voltas, Jordi |
| format |
artículo |
| topic_facet |
Pinus halepensis SNPs Genome-wide association studies Genomics Remote sensing; unmanned aerial vehicle (UAV) |
| author |
Santini, Filippo Kefauver, Shawn C. Araus, José Luis Resco de Dios, Víctor Martín García, Saray Grivet, Delphine Voltas, Jordi |
| author_sort |
Santini, Filippo |
| title |
Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| title_short |
Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| title_full |
Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| title_fullStr |
Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| title_full_unstemmed |
Bridging the genotype-phenotype gap for a Mediterranean pine by semi-automatic crown identification and multispectral imagery |
| title_sort |
bridging the genotype-phenotype gap for a mediterranean pine by semi-automatic crown identification and multispectral imagery |
| publisher |
John Wiley & Sons |
| publishDate |
2021-02 |
| url |
http://hdl.handle.net/10261/272161 http://dx.doi.org/10.13039/501100003329 https://api.elsevier.com/content/abstract/scopus_id/85090199299 |
| work_keys_str_mv |
AT santinifilippo bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT kefauvershawnc bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT arausjoseluis bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT rescodediosvictor bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT martingarciasaray bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT grivetdelphine bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery AT voltasjordi bridgingthegenotypephenotypegapforamediterraneanpinebysemiautomaticcrownidentificationandmultispectralimagery |
| _version_ |
1802819630490714112 |