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Euphytica

, 213:264 | Cite as

Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

  • Pietro Gramazio
  • Jaime Prohens
  • Dionís Borràs
  • Mariola Plazas
  • Francisco Javier Herraiz
  • Santiago Vilanova
Article

Abstract

Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers are amongst the most common markers of choice for studies of diversity and relationships in horticultural species. We have used 11 SSR and 35 SNP markers derived from transcriptome sequencing projects to fingerprint 48 accessions of a collection of brinjal (Solanum melongena), gboma (S. macrocarpon) and scarlet (S. aethiopicum) eggplant complexes, which also include their respective wild relatives S. incanum, S. dasyphyllum and S. anguivi. All SSR and SNP markers were polymorphic and 34 and 36 different genetic fingerprints were obtained with SSRs and SNPs, respectively. When combining both markers all accessions but two had different genetic profiles. Although on average SSRs were more informative than SNPs, with a higher number of alleles, genotypes and polymorphic information content (PIC), and expected heterozygosity (H e ) values, SNPs have proved highly informative in our materials. Low observed heterozygosity (H o ) and high fixation index (f) values confirm the high degree of homozygosity of eggplants. Genetic identities within groups of each complex were higher than with groups of other complexes, although differences in the ranks of genetic identity values among groups were observed between SSR and SNP markers. For low and intermediate values of pair-wise SNP genetic distances, a moderate correlation between SSR and SNP genetic distances was observed (r2 = 0.592), but for high SNP genetic distances the correlation was low (r2 = 0.080). The differences among markers resulted in different phenogram topologies, with a different eggplant complex being basal (gboma eggplant for SSRs and brinjal eggplant for SNPs) to the two others. Overall the results reveal that both types of markers are complementary for eggplant fingerprinting and that interpretation of relationships among groups may be greatly affected by the type of marker used.

Keywords

Eggplants Simple sequence repeats Single nucleotide polymorphisms Fingerprinting Genetic diversity Cluster analysis 

Notes

Acknowledgements

This work has been funded by European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economía y Competitividad and Fondo Europeo de Desarrollo Regional (Grant AGL2015-64755-R from MINECO/FEDER). Pietro Gramazio is grateful to Universitat Politècnica de València for a pre-doctoral contract (Programa FPI de la UPV-Subprograma 1/2013 call). Mariola Plazas is grateful to Spanish Ministerio de Economía, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva-Formación programme (FJCI-2015-24835).

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Authors and Affiliations

  1. 1.Instituto de Conservación y Mejora de la Agrodiversidad ValencianaUniversitat Politècnica de ValènciaValenciaSpain
  2. 2.Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de ValènciaValenciaSpain

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