Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

Viruel Juan, Haguenauer Anne, Juin Marianick, Mirleau Fatma, Bouteiller Delphine, Boudagher-Kharrat Magda, Ouahmane Lahcen, La Malfa Stefano, Médail Frédéric, Sanguin Hervé, Feliner Gonzalo Nieto, Baumel Alex. 2018. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). Applications in Plant Sciences, 6 (12):e1201, 10 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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Quartile : Q3, Sujet : PLANT SCIENCES

Abstract : Premise of the Study: Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. Methods: In this study, we implemented a next‐generation sequencing–based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. Results: The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single‐nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. Discussion: Next‐generation sequencing allows the detection and scoring of SSRs, single‐nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.

Mots-clés libres : Carob tree, Microsatellite, Genotyping by sequencing

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Viruel Juan, Royal Botanic Garden (GBR) - auteur correspondant
  • Haguenauer Anne, IMBE (FRA)
  • Juin Marianick, IMBE (FRA)
  • Mirleau Fatma, IMBE (FRA)
  • Bouteiller Delphine, Hôpital Pitié Salpêtrière (FRA)
  • Boudagher-Kharrat Magda, Université Saint-Joseph (LBN)
  • Ouahmane Lahcen, CIRAD-BIOS-UMR LSTM (FRA)
  • La Malfa Stefano, University of Catania (ITA)
  • Médail Frédéric, IMBE (FRA)
  • Sanguin Hervé, CIRAD-BIOS-UMR LSTM (FRA)
  • Feliner Gonzalo Nieto, Real Jardin Botanico (ESP)
  • Baumel Alex, IMBE (FRA)

Source : Cirad-Agritrop (

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