Pepper (Capsicum spp.) is an important vegetable crop worldwide. Molecular markers for major traits are an essential tool to expedite the development of new varieties in pepper. Genome sequence assemblies for three Capsicum species have been developed by the short-read sequencing and are available for genetic study and molecular breeding. Our group has developed molecular markers linked to major genes including disease resistance using the genome information. Some of the genes have cloned (or are being) by the genomics-assisted method.

Molecular breeding assisted by genomics tools enabled the efficient selection of target traits and reduced costs of cultivar development. However, current pepper genome sequences need to be improved because they are composed of a large number of small scaffolds with N50. Long-read sequencing can improve genome assemblies for large and complex plant genomes by increasing sequence reads up to 1 Mb. Here, we report a high-quality genome assembly of the sweet pepper C. annuum cultivar ‘Dempsey’ at the chromosomal scale, constructed by integrating single-molecule real-time sequencing, optical mapping, high-throughput chromosome conformation capture technologies, and high-density genetic maps. The new Dempsey genome assembly is more contiguous and complete and features better statistics, such as N50 values, than previous short read-based Capsicum assemblies.

Using the Dempsey genome, we were able to identify genes responsible for various traits. We further demonstrated the utility of the Dempsey genome by performing quantitative trait locus (QTL) and genome-wide association study (GWAS) analyses for the multiple quantitative traits. The high-quality and chromosome-scale Dempsey genome will provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.

Professor Byoung-Cheorl Kang Professor, Dept of Plant Science, College of Agriculture and Life Science, Seoul National University, South Korea

Kang Byoung-Cheorl is a professor at Department of Plant Science, College of Agriculture and Life Science, in Seoul National University, Korea. After completing his PhD in Plant Molecular Genetics from Seoul National University, he conducted his post-doctoral research at Cornell University, Ithaca, New York. Following that, he started his professorship under Seoul National University. Dr. Kang has held several important roles over the years which include being on the technical advisory board of Ministry for Food, Agriculture, Forestry and Fisheries for Korea government and was also previously the director for Plant Genomics and Breeding Institute in SNU. As of now, Dr. Kang is the Director for Vegetable Breeding Research Center and the Associate Dean of Research Affairs in SNU.