Black Raspberry Genomic and Genetic Resource Development to Enable Cultivar Improvement

This project incorporates use of phenotypic, genotypic and genomic data to advance and streamline identification of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis L.). A lack of adapted, disease resistant cultivars has led to the steady decline of the black raspberry (BR) industry in the US. Interest in production and breeding new cultivars has been fueled by news regarding the potential health benefits of black raspberry bioactive compounds. To accomplish our goals, we are developing genomic tools including microsatellite and single nucleotide polymorphism (SNP) markers for construction of linkage and physical maps, and a draft genome assembly. Genotyping by sequencing (GBS) through a custom data pipeline identified over 35,000 SNP loci in population ORUS 4305 parents and 105 progeny. Up to 7,900 loci appear suitable for linkage mapping and have less than 10% missing data. The current genome assembly consists of 2,220 scaffolds. Two related full-sibling populations were replicated and planted at five production sites (OR, WA, OH, NC, and NY). We are taking detailed trait measurements including primocane vigor, flowering and fruiting, disease and aphid tolerance, and plant architecture to assess the influence of environment on genotype (GxE). Initial analysis of GxE on primocane vigor indicated that individual genotypes showed significant variation among sites. A densely populated genetic linkage map will be used to improve the draft genome assembly, for quantitative trait locus (QTL) mapping, and comparative genomic studies with other Rosaceae species.