Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing

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dc.contributor.authorHu, Yingen
dc.contributor.authorResende Jr., Marcio F. R.en
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.authorBrym, Mariaen
dc.contributor.authorBassil, Eliasen
dc.contributor.authorChambers, Alan H.en
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2019-07-23T17:51:51Zen
dc.date.available2019-07-23T17:51:51Zen
dc.date.issued2019-03-04en
dc.description.abstractDemand for all-natural vanilla flavor is increasing, but its botanical source, Vanilla planifolia, faces critical challenges arising from a narrow germplasm base and supply limitations. Genomics tools are the key to overcoming these limitations by enabling advanced genetics and plant breeding for new cultivars with improved yield and quality. The objective of this work was to establish the genomic resources needed to facilitate analysis of diversity among Vanilla accessions and to provide a resource to analyze other Vanilla collections. A V. planifolia draft genome was assembled and used to identify 521,732 single nucleotide polymorphism (SNP) markers using Genotyping-By-Sequencing (GBS). The draft genome had a size of 2.20 Gb representing 97% of the estimated genome size. A filtered set of 5,082 SNPs was used to genotype a living collection of 112 Vanilla accessions from 23 species including native Florida species. Principal component analysis of the genetic distances, population structure, and the maternally inherited rbcL gene identified putative hybrids, misidentified accessions, significant diversity within V. planifolia, and evidence for 12 clusters that separate accessions by species. These results validate the efficiency of genomics-based tools to characterize and identify genetic diversity in Vanilla and provide a significant tool for genomics-assisted plant breeding.en
dc.description.notesFunding for this research was provided by the University of Florida Dean for Research. We also acknowledge Advanced Research Computing (ARC) for use of the CASCADES supercomputing resource at Virginia Tech.en
dc.description.sponsorshipUniversity of Florida Dean for Researchen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41598-019-40144-1en
dc.identifier.issn2045-2322en
dc.identifier.other3416en
dc.identifier.pmid30833623en
dc.identifier.urihttp://hdl.handle.net/10919/91928en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectcultivated vanillaen
dc.subjectgene-sequencesen
dc.subjectphylogenetic analysisen
dc.subjecthybridizationen
dc.subjectorchidaceaeen
dc.subjectvanilloideaeen
dc.subjecttahitensisen
dc.subjectnuclearen
dc.subjectandrewsen
dc.subjecttoolen
dc.titleGenomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencingen
dc.title.serialScientific Reportsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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