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Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

TitoloSingle Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm
Tipo di pubblicazioneArticolo su Rivista peer-reviewed
Anno di Pubblicazione2019
AutoriBarchi, L., Acquadro A., Alonso D., Aprea Giuseppe, Bassolino L., Demurtas Olivia Costantina, Ferrante Paola, Gramazio P., Mini P., Portis E., Scaglione D., Toppino L., Vilanova S., Díez M.J., Rotino G.L., Lanteri S., Prohens J., and Giuliano Giovanni
RivistaFrontiers in Plant Science

Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks. © Copyright © 2019 Barchi, Acquadro, Alonso, Aprea, Bassolino, Demurtas, Ferrante, Gramazio, Mini, Portis, Scaglione, Toppino, Vilanova, Díez, Rotino, Lanteri, Prohens and Giuliano.


cited By 21

Citation KeyBarchi2019