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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

dc.contributor.author	Xanthopoulou, Aliki
dc.contributor.author	Montero Pau, Javier
dc.contributor.author	Mellidou, Ifigeneia
dc.contributor.author	Kissoudis, Christos
dc.contributor.author	Blanca, José
dc.contributor.author	Picó, Belén
dc.contributor.author	Tsaballa, Aphrodite
dc.contributor.author	Tsaliki, Eleni
dc.contributor.author	Dalakouras, Athanasios
dc.contributor.author	Paris, Harry S.
dc.contributor.author	Ganopoulou, Maria
dc.contributor.author	Moysiadis, Theodoros
dc.contributor.author	Osathanunkul, Maslin
dc.contributor.author	Tsaftaris, Athanasios
dc.contributor.author	Madesis, Panagiotis
dc.contributor.author	Kalivas, Apostolos
dc.contributor.author	Ganopoulos, Ioannis
dc.date.accessioned	2019-09-09T12:50:00Z
dc.date.available	2019-09-09T12:50:00Z
dc.date.issued	2019
dc.identifier.citation	Xanthopoulou, Aliki Montero Pau, Javier Mellidou, Ifigeneia Kissoudis, Christos Blanca, José Picó, Belén Tsaballa, Aphrodite Tsaliki, Eleni Dalakouras, Athanasios Paris, Harry S. Ganopoulou, Maria Moysiadis, Theodoros Osathanunkul, Maslin Tsaftaris, Athanasios Madesis, Panagiotis Kalivas, Apostolos Ganopoulos, Ioannis 2019 Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits Horticulture Research 6 94 94-1 94-17
dc.identifier.uri	https://hdl.handle.net/10550/71410
dc.description.abstract	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.
dc.language.iso	eng
dc.relation.ispartof	Horticulture Research, 2019, vol. 6, num. 94, p. 94-1-94-17
dc.subject	Genòmica
dc.subject	Plantes
dc.title	Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits
dc.type	journal article	es_ES
dc.date.updated	2019-09-09T12:50:01Z
dc.identifier.doi	10.1038/s41438-019-0176-9
dc.identifier.idgrec	134007
dc.rights.accessRights	open access	es_ES