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

Authors: WILLMAN, MATTHEW - The Ohio State University; Bushakra, Jill; Bassil, Nahla; Finn, Chad; DOSSETT, MICHAEL - British Columbia Blueberry Council; FERNANDEZ, GINA - North Carolina State University; WEBER, COURTNEY - Cornell University; SCHEERENS, JOE - The Ohio State University; DUNLAP, LISA - The Ohio State University; FRESNEDO-RAMIREZ, JONATHAN - The Ohio State University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2020
Publication Date: 7/1/2020
Citation: Willman, M., Bushakra, J., Bassil, N.V., Finn, C.E., Dossett, M., Fernandez, G., Weber, C., Scheerens, J., Dunlap, L., Fresnedo-Ramirez, J. 2020. Genetic analysis of drupelet count in black raspberry (Rubus occidentalis). Acta Horticulturae. 1277:65-72. https://doi.org/10.17660/ActaHortic.2020.1277.9.
DOI: https://doi.org/10.17660/ActaHortic.2020.1277.9

Interpretive Summary: Black raspberry production is limited by narrow adaptation of current cultivars. In this paper we describe preliminary results of analyzing genotype by environment interaction of drupelet count in one mapping population 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. Genetic maps were reconstructed using single nucleotide polymorphism markers and the latest genome assembly for black raspberry. Pedigree verification led to construction of reliable genetic maps, and a region controlling drupelet count was identified on chromosome 1. This region has a stable influence over drupelet count over environments. These results and related findings are expected to guide further genetic characterization of black raspberry fruit quality, management of breeding germplasm, and development of improved cultivars for U.S. production.

Technical 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.