K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
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| dc.contributor.author | Ziarsolo, Peio
|
es_ES |
| dc.contributor.author | Hasing, Tomas
|
es_ES |
| dc.contributor.author | Hilario, Rebeca
|
es_ES |
| dc.contributor.author | García-Carpintero, Víctor
|
es_ES |
| dc.contributor.author | Blanca Postigo, José Miguel
|
es_ES |
| dc.contributor.author | Bombarely, Aureliano
|
es_ES |
| dc.contributor.author | Cañizares Sales, Joaquín
|
es_ES |
| dc.date.accessioned | 2022-09-29T18:04:51Z | |
| dc.date.available | 2022-09-29T18:04:51Z | |
| dc.date.issued | 2021-03-25 | es_ES |
| dc.identifier.issn | 1746-4811 | es_ES |
| dc.identifier.uri | http://hdl.handle.net/10251/186756 | |
| dc.description.abstract | [EN] Background: K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results: As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion: K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies. | es_ES |
| dc.description.sponsorship | This work was supported by the University Polytechnic of Valencia, Grant Number 20180051 "Desarrollo de herramientas para la identificacion de genes y loci de interes en la mejora genetica del tomate y otras horticolas". | es_ES |
| dc.language | Inglés | es_ES |
| dc.publisher | Springer (Biomed Central Ltd.) | es_ES |
| dc.relation.ispartof | Plant Methods | es_ES |
| dc.rights | Reconocimiento (by) | es_ES |
| dc.subject | Klenow polymerase | es_ES |
| dc.subject | K-seq | es_ES |
| dc.subject | K-mer | es_ES |
| dc.subject | Low cost | es_ES |
| dc.subject | SNP | es_ES |
| dc.subject | Genotyping | es_ES |
| dc.subject | GRR | es_ES |
| dc.subject | NGS | es_ES |
| dc.subject.classification | GENETICA | es_ES |
| dc.title | K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology | es_ES |
| dc.type | Artículo | es_ES |
| dc.identifier.doi | 10.1186/s13007-021-00733-6 | es_ES |
| dc.relation.projectID | info:eu-repo/grantAgreement/UPV//20180051//Desarrollo de herramientas para la identificación de genes y loci de interés en la mejora genética del tomate y otras hortícolas/ | es_ES |
| dc.rights.accessRights | Abierto | es_ES |
| dc.contributor.affiliation | Universitat Politècnica de València. Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana - Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana | es_ES |
| dc.contributor.affiliation | Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia | es_ES |
| dc.contributor.affiliation | Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes | es_ES |
| dc.description.bibliographicCitation | Ziarsolo, P.; Hasing, T.; Hilario, R.; García-Carpintero, V.; Blanca Postigo, JM.; Bombarely, A.; Cañizares Sales, J. (2021). K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology. Plant Methods. 17(1):1-11. https://doi.org/10.1186/s13007-021-00733-6 | es_ES |
| dc.description.accrualMethod | S | es_ES |
| dc.relation.publisherversion | https://doi.org/10.1186/s13007-021-00733-6 | es_ES |
| dc.description.upvformatpinicio | 1 | es_ES |
| dc.description.upvformatpfin | 11 | es_ES |
| dc.type.version | info:eu-repo/semantics/publishedVersion | es_ES |
| dc.description.volume | 17 | es_ES |
| dc.description.issue | 1 | es_ES |
| dc.identifier.pmid | 33766048 | es_ES |
| dc.identifier.pmcid | PMC7993484 | es_ES |
| dc.relation.pasarela | S\432080 | es_ES |
| dc.contributor.funder | Universitat Politècnica de València | es_ES |
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