Plant breeding requires genetic diversity of useful traits for crop improvement. EMS-induced mutation is practiced to generate mutations at loci regulating economically important traits and/or to knock out the genes to elucidate their functions. The present study was aimed to induce mutations in a Korean local land race Capsicum annuum ‘Yuwol-cho’. This accession is pungent and also has advantage to mature early. A total of about 1,500 M2 families were screened and three non-pungent mutants were identified and crossed with wild type ‘Yuwol-cho’. After phenotyping of F2 population for pungency, MutMap approach will be used to identify the genes controlling the pungency in mutants. In addition to this, another C. annuum accession “Micro-Pep” was used to develop a mutant population. Micro-Pep is a small, pungent pepper generally used as ornamental purpose. Having compact growth habit, and small size, it has advantage to handle and utilize easily in mutation study and molecular research. On the basis of preliminary experiment 1.3% of mutagen was used for treatment of pepper seeds and 30% less germination percentage was observed in EMS treated seeds in comparison to control seeds. A total of 4,674 M1 plants are grown under greenhouse condition and M2 population will be studied for characterization of phenotypic variation including fruit color and pungency. Newly constructed mutant populations will be valuable assets for identification of functional genes and molecular breeding of pepper.

Pepper (Capsicum spp.) germplasm shows diverse phenotypic variations including fruit size, color, pungency, and many other horticultural traits. Traditional markers including SSR, AFLP, and RFLP have been used to construct genetic maps using biparental populations. However to assess the genetic diversity of large number of germplasm, a robust and rapid marker development and genotyping approach is needed. We used six pepper accessions including C. annuum, C. chinense, C. baccatum and C. frutescens and performed genotyping-by-sequencing (GBS). To select the most appropriate condition, eight different 2 bp selective nucleotides were used to make GBS libraries. Selective nucleotide ‘OO’ showed the largest number of reads in all samples, and 11,026 to 47,957 high-quality SNPs were called in six accessions. When C. annuum ‘CM334’ genome sequence was used as a reference, C. annuum showed the smallest number of SNPs, while C. baccatum which was known to be a different Capsicum clade showed the largest number of SNPs. Pepper core collection chosen to represent the genetic diversity of whole germplasm will be genotyped by high-density SNPs developed from GBS. We will perform genome-wide association study (GWAS) using genetic and phenotypic variation to identify the functional genetic loci controlling horticultural traits.

Genotyping-by-sequencing (GBS) is a robust and rapid tool to develop SNP markers. Reduced sequencing complexity and multiplex sequencing of GBS has reduced genotyping cost for complex genome. However multiplex sequencing brings low sequencing depth which can lead to reduced number of markers. Therefore to find the appropriate condition for GBS is needed. In this research we demonstrated the use of ApeKI and selective primers for GBS of pepper (Capsicum spp.). Selective primers which amplify the GBS library with one or two flanking sequences to ApeKI site were used to increase sequencing depth. By in silico digestion, we developed six different selective primers amplify 4,000-400,000 regions. We made the GBS library with eight pepper accessions in four species using six selective primers and sequenced. Proper selective primers and pooling rate for each species will be determined. This approach will be useful for genotyping Capsicum breeding lines or populations by developing high quality SNP markers.

Tomato yellow leaf curl disease is a devastating disease of tomato (Solanum lycopersicum), which is caused by begomoviruses generally referred to as tomato yellow leaf curl virus (TYLCV). The breeding for TYLCV resistance has been based on the introgression of the Ty-3 resistance locus. Knowledge about the exact location of the Ty-3 on tomato chromosome 6 is needed to understand the genomic organization of the Ty-3 locus. In this study, we conducted a genetic analysis using a segregating population derived from a cross between resistant accession S. lycopersicum “A45” and susceptible accession S. lycopersicum “A39”. The F1 plants showed resistance to TYLCV and F1 was self-pollinated to produce F2 progeny. To screen the TYLCV resistance in 145 F2 plants, a leaf agroinfiltration method was used. F2 plants showed a classical Mendelian seregation (106 resistance : 39 susceptibility) for resistance to TYLCV respectively. SCAR and CAPS markers linked to the Ty-3 were tested for genotyping F2 plants and .genotyping and agroinfiltration results were cosegregated in the newly developed F2 population.

Capsinoids which were found recently in non-pungent pepper show the same biological effects as capsaicinoid including anticancer and anti-obesity. A precursor of capsaicinoids, vanillyl alcohol, is known to be produced by mutations in the p-aminotransferase (pAMT) gene. In the previous study, we showed that capsinoid production is also controlled by the capsaicin synthase (CS) gene. However correlation between the CS gene expression and capsinoids contents has not been fully understood. This study was conducted to elucidate correlation between the expression level of CS gene and capsinoids contents. Through germplasm screening, we identified one C. chinese pepper cultivar, SNU11-001, which contained capsinoids as much as C. annuum ‘CH-19 Sweet’. SNU11-001 was crossed with five Capsicum cultivars (ECW, Takanotsume, Yuwolcho, Habanero and Jolokia) containing different levels of capsaicin, ‘ECW’ is non-pungent pepper line, and ‘Takanotsume’ and ‘Yuwolcho’ have mild pungency, and ‘Habanero’ and ‘Jolokia’ is known to be included in the most pungent pepper lines. When we analyzed the expression of CS and pAMT genes using the six Capsicum cultivars, the expression levels of CS were higher in pungent Capsicum cultivars. To test whether the expression levels of CS also control capsinoids contents, we will analyze several F2 populations derived from crosses between SNU11-001 and Capsicum cultivars containing different levels of capsaicin.

The Korean people consume a lot of hot peppers. Despite its popularity and importance, genetic mechanism determining the content of capsaicinoid has not been understood yet. Since the inheritance of capsaicinoid content is thought to be controlled by quantitative trait loci (QTLs), a well-constructed genetic population and well-organized approach method to study genetic inheritance are required. Here we show the scheme to find the QTLs controlling capsaicinoid content using a recombinant inbred lines (RILs) obtained from a cross between C. annuum, Perennial and C. annuum, Dempsey. We measured capsaicinoid contents of each line for QTL analysis. In addition, total 24 qualitative and quantitative traits of RILs were phenotyped. Phenotyping data can be used to construct another QTL map controlling agricultural trait. An ultra high density linkage map constructed by sequencing RILs will used for QTL nalaysis. We are expecting that this study will be useful to breed high-quality and pungent pepper cultivars by molecular breeding method.