Single Primer Enrichment Genotyping Highlights the Worldwide Population Structure of Tomato and Eggplant Germplasm. - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Conference Papers Year : 2019

Single Primer Enrichment Genotyping Highlights the Worldwide Population Structure of Tomato and Eggplant Germplasm.

Lorenzo Barchi
  • Function : Author
Alberto Acquadro
  • Function : Author
Ezio Portis
  • Function : Author
Sergio Lanteri
David Alonso
  • Function : Author
Pietro Gramazio
  • Function : Author
Santiago Vilanova
  • Function : Author
Maria Josè Díez
  • Function : Author
Jaime Prohens
Gancho Pasev
Stanislava Grozeva
  • Function : Author
Hatice Filiz Boyaci
  • Function : Author
Abdullah Unlu
  • Function : Author
Laura Toppino
  • Function : Author
Laura Bassolino
  • Function : Author
Giuseppe Leonardo Rotino
  • Function : Author
Andreas Boerner
  • Function : Author
Ronny Brandt
  • Function : Author
Nils Stein
Richard Finkers
Arnaud G Bovy
  • Function : Author
Roland Schafleitner
  • Function : Author
Davide Scaglione
  • Function : Author
Eleonora Di Centa
  • Function : Author
Sara Pinosio
  • Function : Author
Giuseppe Aprea
  • Function : Author
Paola Ferrante
  • Function : Author
Giovanni Giuliano

Abstract

G2P-SOL (http://www.g2p-sol.eu) is an EU-funded project, bringing together the main European and international genebanks hosting germplasm of the four major Solanaceous crops: potato, tomato, pepper and eggplant. 23,900 tomato and 5,900 eggplant accessions, including wild relatives of both crops, have been inventoried within the project. To gain information about population structure of the collections, the novel Single Primer Enrichment Technology (SPET, US Patent 9,650,628) developed by NuGEN was used for genotyping. An SNP/indel panel was developed by assaying 14k probes for tomato and 11k for eggplant, evenly distributed in the gene-rich regions, and selecting the 5k best performing probes for each species. DNA samples were prepared by the genebanks using pre-tested protocols, and genotyping partners (ENEA for tomato and University of Torino for eggplant) performed QC and sample normalization. Genotyping and sequencing was performed by IGA Technology Services. Reads were aligned to the eggplant and tomato reference genomes using BWA-MEM and SNP calling was performed using GATK-4.0. We report on the assessment of the genetic relationships in a wide set of tomato and eggplant accessions maintained in genebanks as well as the extent of duplications and possible mis-classifications. The results suggest that SPET genotyping is a reliable, high-throughput, low cost technology for genetic fingerprinting of crops, with a high degree of cross-transferability to their wild relatives. SPET-based higher density genotyping is being developed to characterize the core collections developed in G2P-SOL for GWAS analyses.

Domains

Genetics
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Dates and versions

hal-03551688 , version 1 (01-02-2022)

Identifiers

  • HAL Id : hal-03551688 , version 1

Cite

Lorenzo Barchi, Alberto Acquadro, Ezio Portis, Sergio Lanteri, David Alonso, et al.. Single Primer Enrichment Genotyping Highlights the Worldwide Population Structure of Tomato and Eggplant Germplasm.. XXVII Plant and Animal Genome Conference, Jan 2019, San Diego (CA), United States. ⟨hal-03551688⟩
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