Theoretical and Applied Genetics

, Volume 115, Issue 7, pp 907–916

Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp.

  • Ana Garcés-Claver
  • Shanna Moore Fellman
  • Ramiro Gil-Ortega
  • Molly Jahn
  • María S. Arnedo-Andrés
Original Paper

DOI: 10.1007/s00122-007-0617-y

Cite this article as:
Garcés-Claver, A., Fellman, S.M., Gil-Ortega, R. et al. Theor Appl Genet (2007) 115: 907. doi:10.1007/s00122-007-0617-y

Abstract

A single nucleotide polymorphism (SNP) associated with pungency was detected within an expressed sequence tag (EST) of 307 bp. This fragment was identified after expression analysis of the EST clone SB2-66 in placenta tissue of Capsicum fruits. Sequence alignments corresponding to this new fragment allowed us to identify an SNP between pungent and non-pungent accessions. Two methods were chosen for the development of the SNP marker linked to pungency: tetra-primer amplification refractory mutation system-PCR (tetra-primer ARMS-PCR) and cleaved amplified polymorphic sequence. Results showed that both methods were successful in distinguishing genotypes. Nevertheless, tetra-primer ARMS-PCR was chosen for SNP genotyping because it was more rapid, reliable and less cost-effective. The utility of this SNP marker for pungency was demonstrated by the ability to distinguish between 29 pungent and non-pungent cultivars of Capsicum annuum. In addition, the SNP was also associated with phenotypic pungent character in the tested genotypes of C. chinense, C. baccatum, C. frutescens, C. galapagoense, C. eximium, C. tovarii and C. cardenasi. This SNP marker is a faster, cheaper and more reproducible method for identifying pungent peppers than other techniques such as panel tasting, and allows rapid screening of the trait in early growth stages.

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Ana Garcés-Claver
    • 1
  • Shanna Moore Fellman
    • 2
  • Ramiro Gil-Ortega
    • 1
  • Molly Jahn
    • 3
  • María S. Arnedo-Andrés
    • 1
  1. 1.Technology for Plant Production DepartmentCentro de Investigación y Tecnología Agroalimentaria (CITA)ZaragozaSpain
  2. 2.Department of Plant Breeding and GeneticsCornell UniversityIthacaUSA
  3. 3.College of Agricultural and Life SciencesUniversity of WisconsinMadisonUSA