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.

• Koeun Han(Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center,College of Agriculture and Life Sciences, Seoul National University)
• Joung-Ho Lee(Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center,College of Agriculture and Life Sciences, Seoul National University)
• Byoung-Cheorl Kang(Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center,College of Agriculture and Life Sciences, Seoul National University) Corresponding Author