Black Raspberry Genomic Resource Development

Since the early 1900s, the black raspberry (Rubus occidentalis L.) industry in the United States has steadily declined due to lack of adapted and disease resistant cultivars. Renewed interest in production and breeding new cultivars has been fueled by research into the use of black raspberry anthocyanin compounds as potential chemopreventative agents for certain cancers. The USDA-ARS NCGR manages and maintains a collection of over 175 black raspberry germplasm accessions, which includes newly collected wild accessions from 130 locations across 27 US states and two Canadian provinces. Evaluation of this wild germplasm led to the identification of four potential sources of aphid resistance, and potential new sources of resistance to the fungal pathogen Verticillium dahliae. We are building the genomic infrastructure for black raspberry by developing, and making available, genomic tools including molecular markers for construction of linkage and physical maps, and a draft genome assembly that will benefit both black and red raspberry breeding programs across the U.S. To date, we have developed over 200 SSR markers polymorphic in the parents of two crosses. Up to 704 Gbp of sequence was generated from six cDNA libraries of five tissues types of ‘Jewel’. A draft genome assembly of 300Mbp was generated from a highly homozygous accession. These genomic resources are essential for building the infrastructure needed for identification of candidate genes or closely linked markers for traits of interest during the development of improved black raspberry cultivars, and will inform decisions regarding germplasm value and usage, crossing, and selection through marker-assisted breeding.