Carotenoids are vital pigments responsible for yellow, orange and red color in plants. In Capsicum, capsanthin-capsorubin synthase (CCS), phytoene synthase (PSY), β-Carotene hydroxylase (CRTZ-2) and lycopene β-cyclase (LCYB) were identified to be involved in the carotenoids synthesis pathway. Previously molecular markers based on the CCS and PSY genes have been developed to distinguish fruit colors in pepper. However these markers can distinguish fruit colors of limited pepper genotypes. Therefore, there is need of developing additional markers for accurate prediction of fruit colors using molecular markers. In this study carotenoids contents of 16 pepper accessions were analyzed and the CCS, PSY, CRTZ-2, LCYB genes were sequenced to identify the genes affecting the fruit color. Among all the analyzed carotenoids, capsanthin was accumulated in much higher amount in red and orange fruits (1100-2500 mAU·min and 30-500 mAU·min respectively) while violaxanthin (20-1200 mAU·min) was accumulated more in yellow fruits. Sequence analysis revealed that deletions and two frame shift mutations in CCS gene for yellow accessions. Frame shift mutations of the PSY gene were detected in two orange accessions. These results show that mutations in CCS and PSY genes affect the fruit colors of pepper, and markers can be developed using mutations of these genes.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, 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 capsinoids 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 high capsinoids contents, 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 parent’s 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 ‘Shinghong’ 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.

Phytophthora capsici an Oomycete pathogen is a major challenge to the pepper (Capsicum spp.) production around the world. Control measures are proved ineffective, so breeding resistant cultivars are the most promising strategy against the pathogen. Resistance against P. capsici is governed by quantitative trait loci (QTL). According to previous studies on QTL detection, the QTL on pepper chromosome 5 is a major contributor to resistance. In this study, to exploit the involvement of this QTL and identify its contributing genes, the F2 population derived from a cross between ECW30R and CM334 was inoculated with a medium virulence P. capsici strain JHAI1-7 zoospores at the 6-8 leaf stage. Composite interval mapping revealed two major QTLs; QTL5-1 from 7 days post inoculation (dpi) and QTL5-2 from 16 dpi on chromosome 5. To characterize and detect interactions of the two QTLs, near isogenic lines (NIL) were constructed by crossing Tean and recombinant inbred line (RIL) derived from a cross between YCM334 and Tean. RILs were screened with P. capsici strain MY-1 and resistant lines were selected. Among the resistance RILs most closely related to Tean were selected using AFLP and SSR genotyping data. These RILs were named as YT39-2 and YT143-2. To develop more advanced NILs, two rounds of marker-assisted backcrossing were done using a high-throughput SNP genotyping system (EPI Fluidigm, USA). Among the NILs derived from YT39-2, YT39-2-64 contains only QTL5-1 whereas YT39-2-61 and YT39-2-69 were identified to have both QTLs. On the other hand, YT143-2-55-7 with the highest Tean genetic background contains QTL5-1 only. In the next step, the 3 different NILs having QTL5-1, QTL5-2 individually and both QTLs will be identified. Furthermore, phenotyping and fine mapping will be done for the analysis of individual and interaction effects of QTLs.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, vanillyl alcohol, is known to be produced by mutations in the p-aminotransferase (p-AMT) gene. In the previous study, SNU11-001 (C. chinense) containing high levels of capsinoids was found in germplasm collections of Seoul National University. We found that this collection has a unique mutation in the p-AMT gene. In order to develop a cultivar containing high capsinoids contents, marker-assisted foreground and background selection were performed in this study. Backcrossing is an effective breeding method for introducing useful traits to an elite cultivar. Compared to conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened to obtain polymorphic SNP markers between ‘Takanotsume (C. annuum)’ and ‘SNU11-001’. Of the 412 SNP markers, 96 polymorphic SNP markers evenly distributed in pepper genome were finally selected. Plants carrying the pAmt/pamt genotype were selected from a BC1F1 population using SCAR markers derived from the unique p-AMT mutation of SNU11-001. BC1F1 plants carrying the pAmt/pamt genotype were subjected to background selection. Multiple genotype analysis was done using Fluidigm platform (BioMark). Once we obtain plants carrying most similar genetic background to recurrent parent, capsinoids contents will be measured and another round of MABC be done to obtain plants containing high levels of capsinoids.

Capsinoids, low-pungent compounds, have the same biological effects as capsaicinoids such as anticancer and anti-obesity. A precursor of capsinoids, vanillyl alcohol, is known to be produced by mutations in the p-aminotransferase (p-AMT) gene. In the previous study, SNU11-001 (C. chinense) containing high levels of capsinoids was found in germplasm collections of Seoul National University. We found that this collection has a unique mutation in the p-AMT gene. In order to develop a cultivar containing high capsinoids contents, marker-assisted foreground and background selection were performed in this study. Backcrossing is an effective breeding method for introducing useful traits to an elite cultivar. Compared to conventional backcrossing, marker-assisted backcrossing (MABC) is extremely useful for recovery of a recurrent parent’s genetic background. To obtain background selection markers, a total of 412 single nucleotide polymorphism (SNP) markers was screened to obtain polymorphic SNP markers between ‘Takanotsume (C. annuum)’ and ‘SNU11-001’. Of the 412 SNP markers, 96 polymorphic SNP markers evenly distributed in pepper genome were finally selected. Plants carrying the pAmt/pamt genotype were selected from a BC1F1 population using SCAR markers derived from the unique p-AMT mutation of SNU11-001. BC1F1 plants carrying the pAmt/pamt genotype were subjected to background selection. Multiple genotype analysis was done using Fluidigm platform (BioMark). Once we obtain plants carrying most similar genetic background to recurrent parent, capsinoids contents will be measured and another round of MABC be done to obtain plants containing high levels of capsinoids