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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

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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

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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

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Título: 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
Autor: Gramazio, Pietro Pereira Días, Leandro Vilanova Navarro, Santiago Prohens Tomás, Jaime Soler Aleixandre, Salvador Esteras Pérez, Francisco Javier Garmendia, Alfonso Díez, María José
Entidad UPV: Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Universitat Politècnica de València. Departamento de Ecosistemas Agroforestales - Departament d'Ecosistemes Agroforestals
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
Fecha difusión:
Resumen:
[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 ...[+]
Derechos de uso: Reconocimiento (by)
Fuente:
Horticulture Research. (eissn: 2052-7276 )
DOI: 10.1038/s41438-020-00395-w
Editorial:
Springer Nature
Versión del editor: https://doi.org/10.1038/s41438-020-00395-w
Código del Proyecto:
info:eu-repo/grantAgreement/EC/H2020/677379/EU/Linking genetic resources, genomes and phenotypes of Solanaceous crops/
info:eu-repo/grantAgreement/JSPS//FY2019/
info:eu-repo/grantAgreement/EC/H2020/774244/EU/Breeding for Resilient, Efficient and Sustainable Organic Vegetable production/
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/
info:eu-repo/grantAgreement/JSPS//P19105/
Agradecimientos:
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 ...[+]
Tipo: Artículo

References

FAO. FAOSTAT Statistics Database. http://www.fao.org/faostat/ (2018).

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).

Rick, C. M. & Fobes, J. F. Allozyme variation in the cultivated tomato and closely related species. Bull. Torre. Bot. Club 102, 376–384 (1975). [+]
FAO. FAOSTAT Statistics Database. http://www.fao.org/faostat/ (2018).

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).

Rick, C. M. & Fobes, J. F. Allozyme variation in the cultivated tomato and closely related species. Bull. Torre. Bot. Club 102, 376–384 (1975).

Blanca, J. et al. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7, e48198 (2012).

Blanca, J. et al. Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genom. 16, 257 (2015).

Razifard, H. et al. Genomic evidence for complex domestication history of the cultivated tomato in latin America. Mol. Biol. Evol. 37, 1118–1132 (2020).

Gao, L. et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51, 1044–1051 (2019).

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 .

Warnock, S. J. Natural habitats of Lycopersicon species. HortScience 26, 466–471 (1991).

Zuriaga, E. et al. Genetic and bioclimatic variation in Solanum pimpinellifolium. Genet. Resour. Crop Evol. 56, 39–51 (2009).

Taylor, I. B. in The Tomato Crop (eds Atherton, J. G. & Rudich, J.) Ch. 1 (Springer, 1986).

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).

Walter, J. M. Hereditary resistance to disease in tomato. Annu. Rev. Phytopathol. 5, 131–160 (1967).

Banerjee, M. K. & Kalloo, M. K. Sources and inheritance of resistance to leaf curl virus in Lycopersicon. Theor. Appl. Genet. 73, 707–710 (1987).

Rao, N. K. S., Bhatt, R. M. & Sadashiva, A. T. Tolerance to water stress in tomato cultivars. Photosynthetica 38, 465–468 (2000).

Razali, R. et al. The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance. Front. Plant Sci. 9, 1402 (2018).

Rick, C. M. Tomato Lycopersicon esculentum (Solanaceae). in Evolution of Crop Plants (ed. Simmonds, N. W.) 268–273 (Longman, London, 1976).

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).

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).

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).

International Plant Genetic Resources Institute (IPGRI). Descriptors for Tomato (Lycopersicon spp.). (Bioversity International, 1996).

R Core Team. A Language and Environment for Statistical Computing. (R Core Team, 2019).

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).

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).

Aronesty, E. Comparison of sequencing utility programs. Open Bioinformat. J. 7, 1–8 (2013).

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).

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

Li, H. et al. The sequence alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Quinlan, A. & Hall, I. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. 1207, 3907. https://arxiv.org/abs/1207.3907 (2012).

Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

Ihaka, R. & Gentleman, R. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299–314 (1996).

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).

Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).

Wickham, H. ggplot2: elegant graphics for data analysis. (Springer-Verlag New York Inc, 2016).

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).

Alexa, A. & Rahnenfuhrer, J. topGO: Enrichment Analysis for Gene Ontology. Bioconductor Improv. 27 (2009).

Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).

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).

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).

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).

Aflitos, S. et al. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 80, 136–148 (2014).

Lin, T. et al. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220–1226 (2014).

Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017).

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).

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).

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).

Allaby, R. G., Ware, R. L. & Kistler, L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12, 29–37 (2019).

Schouten, H. J. et al. Breeding has increased the diversity of cultivated tomato in The Netherlands. Front. Plant Sci. 10, 1606 (2019).

Prohens, J. et al. Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica 213, 158 (2017).

Dempewolf, H. et al. Past and future use of wild relatives in crop breeding. Crop Sci. 57, 1070–1082 (2017).

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).

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).

Sharma, A. et al. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 24, 2452 (2019).

Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840–852 (2013).

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.

Rick, C. M. & Holle, M. Andean Lycopersicon esculentum var. cerasiforme: genetic variation and its evolutionary significance. Econ. Bot. 44, 69–78 (1990).

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).

Díez, M. J. & Nuez F. in Vegetables II. Handbook of Plant Breeding (eds Prohens, J. & Nuez, F.) (Springer, 2008).

Causse, M. et al. Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genom. 14, 791 (2013).

Micheli, F. Pectin methylesterases: cell wall enzymes with important roles in plant physiology. Trends Plant Sci. 6, 414–419 (2001).

Bosch, M. & Hepler, P. K. Pectin methylesterases and pectin dynamics in pollen tubes. Plant Cell 17, 3219–3226 (2005).

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).

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).

Tucker, G. Improving fruit and vegetable texture by genetic transformation. in Texture in Food (ed. Kilcast, D.) (Woodhead Publishing, 2004).

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).

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).

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).

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