Anecdote of homozygosity in black raspberry (Rubus occidentalis)

K. Lust-Moore, G. Fernandez, M.R. Hysong, C. Oschenfeld, C. Britton, R. Rapp, M. Worthington, C. Weber, N. Bassil, J.M. Bushakra, M. Dossett, H. Ashrafi
Blackberries and red raspberries (Rubus spp.) have been successfully developed into commercially produced and commonly consumed small fruits. However, black raspberries (R. occidentalis) have been less successful due to challenges with generating variability for improvement. A single nucleotide polymorphism (SNP) validation study to correlate nucleotide identities with economically important traits uncovered a high level of homozygosity in the tested black raspberry cultivar, ‘Bristol’. Thirty-one public genotypes from five Rubus species were previously sequenced by Pairwise Plant Services Inc. aka. Pairwise. The sequences were mapped to a published black raspberry genome. More than 3.5 million SNPs were discovered using SAMTools and in-house Perl scripts. SNPs were selected from genic regions associated with traits of interest, and their flanking sequences were sent to AgBiotech Inc. (Monterey, CA) for primer design and KASP marker analysis. Traits of interest included primocane fruiting, prickle-free canes, and fruit quality characteristics. Tissues of the 31 genotypes were resampled along with an additional 14 genotypes representing 8 Rubus species. DNA was extracted to validate the congruity between the biological samples and bioinformatically identified SNPs. A total of 174 out of 192 (91%) SNP markers generated scorable data in the cultivar ‘Bristol’. and only 3 of those loci were found to be heterozygous. Compared to the homozygous (XX or YY) allele frequency of 98.3% in the black raspberry, the remainder of the population had an average XX or YY allele frequency of 83.4%. Although it was a single genotype, this extremely high level of homozygosity anecdotally supports the challenge of generating variability observed by Rubus breeders.
Lust-Moore, K., Fernandez, G., Hysong, M.R., Oschenfeld, C., Britton, C., Rapp, R., Worthington, M., Weber, C., Bassil, N., Bushakra, J.M., Dossett, M. and Ashrafi, H. (2024). Anecdote of homozygosity in black raspberry (Rubus occidentalis). Acta Hortic. 1388, 131-134
DOI: 10.17660/ActaHortic.2024.1388.19
breeding, single nucleotide polymorphism, genetic diversity, markers

Acta Horticulturae