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

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.

Validação de marcadores moleculares associados à pungência em pimenta

“…Dentre as características de importância econômica, a pungência é o principal atrativo deste gênero, sendo conferida por substâncias alcalóides denominadas capsaicinóides. Esses alcalóides têm sido amplamente estudados (Henry & Emery, 1986;Caterina, 2000;Blum et al, 2002;Daood et al, 2002) sendo sintetizados no tecido da placenta e armazenados em células epidérmicas (Garcés-Claver et al, 2007;Stewart et al, 2007).…”

“…Nestes casos uma alternativa para avaliação da pungência é o uso de marcadores moleculares, onde a análise pode ser realizada em estágios iniciais de desenvolvimento da plântula, utilizando apenas folhas jovens e, com isso, reduzindo o tempo para verificação dos genótipos (Garcés-Claver et al, 2007). A determinação de pungência através de marcadores moleculares foi realizada a partir do loco Pun1 (Stellari et al, 2010;Wyatt et al, 2012), principal gene responsável pela biossíntese de capsaicinoides, sendo o único loco conhecido, até o momento, com efeito quantitativo sobre o acúmulo de pungência (Blum et al, 2003;Lang et al, 2006;Stellari et al, 2010).…”

Tetra Primer ARMS PCR Optimization to Detect Single Nucleotide Polymorphism of the KLF14 Gene

“…Garce's-Claver and collaborators [24] reported that the smaller fragment of the inner primers is disadvantaged by the formation of larger fragments, resulting in a weaker intensity of the band. In our case, with the same concentrations of inner primers, not only the intensities of the allelic bands were different (the A allele showed higher intensity respect to the G allele) but also the amplification of both alleles was observed in the homozygous G/G by ARMS modified PCR (data not shown).…”

Identification of 'Chunpoong' among Panax ginseng Cultivars Using Real Time PCR and SNP Marker

“…For the plant biotech industry, it represents a useful tool for the determination of copy numbers [13][14], transgenic plants [15], and single nucleotide polymorphisms (SNPs) [16,17]. SNPs are rare, single nucleotide substitutions, and small insertion/deletion (InDel) mutations have been widely used in a variety of research areas, such as molecular markers [18], biodiversity assessment [19], and high-density genome-wide scans [20]. As a powerful tool in plant breeding, the SNP analysis technique, which can analyze any change in nucleotide sequence, allows the identification of the genotype of each plant.…”