Molecular Breeding of Pepper Varieties (Capsicum annuum) Containing High Levels of Capsinoid

Abstract

Capsinoid, low-pungent compounds, have the same biological effects as capsaicinoid such as anticancer and anti-obesity. A precursor of capsinoid, vanillyl alcohol, is known to be produced by mutations in the putative-aminotransferase (pAMT) gene. In the previous study, SNU11-001 (Capsicum chinense) containing high levels of capsinoid was identified in germplasm collections of Capsicum. This collection has a unique mutation in the pAMT gene that can cause dysfunction of this gene. In order to develop pepper varieties containing a high capsinoid content, marker-assisted foreground and background selections were performed during backcross breeding. Compared to the conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parents genetic background. For foreground selection, plants carrying the pAMT/pamt genotype were selected from a BC1F1 and BC2F1 populations using SCAR markers derived from the unique pAMT mutation of SNU11-001. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened on Shinhong parental lines and SNU11-001 to obtain polymorphic SNP markers. Of the 412 SNP markers, 144 and 204 polymorphic SNP markers evenly distributed in pepper genome were finally selected. BC1F1 and BC2F1 plants carrying the pAMT/pamt genotype were subjected to background selection using the selected marker sets. Multiple genotype analysis was done using a high-throughput genotyping system (EP1TM, Fluidigm®, USA). As a result, one BC1F1 plant 84% similar to the recurrent parent and several BC2F1 plants more than 96% recovery rate of the recurrent parent were selected. Genetic backgrounds of the selected BC2F1 plants were evaluated by the genotype-by-sequencing (GBS) method in order to confirm the background selection results using the SNP marker set. GBS results showed that recovery rate and positions of introgressed segments were well matched between two methods demonstrating MABC can be successfully done with a couple hundred SNP markers.