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Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

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Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

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dc.contributor.author Gramazio, Pietro es_ES
dc.contributor.author Yan, Haidong es_ES
dc.contributor.author Hasing, Tomas es_ES
dc.contributor.author Vilanova Navarro, Santiago es_ES
dc.contributor.author Prohens Tomás, Jaime es_ES
dc.contributor.author Bombarely, Aureliano es_ES
dc.date.accessioned 2020-05-16T03:00:40Z
dc.date.available 2020-05-16T03:00:40Z
dc.date.issued 2019-10-08 es_ES
dc.identifier.uri http://hdl.handle.net/10251/143437
dc.description.abstract [EN] Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8x and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding. es_ES
dc.description.sponsorship This work has been funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 677379 (G2P-SOL project: Linking genetic resources, genomes, and phenotypes of Solanaceous crops), by the Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant AGL2015-64755-R), and by the Spanish Ministerio de Ciencia, Innovacion y Universidades (MCIU), Agencia Estatal de Investigacion (AEI), and Fondo Europeo de Desarrollo Regional/European Regional Development Fund (grant RTI2018-09592-B-100). PG is grateful to Universitat Politecnica de Valencia and to Japan Society for the Promotion of Science for their respective postdoctoral grants [PAID-10-18 and FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)]. es_ES
dc.language Inglés es_ES
dc.publisher Frontiers Media SA es_ES
dc.relation.ispartof Frontiers in Plant Science es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Whole-genome resequencing es_ES
dc.subject Solanum melongena es_ES
dc.subject S. incanum es_ES
dc.subject Polymorphisms es_ES
dc.subject Genome characterization es_ES
dc.subject.classification GENETICA es_ES
dc.title Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.3389/fpls.2019.01220 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/UPV//PAID-10-18/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//AGL2015-64755-R/ES/MEJORA GENETICA DE LA CALIDAD FUNCIONAL Y APARENTE DE LA BERENJENA/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-094592-B-I00/ES/INTROGRESION DE TOLERANCIA A LA SEQUIA PROCEDENTE DE ESPECIES SILVESTRES PARA LA MEJORA GENETICA DE LA BERENJENA/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Gramazio, P.; Yan, H.; Hasing, T.; Vilanova Navarro, S.; Prohens Tomás, J.; Bombarely, A. (2019). Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement. Frontiers in Plant Science. 10:1-17. https://doi.org/10.3389/fpls.2019.01220 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.3389/fpls.2019.01220 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 17 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 10 es_ES
dc.identifier.eissn 1664-462X es_ES
dc.identifier.pmid 31649694 es_ES
dc.identifier.pmcid PMC6791922 es_ES
dc.relation.pasarela S\407112 es_ES
dc.contributor.funder Agencia Estatal de Investigación es_ES
dc.contributor.funder Universitat Politècnica de València es_ES
dc.contributor.funder Japan Society for the Promotion of Science es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.description.references Acquadro, A., Barchi, L., Gramazio, P., Portis, E., Vilanova, S., Comino, C., … Lanteri, S. (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLOS ONE, 12(7), e0180774. doi:10.1371/journal.pone.0180774 es_ES
dc.description.references Alonso-Blanco, C., Andrade, J., Becker, C., Bemm, F., Bergelson, J., Borgwardt, K. M., … Ding, W. (2016). 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell, 166(2), 481-491. doi:10.1016/j.cell.2016.05.063 es_ES
dc.description.references Aronesty, E. (2013). Comparison of Sequencing Utility Programs. The Open Bioinformatics Journal, 7(1), 1-8. doi:10.2174/1875036201307010001 es_ES
dc.description.references Barchi, L., Lanteri, S., Portis, E., Acquadro, A., Valè, G., Toppino, L., & Rotino, G. L. (2011). Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics, 12(1). doi:10.1186/1471-2164-12-304 es_ES
dc.description.references Barchi, L., Pietrella, M., Venturini, L., Minio, A., Toppino, L., Acquadro, A., … Rotino, G. L. (2019). A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Scientific Reports, 9(1). doi:10.1038/s41598-019-47985-w es_ES
dc.description.references Barchi, L., Acquadro, A., Alonso, D., Aprea, G., Bassolino, L., Demurtas, O., … Giuliano, G. (2019). Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.01005 es_ES
dc.description.references Bao, G., Zhuo, C., Qian, C., Xiao, T., Guo, Z., & Lu, S. (2015). Co-expression ofNCEDandALOimproves vitamin C level and tolerance to drought and chilling in transgenic tobacco and stylo plants. Plant Biotechnology Journal, 14(1), 206-214. doi:10.1111/pbi.12374 es_ES
dc.description.references Brozynska, M., Furtado, A., & Henry, R. J. (2015). Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnology Journal, 14(4), 1070-1085. doi:10.1111/pbi.12454 es_ES
dc.description.references Cao, J., Schneeberger, K., Ossowski, S., Günther, T., Bender, S., Fitz, J., … Weigel, D. (2011). Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics, 43(10), 956-963. doi:10.1038/ng.911 es_ES
dc.description.references Causse, M., Desplat, N., Pascual, L., Le Paslier, M.-C., Sauvage, C., Bauchet, G., … Bouchet, J.-P. (2013). Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics, 14(1), 791. doi:10.1186/1471-2164-14-791 es_ES
dc.description.references Cavanagh, C., Morell, M., Mackay, I., & Powell, W. (2008). From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Current Opinion in Plant Biology, 11(2), 215-221. doi:10.1016/j.pbi.2008.01.002 es_ES
dc.description.references Cericola, F., Portis, E., Toppino, L., Barchi, L., Acciarri, N., Ciriaci, T., … Lanteri, S. (2013). The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin. PLoS ONE, 8(9), e73702. doi:10.1371/journal.pone.0073702 es_ES
dc.description.references Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., … Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6(2), 80-92. doi:10.4161/fly.19695 es_ES
dc.description.references Conesa, A., Gotz, S., Garcia-Gomez, J. M., Terol, J., Talon, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674-3676. doi:10.1093/bioinformatics/bti610 es_ES
dc.description.references Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., … DePristo, M. A. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. doi:10.1093/bioinformatics/btr330 es_ES
dc.description.references Dempewolf, H., Baute, G., Anderson, J., Kilian, B., Smith, C., & Guarino, L. (2017). Past and Future Use of Wild Relatives in Crop Breeding. Crop Science, 57(3), 1070-1082. doi:10.2135/cropsci2016.10.0885 es_ES
dc.description.references Deng, Y., Srivastava, R., & Howell, S. H. (2013). Protein kinase and ribonuclease domains of IRE1 confer stress tolerance, vegetative growth, and reproductive development in Arabidopsis. Proceedings of the National Academy of Sciences, 110(48), 19633-19638. doi:10.1073/pnas.1314749110 es_ES
dc.description.references Jadhav, S. K., Tiwari, K. L., & Gupta, S. (2012). Modified CTAB Technique for Isolation of DNA from some Medicinal Plants. Research Journal of Medicinal Plant, 6(1), 65-73. doi:10.3923/rjmp.2012.65.73 es_ES
dc.description.references Du, X., Huang, G., He, S., Yang, Z., Sun, G., Ma, X., … Li, F. (2018). Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature Genetics, 50(6), 796-802. doi:10.1038/s41588-018-0116-x es_ES
dc.description.references Felcher, K. J., Coombs, J. J., Massa, A. N., Hansey, C. N., Hamilton, J. P., Veilleux, R. E., … Douches, D. S. (2012). Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS ONE, 7(4), e36347. doi:10.1371/journal.pone.0036347 es_ES
dc.description.references Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28(23), 3150-3152. doi:10.1093/bioinformatics/bts565 es_ES
dc.description.references Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., … Fei, Z. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51(6), 1044-1051. doi:10.1038/s41588-019-0410-2 es_ES
dc.description.references Gisbert, C., Prohens, J., Raigón, M. D., Stommel, J. R., & Nuez, F. (2011). Eggplant relatives as sources of variation for developing new rootstocks: Effects of grafting on eggplant yield and fruit apparent quality and composition. Scientia Horticulturae, 128(1), 14-22. doi:10.1016/j.scienta.2010.12.007 es_ES
dc.description.references Gong, Z., Lee, H., Xiong, L., Jagendorf, A., Stevenson, B., & Zhu, J.-K. (2002). RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proceedings of the National Academy of Sciences, 99(17), 11507-11512. doi:10.1073/pnas.172399299 es_ES
dc.description.references Gramazio, P., Prohens, J., Plazas, M., Andújar, I., Herraiz, F. J., Castillo, E., … Vilanova, S. (2014). Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biology, 14(1). doi:10.1186/s12870-014-0350-z es_ES
dc.description.references Gramazio, P., Blanca, J., Ziarsolo, P., Herraiz, F. J., Plazas, M., Prohens, J., & Vilanova, S. (2016). Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics, 17(1). doi:10.1186/s12864-016-2631-4 es_ES
dc.description.references Gramazio, P., Prohens, J., Plazas, M., Mangino, G., Herraiz, F. J., & Vilanova, S. (2017). Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. Frontiers in Plant Science, 8. doi:10.3389/fpls.2017.01477 es_ES
dc.description.references Gramazio, P., Prohens, J., Borràs, D., Plazas, M., Herraiz, F. J., & Vilanova, S. (2017). Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants. Euphytica, 213(12). doi:10.1007/s10681-017-2057-3 es_ES
dc.description.references GRAMAZIO, P., PROHENS, J., PLAZAS, M., MANGINO, G., HERRAIZ, F. J., GARCÍA-FORTEA, E., & VILANOVA, S. (2018). Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 46(1), 1-13. doi:10.15835/nbha46110936 es_ES
dc.description.references Grzebelus, D., Gładysz, M., Macko-Podgórni, A., Gambin, T., Golis, B., Rakoczy, R., & Gambin, A. (2009). Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene, 448(2), 214-220. doi:10.1016/j.gene.2009.06.004 es_ES
dc.description.references Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J., Zhang, H., … Wang, Z. (2012). The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics, 45(1), 51-58. doi:10.1038/ng.2470 es_ES
dc.description.references Hill, T. A., Ashrafi, H., Reyes-Chin-Wo, S., Yao, J., Stoffel, K., Truco, M.-J., … Van Deynze, A. (2013). Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip. PLoS ONE, 8(2), e56200. doi:10.1371/journal.pone.0056200 es_ES
dc.description.references Hirakawa, H., Shirasawa, K., Miyatake, K., Nunome, T., Negoro, S., Ohyama, A., … Fukuoka, H. (2014). Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World. DNA Research, 21(6), 649-660. doi:10.1093/dnares/dsu027 es_ES
dc.description.references Hu, J., Manduzio, S., & Kang, H. (2019). Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. Frontiers in Plant Science, 10. doi:10.3389/fpls.2019.00500 es_ES
dc.description.references Huang, X., Wei, X., Sang, T., Zhao, Q., Feng, Q., Zhao, Y., … Han, B. (2010). Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42(11), 961-967. doi:10.1038/ng.695 es_ES
dc.description.references Hulse-Kemp, A. M., Ashrafi, H., Plieske, J., Lemm, J., Stoffel, K., Hill, T., … Van Deynze, A. (2016). A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. Horticulture Research, 3(1). doi:10.1038/hortres.2016.36 es_ES
dc.description.references Hurtado, M., Vilanova, S., Plazas, M., Gramazio, P., Andújar, I., Herraiz, F. J., … Prohens, J. (2014). Enhancing conservation and use of local vegetable landraces: the Almagro eggplant (Solanum melongena L.) case study. Genetic Resources and Crop Evolution, 61(4), 787-795. doi:10.1007/s10722-013-0073-2 es_ES
dc.description.references Ihaka, R., & Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics, 5(3), 299-314. doi:10.1080/10618600.1996.10474713 es_ES
dc.description.references Kim, C., Guo, H., Kong, W., Chandnani, R., Shuang, L.-S., & Paterson, A. H. (2016). Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science, 242, 14-22. doi:10.1016/j.plantsci.2015.04.016 es_ES
dc.description.references Kim, S., Park, M., Yeom, S.-I., Kim, Y.-M., Lee, J. M., Lee, H.-A., … Kim, K.-T. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 46(3), 270-278. doi:10.1038/ng.2877 es_ES
dc.description.references Knapp, S., Vorontsova, M. S., & Prohens, J. (2013). Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group. PLoS ONE, 8(2), e57039. doi:10.1371/journal.pone.0057039 es_ES
dc.description.references Kouassi, B., Prohens, J., Gramazio, P., Kouassi, A. B., Vilanova, S., Galán-Ávila, A., … Plazas, M. (2016). Development of backcross generations and new interspecific hybrid combinations for introgression breeding in eggplant ( Solanum melongena ). Scientia Horticulturae, 213, 199-207. doi:10.1016/j.scienta.2016.10.039 es_ES
dc.description.references Lam, H.-M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F.-L., … Zhang, G. (2010). Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics, 42(12), 1053-1059. doi:10.1038/ng.715 es_ES
dc.description.references Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. doi:10.1038/nmeth.1923 es_ES
dc.description.references Levin, H. L., & Moran, J. V. (2011). Dynamic interactions between transposable elements and their hosts. Nature Reviews Genetics, 12(9), 615-627. doi:10.1038/nrg3030 es_ES
dc.description.references Lewicki, T. (1974). West African Food in the Middle Ages. doi:10.1017/cbo9780511759796 es_ES
dc.description.references Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352 es_ES
dc.description.references Li, H. (2014). Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics, 30(20), 2843-2851. doi:10.1093/bioinformatics/btu356 es_ES
dc.description.references Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., … Huang, S. (2014). Genomic analyses provide insights into the history of tomato breeding. Nature Genetics, 46(11), 1220-1226. doi:10.1038/ng.3117 es_ES
dc.description.references Liu, J., Zheng, Z., Zhou, X., Feng, C., & Zhuang, Y. (2014). Improving the resistance of eggplant (Solanum melongena) to Verticillium wilt using wild species Solanum linnaeanum. Euphytica, 201(3), 463-469. doi:10.1007/s10681-014-1234-x es_ES
dc.description.references Mahesh, S., & Udayakumar, M. (2017). Peanut RNA Helicase AhRH47 Sustains Protein Synthesis Under Stress and Improves Stress Adaptation in Arabidopsis. Plant Molecular Biology Reporter, 36(1), 58-70. doi:10.1007/s11105-017-1056-9 es_ES
dc.description.references Meyer, R. S., Karol, K. G., Little, D. P., Nee, M. H., & Litt, A. (2012). Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Molecular Phylogenetics and Evolution, 63(3), 685-701. doi:10.1016/j.ympev.2012.02.006 es_ES
dc.description.references Meyer, R. S., Whitaker, B. D., Little, D. P., Wu, S.-B., Kennelly, E. J., Long, C.-L., & Litt, A. (2015). Parallel reductions in phenolic constituents resulting from the domestication of eggplant. Phytochemistry, 115, 194-206. doi:10.1016/j.phytochem.2015.02.006 es_ES
dc.description.references Michalovova, M., Vyskot, B., & Kejnovsky, E. (2013). Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization. Heredity, 111(4), 314-320. doi:10.1038/hdy.2013.51 es_ES
dc.description.references Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., & Nuez, F. (2008). Characterization, diversity, and relationships of the Spanish striped (Listada) eggplants: a model for the enhancement and protection of local heirlooms. Euphytica, 164(2), 405-419. doi:10.1007/s10681-008-9688-3 es_ES
dc.description.references Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., Ribas, F., Castro, A., & Nuez, F. (2008). Distinguishing a protected geographical indication vegetable (Almagro eggplant) from closely related varieties with selected morphological traits and molecular markers. Journal of the Science of Food and Agriculture, 89(2), 320-328. doi:10.1002/jsfa.3452 es_ES
dc.description.references Muñoz-Falcón, J. E., Prohens, J., Vilanova, S., & Nuez, F. (2009). Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders’ gene pool. Annals of Applied Biology, 154(3), 453-465. doi:10.1111/j.1744-7348.2009.00314.x es_ES
dc.description.references Naito, K., Cho, E., Yang, G., Campbell, M. A., Yano, K., Okumoto, Y., … Wessler, S. R. (2006). Dramatic amplification of a rice transposable element during recent domestication. Proceedings of the National Academy of Sciences, 103(47), 17620-17625. doi:10.1073/pnas.0605421103 es_ES
dc.description.references Nelson, M. G., Linheiro, R. S., & Bergman, C. M. (2017). McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. G3: Genes|Genomes|Genetics, 7(8), 2763-2778. doi:10.1534/g3.117.043893 es_ES
dc.description.references Nidumukkala, S., Tayi, L., Chittela, R. K., Vudem, D. R., & Khareedu, V. R. (2019). DEAD box helicases as promising molecular tools for engineering abiotic stress tolerance in plants. Critical Reviews in Biotechnology, 39(3), 395-407. doi:10.1080/07388551.2019.1566204 es_ES
dc.description.references Pascual, L., Desplat, N., Huang, B. E., Desgroux, A., Bruguier, L., Bouchet, J.-P., … Causse, M. (2014). Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnology Journal, 13(4), 565-577. doi:10.1111/pbi.12282 es_ES
dc.description.references Paterson, A. H., Bowers, J. E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., … Rokhsar, D. S. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229), 551-556. doi:10.1038/nature07723 es_ES
dc.description.references Plazas, M., Vilanova, S., Gramazio, P., Rodríguez-Burruezo, A., Fita, A., Herraiz, F. J., … Prohens, J. (2016). Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools. Journal of the American Society for Horticultural Science, 141(1), 34-44. doi:10.21273/jashs.141.1.34 es_ES
dc.description.references (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475(7355), 189-195. doi:10.1038/nature10158 es_ES
dc.description.references Prohens, J., Gramazio, P., Plazas, M., Dempewolf, H., Kilian, B., Díez, M. J., … Vilanova, S. (2017). Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica, 213(7). doi:10.1007/s10681-017-1938-9 es_ES
dc.description.references Prohens, J., Whitaker, B. D., Plazas, M., Vilanova, S., Hurtado, M., Blasco, M., … Stommel, J. R. (2013). Genetic diversity in morphological characters and phenolic acids content resulting from an interspecific cross between eggplant,Solanum melongena, and its wild ancestor (S. incanum). Annals of Applied Biology, 162(2), 242-257. doi:10.1111/aab.12017 es_ES
dc.description.references Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., … Huang, S. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics, 45(12), 1510-1515. doi:10.1038/ng.2801 es_ES
dc.description.references Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi:10.1093/bioinformatics/btq033 es_ES
dc.description.references Ranil, R. H. G., Niran, H. M. L., Plazas, M., Fonseka, R. M., Fonseka, H. H., Vilanova, S., … Prohens, J. (2015). Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design. Scientia Horticulturae, 193, 174-181. doi:10.1016/j.scienta.2015.07.030 es_ES
dc.description.references Salas, P., Prohens, J., & Seguí-Simarro, J. M. (2011). Evaluation of androgenic competence through anther culture in common eggplant and related species. Euphytica, 182(2), 261-274. doi:10.1007/s10681-011-0490-2 es_ES
dc.description.references Salikhov, K., Sacomoto, G., & Kucherov, G. (2014). Using cascading Bloom filters to improve the memory usage for de Brujin graphs. Algorithms for Molecular Biology, 9(1), 2. doi:10.1186/1748-7188-9-2 es_ES
dc.description.references Särkinen, T., Bohs, L., Olmstead, R. G., & Knapp, S. (2013). A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree. BMC Evolutionary Biology, 13(1), 214. doi:10.1186/1471-2148-13-214 es_ES
dc.description.references Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., … Graves, T. A. (2009). The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science, 326(5956), 1112-1115. doi:10.1126/science.1178534 es_ES
dc.description.references Shi, L., Wu, Y., & Sheen, J. (2018). TOR signaling in plants: conservation and innovation. Development, 145(13), dev160887. doi:10.1242/dev.160887 es_ES
dc.description.references Shivakumara, T. N., Sreevathsa, R., Dash, P. K., Sheshshayee, M. S., Papolu, P. K., Rao, U., … UdayaKumar, M. (2017). Overexpression of Pea DNA Helicase 45 (PDH45) imparts tolerance to multiple abiotic stresses in chili (Capsicum annuum L.). Scientific Reports, 7(1). doi:10.1038/s41598-017-02589-0 es_ES
dc.description.references Sim, S.-C., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Van Deynze, A., … Francis, D. M. (2012). Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato. PLoS ONE, 7(7), e40563. doi:10.1371/journal.pone.0040563 es_ES
dc.description.references Sim, S.-C., Van Deynze, A., Stoffel, K., Douches, D. S., Zarka, D., Ganal, M. W., … Francis, D. M. (2012). High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding. PLoS ONE, 7(9), e45520. doi:10.1371/journal.pone.0045520 es_ES
dc.description.references Stommel, J. R., & Whitaker, B. D. (2003). Phenolic Acid Content and Composition of Eggplant Fruit in a Germplasm Core Subset. Journal of the American Society for Horticultural Science, 128(5), 704-710. doi:10.21273/jashs.128.5.0704 es_ES
dc.description.references Studer, A., Zhao, Q., Ross-Ibarra, J., & Doebley, J. (2011). Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics, 43(11), 1160-1163. doi:10.1038/ng.942 es_ES
dc.description.references Subbaiyan, G. K., Waters, D. L. E., Katiyar, S. K., Sadananda, A. R., Vaddadi, S., & Henry, R. J. (2012). Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing. Plant Biotechnology Journal, 10(6), 623-634. doi:10.1111/j.1467-7652.2011.00676.x es_ES
dc.description.references Syfert, M. M., Castañeda-Álvarez, N. P., Khoury, C. K., Särkinen, T., Sosa, C. C., Achicanoy, H. A., … Knapp, S. (2016). Crop wild relatives of the brinjal eggplant (Solanum melongena): Poorly represented in genebanks and many species at risk of extinction. American Journal of Botany, 103(4), 635-651. doi:10.3732/ajb.1500539 es_ES
dc.description.references Toppino, L., Valè, G., & Rotino, G. L. (2008). Inheritance of Fusarium wilt resistance introgressed from Solanum aethiopicum Gilo and Aculeatum groups into cultivated eggplant (S. melongena) and development of associated PCR-based markers. Molecular Breeding, 22(2), 237-250. doi:10.1007/s11032-008-9170-x es_ES
dc.description.references Toppino, L., Barchi, L., Lo Scalzo, R., Palazzolo, E., Francese, G., Fibiani, M., … Rotino, G. L. (2016). Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.). Frontiers in Plant Science, 7. doi:10.3389/fpls.2016.00256 es_ES
dc.description.references Tranchida-Lombardo, V., Aiese Cigliano, R., Anzar, I., Landi, S., Palombieri, S., Colantuono, C., … Grillo, S. (2017). Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. DNA Research, 25(2), 149-160. doi:10.1093/dnares/dsx045 es_ES
dc.description.references Vashisht, A. A., Pradhan, A., Tuteja, R., & Tuteja, N. (2005). Cold- and salinity stress-induced bipolar pea DNA helicase 47 is involved in protein synthesis and stimulated by phosphorylation with protein kinase C. The Plant Journal, 44(1), 76-87. doi:10.1111/j.1365-313x.2005.02511.x es_ES
dc.description.references Vilanova, S., Manzur, J. P., & Prohens, J. (2011). Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Molecular Breeding, 30(2), 647-660. doi:10.1007/s11032-011-9650-2 es_ES
dc.description.references Víquez-Zamora, M., Vosman, B., van de Geest, H., Bovy, A., Visser, R. G., Finkers, R., & van Heusden, A. W. (2013). Tomato breeding in the genomics era: insights from a SNP array. BMC Genomics, 14(1), 354. doi:10.1186/1471-2164-14-354 es_ES
dc.description.references Vorontsova, M. S., Stern, S., Bohs, L., & Knapp, S. (2013). African spinySolanum(subgenusLeptostemonum, Solanaceae): a thorny phylogenetic tangle. Botanical Journal of the Linnean Society, 173(2), 176-193. doi:10.1111/boj.12053 es_ES
dc.description.references Vos, P. G., Uitdewilligen, J. G. A. M. L., Voorrips, R. E., Visser, R. G. F., & van Eck, H. J. (2015). Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theoretical and Applied Genetics, 128(12), 2387-2401. doi:10.1007/s00122-015-2593-y es_ES
dc.description.references Wang, Y., Pang, C., Li, X., Hu, Z., Lv, Z., Zheng, B., & Chen, P. (2017). Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis. BMC Plant Biology, 17(1). doi:10.1186/s12870-017-1206-0 es_ES
dc.description.references Weigel, D., & Mott, R. (2009). The 1001 Genomes Project for Arabidopsis thaliana. Genome Biology, 10(5), 107. doi:10.1186/gb-2009-10-5-107 es_ES
dc.description.references Wheeler, G. L., Jones, M. A., & Smirnoff, N. (1998). The biosynthetic pathway of vitamin C in higher plants. Nature, 393(6683), 365-369. doi:10.1038/30728 es_ES
dc.description.references Xu, X., Liu, X., Ge, S., Jensen, J. D., Hu, F., Li, X., … Wang, W. (2011). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 30(1), 105-111. doi:10.1038/nbt.2050 es_ES
dc.description.references Yan, J., Yang, X., Shah, T., Sánchez-Villeda, H., Li, J., Warburton, M., … Xu, Y. (2009). High-throughput SNP genotyping with the GoldenGate assay in maize. Molecular Breeding, 25(3), 441-451. doi:10.1007/s11032-009-9343-2 es_ES
dc.description.references Yang, X., Cheng, Y.-F., Deng, C., Ma, Y., Wang, Z.-W., Chen, X.-H., & Xue, L.-B. (2014). Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis. BMC Genomics, 15(1), 412. doi:10.1186/1471-2164-15-412 es_ES
dc.description.references Yu, J. (2002). A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). Science, 296(5565), 79-92. doi:10.1126/science.1068037 es_ES
dc.description.references Zhou, X., Bao, S., Liu, J., & Zhuang, Y. (2016). De Novo Sequencing and Analysis of the Transcriptome of the Wild Eggplant Species Solanum Aculeatissimum in Response to Verticillium dahliae. Plant Molecular Biology Reporter, 34(6), 1193-1203. doi:10.1007/s11105-016-0998-7 es_ES
dc.description.references Zhuang, J., Wang, J., Theurkauf, W., & Weng, Z. (2014). TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Research, 42(11), 6826-6838. doi:10.1093/nar/gku323 es_ES
dc.description.references Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., … Tian, Z. (2015). Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnology, 33(4), 408-414. doi:10.1038/nbt.3096 es_ES


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