Genetic analysis of drupelet count in black raspberry (Rubus occidentalis)

Abstract

U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. Improved understanding of genetic control and genotype-by-environment interactions (GEI) of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, analysis of a multi-environment trial of two BR mapping populations derived from crosses of commercial cultivars with wild accessions is providing insights into genetic variation, quantitative trait loci (QTL), and GEI related to traits of horticultural value. Twenty-six horticultural and fruit quality traits were evaluated in two mapping populations over three years at four distinct locations representative of current U.S. BR production. One fruit quality trait, drupelet count, has been analyzed, and nine additional fruit quality traits are being analyzed. Random factor analysis of genetic effect was used to account for missing data. GEI analysis was performed using a Bayesian approach to Finlay-Wilkinson regression and genotyping-by-sequencing (GBS)-derived genomic relationship matrices, with the purpose of verifying relatedness and identifying genotypes with stable performance over environments. Genetic maps were reconstructed using GBS-derived markers and the latest genome assembly for BR. Among relevant results, pedigree verification led to construction of reliable linkage maps, and a QTL spanning a one to five megabase region containing several hundred genes was identified on chromosome 1. This region has a stable influence over drupelet count over environments (location by year). These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production.