- -

Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interespecific tomato MAGIC population

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interespecific tomato MAGIC population

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Gramazo;Perera-Da ...
Tamaño: 1.295Mb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Pereira Días, Leandro es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Soler Aleixandre, Salvador es_ES
dc.contributor.author Esteras Pérez, Francisco Javier es_ES
dc.contributor.author Garmendia, Alfonso es_ES
dc.contributor.author Díez, María José es_ES
dc.date.accessioned 2021-07-02T03:30:53Z
dc.date.available 2021-07-02T03:30:53Z
dc.date.issued 2020-11-01 es_ES
dc.identifier.uri http://hdl.handle.net/10251/168674
dc.description.abstract [EN] The wild Solanum pimpinellifolium (SP) and the weedy S. lycopersicum var. cerasiforme (SLC) are largely unexploited genetic reservoirs easily accessible to breeders, as they are fully cross-compatible with cultivated tomato (S. lycopersicum var. lycopersicum). We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions, selected to maximize the range of variation of both taxa. These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross (MAGIC) population. The morphoagronomic characterization was carried out with 39 descriptors to assess plant, inflorescence, fruit and agronomic traits, revealing the broad range of diversity captured. Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments, while in the case of SLC to both human activity and adaptation to the environment. Whole-genome resequencing of the eight accessions revealed over 12 million variants, ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP, being 46.3% of them (4,897,803) private variants. The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC. This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa. The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding. The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes. es_ES
dc.description.sponsorship This work has been funded by the Spanish Ministerio de Economia y Competitividad and the Fondo Europeo de Desarrollo Regional/European Regional Development Fund, Grant AGL2015-71011-R. Authors also thank the G2P-SOL (linking genetic resources, genomes, and phenotypes of solanaceous crops) and BRESOV (breeding for resilient, efficient, and sustainable organic vegetable production) projects for support. G2P-SOL and BRESOV projects have received funding from the European Union's Horizon 2020 research and innovation programme under grant agreements 677379 (G2P-SOL), and 774244 (BRESOV). P.G. is grateful to Japan Society for the Promotion of Science for a postdoctoral grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)). We thank Aureliano Bombarely for the support in the bioinformatic analyses. es_ES
dc.language Inglés es_ES
dc.publisher Springer Nature es_ES
dc.relation.ispartof Horticulture Research es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject.classification GENETICA es_ES
dc.subject.classification BOTANICA es_ES
dc.title Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interespecific tomato MAGIC population es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/s41438-020-00395-w es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/677379/EU/Linking genetic resources, genomes and phenotypes of Solanaceous crops/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/JSPS//FY2019/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/774244/EU/Breeding for Resilient, Efficient and Sustainable Organic Vegetable production/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2015-71011-R/ES/NUEVA VARIABILIDAD EN SOLANUM PIMPINELLIFOLIUM Y S. LYCOPERSICUM VAR. CERASIFORME PARA LA MEJORA DE CARACTERES AGRONOMICOS Y RESISTENCIA A ESTRESES EN TOMATE/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/JSPS//P19105/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ecosistemas Agroforestales - Departament d'Ecosistemes Agroforestals es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Gramazio, P.; Pereira Días, L.; Vilanova Navarro, S.; Prohens Tomás, J.; Soler Aleixandre, S.; Esteras Pérez, FJ.; Garmendia, A.... (2020). Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interespecific tomato MAGIC population. Horticulture Research. 7(1):1-16. https://doi.org/10.1038/s41438-020-00395-w es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/s41438-020-00395-w es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 16 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 7 es_ES
dc.description.issue 1 es_ES
dc.identifier.eissn 2052-7276 es_ES
dc.identifier.pmid 33328432 es_ES
dc.identifier.pmcid PMC7603519 es_ES
dc.relation.pasarela S\422560 es_ES
dc.contributor.funder European Regional Development Fund es_ES
dc.contributor.funder European Commission es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Japan Society for the Promotion of Science es_ES
dc.description.references FAO. FAOSTAT Statistics Database. http://www.fao.org/faostat/ (2018). es_ES
dc.description.references Peralta, I., Spooner, D. & Knapp, S. Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Syst. Bot. Monogr. 84, 1–186 (2008). es_ES
dc.description.references Rick, C. M. & Fobes, J. F. Allozyme variation in the cultivated tomato and closely related species. Bull. Torre. Bot. Club 102, 376–384 (1975). es_ES
dc.description.references Blanca, J. et al. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7, e48198 (2012). es_ES
dc.description.references Blanca, J. et al. Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genom. 16, 257 (2015). es_ES
dc.description.references Razifard, H. et al. Genomic evidence for complex domestication history of the cultivated tomato in latin America. Mol. Biol. Evol. 37, 1118–1132 (2020). es_ES
dc.description.references Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 1044–1051 (2019). es_ES
dc.description.references Bauchet, G. & Causse, M. Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. in Genetic Diversity in Plants (ed. Caliskan, M.) 133–162 (IntechOpen, 2012). https://doi.org/10.5772/2640 . es_ES
dc.description.references Warnock, S. J. Natural habitats of Lycopersicon species. HortScience 26, 466–471 (1991). es_ES
dc.description.references Zuriaga, E. et al. Genetic and bioclimatic variation in Solanum pimpinellifolium. Genet. Resour. Crop Evol. 56, 39–51 (2009). es_ES
dc.description.references Taylor, I. B. in The Tomato Crop (eds Atherton, J. G. & Rudich, J.) Ch. 1 (Springer, 1986). es_ES
dc.description.references Alexander, L. & Hoover, M. Disease resistance in wild species of tomato: report of the National Screening Committee. Agric. Exp. Stn. Res. Bull. 752, 1–76 (1955). es_ES
dc.description.references Walter, J. M. Hereditary resistance to disease in tomato. Annu. Rev. Phytopathol. 5, 131–160 (1967). es_ES
dc.description.references Banerjee, M. K. & Kalloo, M. K. Sources and inheritance of resistance to leaf curl virus in Lycopersicon. Theor. Appl. Genet. 73, 707–710 (1987). es_ES
dc.description.references Rao, N. K. S., Bhatt, R. M. & Sadashiva, A. T. Tolerance to water stress in tomato cultivars. Photosynthetica 38, 465–468 (2000). es_ES
dc.description.references Razali, R. et al. The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance. Front. Plant Sci. 9, 1402 (2018). es_ES
dc.description.references Rick, C. M. Tomato Lycopersicon esculentum (Solanaceae). in Evolution of Crop Plants (ed. Simmonds, N. W.) 268–273 (Longman, London, 1976). es_ES
dc.description.references Ciccarese, F., Amenduni, M., Schiavone, D. & Cirulli, M. Occurrence and inheritance of resistance to powdery mildew (Oidium lycopersici) in Lycopersicon species. Plant Pathol. 47, 417–419 (1998). es_ES
dc.description.references Arellano Rodríguez, L. J. et al. Evaluation of the resistance against Phytophthora infestans of wild populations of Solanum lycopersicum var cerasiforme. Rev. Mex. Cienc. Agrícolas 4, 753–766 (2013). es_ES
dc.description.references Martínez-Cuenca, M. R. et al. Adaptation to water and salt stresses of Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme. Agronomy 10, 1169. https://doi.org/10.3390/agronomy10081169 (2020). es_ES
dc.description.references International Plant Genetic Resources Institute (IPGRI). Descriptors for Tomato (Lycopersicon spp.). (Bioversity International, 1996). es_ES
dc.description.references R Core Team. A Language and Environment for Statistical Computing. (R Core Team, 2019). es_ES
dc.description.references Vilanova, S. et al. SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. Plant Methods 16, 110. https://doi.org/10.1186/s13007-020-00652-y (2020). es_ES
dc.description.references Metsalu, T. & Vilo, J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 43, W566–W570 (2015). es_ES
dc.description.references Aronesty, E. Comparison of sequencing utility programs. Open Bioinformat. J. 7, 1–8 (2013). es_ES
dc.description.references Hosmani, P. S. et al. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. 767764. https://doi.org/10.1101/767764 (2019). es_ES
dc.description.references Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). es_ES
dc.description.references Li, H. et al. The sequence alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). es_ES
dc.description.references Quinlan, A. & Hall, I. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010). es_ES
dc.description.references Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. 1207, 3907. https://arxiv.org/abs/1207.3907 (2012). es_ES
dc.description.references Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011). es_ES
dc.description.references Ihaka, R. & Gentleman, R. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299–314 (1996). es_ES
dc.description.references Knaus, B. J. & Grünwald, N. J. VCFR: a package to manipulate and visualize variant call format data in R. Mol. Ecol. Resour. 17, 44–53 (2017). es_ES
dc.description.references Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008). es_ES
dc.description.references Wickham, H. ggplot2: elegant graphics for data analysis. (Springer-Verlag New York Inc, 2016). es_ES
dc.description.references Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80–92 (2012). es_ES
dc.description.references Alexa, A. & Rahnenfuhrer, J. topGO: Enrichment Analysis for Gene Ontology. Bioconductor Improv. 27 (2009). es_ES
dc.description.references Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011). es_ES
dc.description.references Vilanova, S. et al. Whole-genome resequencing of the eight Solanum lycopersicum var. cerasiforme and S. pimpinellifolium parents of a MAGIC population. in XVI Solanaceae Conference (Jerusalem, Israel, 2019). es_ES
dc.description.references Pascual, L. et al. Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Sci. 242, 120–130 (2016). es_ES
dc.description.references Zaw, H. et al. Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population. Sci. Rep. 9, 1–11 (2019). es_ES
dc.description.references Aflitos, S. et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 80, 136–148 (2014). es_ES
dc.description.references Lin, T. et al. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220–1226 (2014). es_ES
dc.description.references Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). es_ES
dc.description.references Pascual, L. et al. Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol. J. 13, 565–577 (2015). es_ES
dc.description.references Thyssen, G. N. et al. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Theor. Appl. Genet. 132, 989–999 (2019). es_ES
dc.description.references Han, Z. et al. Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population. Theor. Appl. Genet. 133, 59–71 (2020). es_ES
dc.description.references Allaby, R. G., Ware, R. L. & Kistler, L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12, 29–37 (2019). es_ES
dc.description.references Schouten, H. J. et al. Breeding has increased the diversity of cultivated tomato in The Netherlands. Front. Plant Sci. 10, 1606 (2019). es_ES
dc.description.references Prohens, J. et al. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica 213, 158 (2017). es_ES
dc.description.references Dempewolf, H. et al. Past and future use of wild relatives in crop breeding. Crop Sci. 57, 1070–1082 (2017). es_ES
dc.description.references Rick, C. M., Holle, M. & Thorp, R. W. Rates of cross-pollination in Lycopersicon pimpinellifolium: impact of genetic variation in floral characters. Plant Syst. Evol. 129, 31–44 (1978). es_ES
dc.description.references Nakazato, T., Bogonovich, M. & Moyle, L. C. Environmental factors predict adaptive phenotypic differentiation within and between two wild Andean tomatoes. Evolution 62, 774–792 (2008). es_ES
dc.description.references Sharma, A. et al. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 24, 2452 (2019). es_ES
dc.description.references Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013). es_ES
dc.description.references Vargas, C. D. et al. Adaptación climática de Lycopersicum en el occidente de México. Av. en la Investig. Científica en el CUCBA 207–210 (2005). XVI Semana de la Investigación Científica. es_ES
dc.description.references Rick, C. M. & Holle, M. Andean Lycopersicon esculentum var. cerasiforme: genetic variation and its evolutionary significance. Econ. Bot. 44, 69–78 (1990). es_ES
dc.description.references Mata-Nicolás, E. et al. Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection. Hortic. Res. 7, 1–14 (2020). es_ES
dc.description.references Díez, M. J. & Nuez F. in Vegetables II. Handbook of Plant Breeding (eds Prohens, J. & Nuez, F.) (Springer, 2008). es_ES
dc.description.references Causse, M. et al. Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom. 14, 791 (2013). es_ES
dc.description.references Micheli, F. Pectin methylesterases: cell wall enzymes with important roles in plant physiology. Trends Plant Sci. 6, 414–419 (2001). es_ES
dc.description.references Bosch, M. & Hepler, P. K. Pectin methylesterases and pectin dynamics in pollen tubes. Plant Cell 17, 3219–3226 (2005). es_ES
dc.description.references Wang, Y., Li, T., Meng, H. & Sun, X. Optimal and spatial analysis of hormones, degrading enzymes and isozyme profiles in tomato pedicel explants during ethylene-induced abscission. Plant Growth Regul. 46, 97–107 (2005). es_ES
dc.description.references Körner, E., Von Dahl, C. C., Bonaventure, G. & Baldwin, I. T. Pectin methylesterase NaPME1 contributes to the emission of methanol during insect herbivory and to the elicitation of defence responses in Nicotiana attenuata. J. Exp. Bot. 60, 2631–2640 (2009). es_ES
dc.description.references Tucker, G. Improving fruit and vegetable texture by genetic transformation. in Texture in Food (ed. Kilcast, D.) (Woodhead Publishing, 2004). es_ES
dc.description.references Phan, T. D., Bo, W., West, G., Lycett, G. W. & Tucker, G. A. Silencing of the major salt-dependent isoform of pectinesterase in tomato alters fruit softening. Plant Physiol. 144, 1960–1967 (2007). es_ES
dc.description.references de Freitas, S. T., Handa, A. K., Wu, Q., Park, S. & Mitcham, E. J. Role of pectin methylesterases in cellular calcium distribution and blossom-end rot development in tomato fruit. Plant J. 71, 824–835 (2012). es_ES
dc.description.references van der Knaap, E. et al. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Front. Plant Sci. 5, 227 (2014). es_ES
dc.subject.ods 02.- Poner fin al hambre, conseguir la seguridad alimentaria y una mejor nutrición, y promover la agricultura sostenible es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem