Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp.
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.
Garcés-Claver
Ana
A
Technology for Plant Production Department, Centro de Investigación y Tecnología Agroalimentaria (CITA), Apdo 727, 50080, Zaragoza, Spain.
Fellman
Shanna Moore
SM
Gil-Ortega
Ramiro
R
Jahn
Molly
M
Arnedo-Andrés
María S
MS
D054458:Amplified Fragment Length Polymorphism Analysis; D001483:Base Sequence; D002211:Capsaicin / Q000378:metabolism*; D002212:Capsicum / Q000235:genetics*; D005819:Genetic Markers; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
D005819:Genetic Markers; D002211:Capsaicin