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Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

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Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

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dc.contributor.author Xanthopoulou, Aliki es_ES
dc.contributor.author Montero-Pau, Javier es_ES
dc.contributor.author Mellidou, Ifigeneia es_ES
dc.contributor.author Kissoudis, Christos es_ES
dc.contributor.author Blanca Postigo, José Miguel es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.contributor.author Tsaballa, Aphrodite es_ES
dc.contributor.author Tsaliki, Eleni es_ES
dc.contributor.author Dalakouras, Athanasios es_ES
dc.contributor.author Paris, Harry S. es_ES
dc.contributor.author Ganopoulou, Maria es_ES
dc.contributor.author Moysiadis, Theodoros es_ES
dc.contributor.author Osathanunkul, Maslin es_ES
dc.contributor.author Tsaftaris, Athanasios es_ES
dc.contributor.author Madesis, Panagiotis es_ES
dc.date.accessioned 2020-12-12T04:32:28Z
dc.date.available 2020-12-12T04:32:28Z
dc.date.issued 2019-08-11 es_ES
dc.identifier.uri http://hdl.handle.net/10251/156948
dc.description.abstract [EN] Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance. es_ES
dc.description.sponsorship This work has been supported by Hellenic Agricultural Organization (ELGO) Demeter. Furthermore, we thank the Conselleria de Educacio, Investigacio, Cultura i Esport (Generalitat Valenciana) for funding Project Prometeo 2017/078 "Seleccion de Variedades Tradicionales y Desarrollo de Nuevas Variedades de Cucurbitaceas Adaptadas a la Produccion Ecologica". Also, this work was supported by Chiang Mai University. 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 Yabby gene family es_ES
dc.subject Fruit shape es_ES
dc.subject Candidate genes es_ES
dc.subject Reveals es_ES
dc.subject Evolution es_ES
dc.subject Homologs es_ES
dc.subject Common es_ES
dc.subject Size es_ES
dc.subject Sun es_ES
dc.subject.classification GENETICA es_ES
dc.title Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1038/s41438-019-0176-9 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//PROMETEO%2F2017%2F078/ES/Selección de variedades tradicionales y desarrollo de nuevas variedades de cucurbitáceas adaptadas a la producción ecológica/ 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 Xanthopoulou, A.; Montero-Pau, J.; Mellidou, I.; Kissoudis, C.; Blanca Postigo, JM.; Picó Sirvent, MB.; Tsaballa, A.... (2019). Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits. Horticulture Research. 6:1-17. https://doi.org/10.1038/s41438-019-0176-9 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1038/s41438-019-0176-9 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 6 es_ES
dc.identifier.eissn 2052-7276 es_ES
dc.identifier.pmid 31645952 es_ES
dc.identifier.pmcid PMC6804688 es_ES
dc.relation.pasarela S\410034 es_ES
dc.contributor.funder Chiang Mai University es_ES
dc.contributor.funder Generalitat Valenciana es_ES
dc.contributor.funder Hellenic Agricultural Organization (ELGO) Demeter es_ES
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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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