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First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.)

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First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.)

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dc.contributor.author Pomares-Viciana, T es_ES
dc.contributor.author Del Rio-Celestino, M es_ES
dc.contributor.author Roman, B es_ES
dc.contributor.author Die, J es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.contributor.author Gómez, P es_ES
dc.date.accessioned 2020-11-07T04:32:10Z
dc.date.available 2020-11-07T04:32:10Z
dc.date.issued 2019-02-06 es_ES
dc.identifier.issn 1471-2229 es_ES
dc.identifier.uri http://hdl.handle.net/10251/154378
dc.description.abstract [EN] Background: Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. Results: RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. Conclusion: This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini. es_ES
dc.description.sponsorship Research worked is supported by the project RTA2014-00078 from the Spanish Institute of Agronomy Research INIA (Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria) and also PP.AVA.AVA201601.7, FEDER y FSE (Programa Operativo FSE de Andalucia 2007-2013 "Andalucia se mueve con Europa"). TPV is supported by a FPI scholarship from RTA2011-00044-C02-01/02 project of INIA. The funding agencies were not involved in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript. es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Plant Biology es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Cucurbita pepo es_ES
dc.subject Zucchini es_ES
dc.subject Parthenocarpy es_ES
dc.subject Fruit set es_ES
dc.subject Differential gene expression es_ES
dc.subject RNA-seq es_ES
dc.subject.classification GENETICA es_ES
dc.title First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.) es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12870-019-1632-2 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RTA2011-00044-C02-01/ES/Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortaliza/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//RTA2014-00078-00-00/ES/Mejora de la calidad y resistencia de calabacín: aproximación genómica/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/Junta de Andalucía//PP.AVA.AVA201601.7/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//RTA2011-00044-C02-02/ES/Desarrollo competitivo de nuevos cultivares de calabacín y ampliación de la plataforma genómica para la mejora de esta hortaliza/ 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 Pomares-Viciana, T.; Del Rio-Celestino, M.; Roman, B.; Die, J.; Picó Sirvent, MB.; Gómez, P. (2019). First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC Plant Biology. 19:1-20. https://doi.org/10.1186/s12870-019-1632-2 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12870-019-1632-2 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 20 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 19 es_ES
dc.identifier.pmid 30727959 es_ES
dc.identifier.pmcid PMC6366093 es_ES
dc.relation.pasarela S\383955 es_ES
dc.contributor.funder Junta de Andalucía es_ES
dc.contributor.funder European Regional Development Fund es_ES
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.description.references Varga A, Bruinsma J. Tomato. In: Monselise SP, editor. CRC Handbook of Fruit Set and Development. Boca Raton: CRC Press; 1986. p. 461–80. es_ES
dc.description.references Nepi M, Cresti L, Guarnieri M, Pacini E. Effect of relative humidity on water content, viability and carbohydrate profile of Petunia hybrid and Cucurbita pepo pollen. Plant Syst Evol. 2010;284:57–64. es_ES
dc.description.references Gustafson FG. Parthenocarpy: natural and artificial. Bot Rev. 1942;8:599–654. es_ES
dc.description.references Robinson RW, Reiners S. Parthenocarpy in summer squash. Hortscience. 1999;34:715–7. es_ES
dc.description.references Pomares-Viciana T, Die J, Del Río-Celestino M, Román B, Gómez P. Auxin signalling regulation during induced and parthenocarpic fruit set in zucchini. Mol Breeding. 2017;37:56. es_ES
dc.description.references Ozga JA, Reinecke DM. Hormonal interactions in fruit development. J Plant Growth Regul. 2003;22:73–81. es_ES
dc.description.references Kim IS, Okubo H, Fujieda K. Endogenous levels of IAA in relation to parthenocarpy in cucumber (Cucumis sativus L). Sci Hortic. 1992;52:1–8. es_ES
dc.description.references Olimpieri I, Siligato F, Caccia R, Mariotti L, Ceccarelli N, Soressi GP, et al. Tomato fruit set driven by pollination or by the parthenocarpic fruit allele are mediated by transcriptionally regulated gibberellin biosynthesis. Planta. 2007;226:877–88. es_ES
dc.description.references Cui L, Zhang T, Li J, Lou Q, Chen J. Cloning and expression analysis of Cs-TIR1/AFB2: the fruit development-related genes of cucumber (Cucumis sativus L.). Acta Physiol Plant. 2014;36:139–49. es_ES
dc.description.references De Jong M, Wolters-Arts J, Feron R, Mariani C, Vriezen WH. The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signalling during tomato fruit set and development. Plant J. 2009;57:160–70. es_ES
dc.description.references Wang H, Jones B, Li Z, Frasse P, Delalande C, Regad F, Chaabouni S, Latché A, Pech JC, Bouzayen M. The tomato aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell. 2005;17(10):2676–92. es_ES
dc.description.references Goetz M, Vivian-Smith A, Johnson SD, Koltunow AM. AUXIN RESPONSE FACTOR 8 is a negative regulator of fruit initiation in Arabidopsis. Plant Cell. 2006;18(8):1873–86. es_ES
dc.description.references Mazzucato A, Cellini F, Bouzayen M, Zouine M, Mila I, Minoia S et al. A TILLING allele of the tomato aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. Mol Breeding. 2015; 35(22):1-15. es_ES
dc.description.references Blanca J, Cañizares J, Roig C, Ziarsolo P, Nuez F, Picó B. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 2011;12:104. es_ES
dc.description.references Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63. es_ES
dc.description.references Da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, et al. Next-generation biology: sequencing and data analysis approaches for non-model organisms. Mar Genomics. 2016;30:3–13. es_ES
dc.description.references Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 2016;17:13. es_ES
dc.description.references Li J, Cui ZWJ, Zhang T, Guo Q, Xu J, Li J, et al. Transcriptome comparison of global distinctive features between pollination and parthenocarpic fruit set reveals transcriptional phytohormone cross-talk in cucumber (Cucumis sativus L). Plant Cell Physiol. 2014;55(7):1325–42. es_ES
dc.description.references Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2. es_ES
dc.description.references Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí-Gómez C, et al. De novo assembly of the zucchini genome reveals a whole genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol J. 2017. https://doi.org/10.1111/pbi.12860 . es_ES
dc.description.references Vriezen WH, Feron R, Maretto F, Keijman J, Mariani C. Changes in tomato ovary transcriptome demonstrate complex hormonal regulation of fruit set. New Phytol. 2008;177:60–76. es_ES
dc.description.references Tang N, Deng W, Hu G, Hu N, Li Z. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin. PLoS One. 2015;10(4):e0125355. es_ES
dc.description.references Li J, Yan S, Yang W, Li Y, Xia M, Chen Z, et al. Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.). Sci Rep. 2015;26(5):8031. es_ES
dc.description.references Mironov V, De Veylder L, Van Montagu M, Inze D. Cyclin-dependent kinases and cell division in plants- the nexus. Plant Cell. 1999;11(4):509–22. es_ES
dc.description.references Perrot-Rechenmann C. Cellular responses to auxin: division versus expansion. Cold Spring Harb Perspect Biol. 2010;2(5):a001446. es_ES
dc.description.references De Veylder L, Beeckman T, Beemster GT, Krols L, Terras F, Landrieu I, et al. Functional analysis of cyclin-dependent kinase inhibitors of Arabidopsis. Plant Cell. 2001;13:1653–68. es_ES
dc.description.references Nieuwland J, Menges M, Murray JAH. The plant cyclins. In: Inze D, editor. Cell cycle control and plant development, vol. 2007. Oxford: Wiley-Blackwell Publishing; 2007. p. 33–61. es_ES
dc.description.references Menges M, Samland AK, Planchais S, Murray JA. The D-type cyclin CYCD3;1 is limiting for the G1-to-S-phasetransition in Arabidopsis. Plant Cell. 2006;18:893–906. es_ES
dc.description.references Boruc J, Mylle E, Duda M, De Clercq R, Rombauts S, Geelen D, et al. Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes. Plant Physiol. 2010;152(2):553–65. es_ES
dc.description.references Sampedro J, Cosgrove DJ. The expansin superfamily. Genome Biol. 2005;6:242. es_ES
dc.description.references Esmon CA, Tinsley AG, Ljung K, Sandberg G, Hearne LB, Liscum E. A gradient of auxin and auxin-dependent transcription precedes tropic growth responses. Proc Natl Acad Sci. 2006;103:236–41. es_ES
dc.description.references De Folter S, Busscher J, Colombo L, Losa A, Angenent GC. Transcript profiling of transcription factors genes during siliques development in Arabidopsis. Plant Mol Bio. 2004;56:351–3662004. es_ES
dc.description.references Son O, Cho HY, Kim MR, Lee H, Lee MS, Song E, et al. Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots. Biochem Biophys Res Commun. 2005;326(1):203–9. es_ES
dc.description.references Olsson ASB, Engstroem P, Seoderman E. The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Mol Biol. 2004;55:663–77. es_ES
dc.description.references Merrow SB, Hopp RJ. Storage effects on winter squashes. Associations between the sugar and starch content of and the degree of preference for winter squashes. J Agric Food Chem. 1961;9:321–6. es_ES
dc.description.references Berg JM, Tymoczko JL, Stryer L. Carbohydrates. In: Freeman WH, editor. Biochemistry. 5th ed. New York: W H Freeman; 2002. es_ES
dc.description.references Prabhakar V, Löttgert T, Gigolashvili T, Bell K, Flügge UI, Häusler RE. Molecular and functional characterization of the plastid-localized phosphoenolpyruvate enolase (ENO1) from Arabidopsis thaliana. FEBS Lett. 2009;583(6):983–91. es_ES
dc.description.references Rius SP, Casati P, Iglesias AA, Gomez-Casati DF. Characterization of Arabidopsis lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase. Plant Physiol. 2008;148(3):1655–67. es_ES
dc.description.references Van der Linde K, Gutsche N, Leffers HM, Lindermayr C, Müller B, Holtgrefe S, et al. Regulation of plant cytosolic aldolase functions by redox-modifications. Plant Physiol Biochem. 2011;49(9):946–57. es_ES
dc.description.references Lim H, Cho MH, Jeon JS, Bhoo SH, Kwon YK, Hahn TR. Altered expression of pyrophosphate: fructose-6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants. Mol Cells. 2009;27(6):641–9. es_ES
dc.description.references Baud S, Wuillème S, Dubreucq B, De Almeida A, Vuagnat C, Lepiniec L, et al. Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana. Plant J. 2007;52:405–19. es_ES
dc.description.references De Jong M, Mariani C, Vriezen WH. The role of auxin and gibberellin in tomato fruit set. J Exp Bot. 2009;60(5):1523–32. es_ES
dc.description.references Martínez C, Manzano S, Megías Z, Garrido D, Picó B, Jamilena M. Involvement of ethylene biosynthesis and signalling in fruit set and early fruit development in zucchini squash (Cucurbita pepo L.). BMC Plant Biol. 2013;13:139. es_ES
dc.description.references Serrani JC, Fos M, Atarés A, Garcia-martinez JL. Effect of gibberellin and auxin on parthenocarpic fruit growth induction in the cv. micro-tom of tomato. J Plant Growth Regul. 2007;26:211–21. es_ES
dc.description.references Mapelli S. Changes in cytokinin in the fruits of parthenocarpic and normal tomatoes. Plant Sci Lett. 1981;22:227–33. es_ES
dc.description.references Ulmasov T, Hagen G, Guilfoyle TJ. Activation and repression of transcription by auxin-response factors. Proc Natl Acad Sci U S A. 1999;96:5844–9. es_ES
dc.description.references Ulmasov T, Hagen G, Guilfoyle TJ. Dimerization and DNA binding of auxin response factors. Plant J. 1999;19:309–19. es_ES
dc.description.references Tiwari SB, Hagen G, Guilfoyle TJ. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell. 2004;16:533–43. es_ES
dc.description.references Switzenberg JA, Beaudry RM, Grumet R. Effect of CRC:: etr1-1 transgene expression on ethylene production, sex expression, fruit set and fruit ripening in transgenic melon (Cucumis melo L.). Transgenic Res. 2015;24(3):497-507. es_ES
dc.description.references Nitsch LM, Oplaat C, Feron R, Ma Q, Wolters-Arts M, Hedden P, et al. Abscisic acid levels in tomato ovaries are regulated by LeNCED1 and SlCYP707A1. Planta. 2009;229(6):1335–46. es_ES
dc.description.references Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods. 2008;5(7):621–8. es_ES
dc.description.references Robinson MD, McCarthy DJ, Smyth GK. Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2008;26(1):139–40. es_ES
dc.description.references Raza K, Mishra A. A novel anticlustering filtering algorithm for the prediction of genes as a drug target. Am J Bio Engi. 2012;2(5):206–11. es_ES
dc.description.references Van Iterson M, Boer JM, Menezes RX. Filtering, FDR and power. BMCBioinformatics. 2010;11:450. es_ES
dc.description.references Conesa A, Götz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21:3674–6. es_ES
dc.description.references Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis. 2015. https://doi.org/10.1002/dvg.22877 . es_ES
dc.description.references Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL. Nucleic Acids Res. 2000;28(1):45–8. es_ES
dc.description.references Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST: a better web interface. Nucleic Acids Res. 2008;36:W5–9. es_ES
dc.description.references Wyatt LE, Strickler SR, Mueller LA, Mazourek M. An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. Hortic Res. 2015;2:14070. https://doi.org/10.1038/hortres.2014.70 . es_ES
dc.description.references Zhang A, Ren GA, Sun YA, Guo H, Zhang SA, Zhang FA, et al. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.). BMC Genomics. 2015;16:1101. es_ES
dc.description.references Finn RD, Attwood TK, Babbit AB, Bork P, Bridge AJ, Chang HY. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. https://doi.org/10.1093/nar/gkw1107 . es_ES
dc.description.references Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9. es_ES
dc.description.references Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:480–4. 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


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