Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

Authors: Clare, Shaun; King, Ryan; Hardigan, Michael; DOSSETT, MICHAEL - British Columbia Blueberry Council; MONTANARI, SARA - New Zealand Institute Of Plant & Food Research; CHAGNE, DAVID - New Zealand Institute Of Plant & Food Research; OCHSENFELD, CHERIE - Pairwise; BRITTON, CAITLIN - Pairwise; RAPP, RYAN - Pairwise; Bassil, Nahla

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2023
Publication Date: 9/7/2023
Citation: Clare, S.J., King, R., Hardigan, M.A., Dossett, M., Montanari, S., Chagne, D., Ochsenfeld, C., Britton, C., Rapp, R., Bassil, N.V. 2023. Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.). Plant Breeding. 142(6):798-808. https://doi.org/10.1111/pbr.13141.
DOI: https://doi.org/10.1111/pbr.13141

Interpretive Summary: A reliable and economic genotyping platform is needed to facilitate clonal/variety identification in red raspberry. DNA markers based on single nucleotide polymorphisms (SNPs), despite having lower diversity, are numerous across the genome and more easily converted to high-throughput assays restoring differential power. In this study we use the kompetitive allele-specific PCR (KASP™) chemistry, an affordable and high-throughput platform, to develop a panel of these DNA markers to distinguish a diverse collection of red raspberry accessions for clonal identification. The panel consists of 48 markers that show high concordance with whole genome sequencing and recovery rate, as well as a minimal set of 24 markers that distinguished the same accessions differentiated by the larger panel.

Technical Abstract: Red raspberry is an economically important horticultural crop that is known for its fruit’s sweet flavor and nutritional value. A reliable and economic genotyping platform is needed to facilitate clonal/variety identification. Previous attempts for clonal identification utilized morphological traits or low-throughput, difficult to score dinucleotide-containing simple sequence repeat molecular markers. Single nucleotide polymorphisms (SNPs), despite having lower allelic diversity, are numerous across the genome and more easily converted to high-throughput assays restoring differential power. In this study we use the kompetitive allele-specific PCR (KASP™) chemistry, an affordable and high-throughput platform, to develop a panel of SNPs to distinguish a diverse collection of red raspberry accessions for clonal identification. The panel consists of 48 KASP assays that show high concordance with whole genome sequencing, allelic balance, and recovery rate, and a minimal set of 24 assays that distinguished the same accessions differentiated by the larger panel.