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

Author:

Clare Shaun J.1ORCID,King Ryan M.1,Hardigan Michael2,Dossett Michael3,Montanari Sara4,Chagné David5,Ochsenfeld Cherie6,Britton Caitlin6,Rapp Ryan6,Bassil Nahla1

Affiliation:

1. National Clonal Germplasm Repository USDA‐ARS Corvallis Oregon USA

2. Horticultural Crops Production and Genetic Improvement Research Unit USDA‐ARS Corvallis Oregon USA

3. BC Berry Cultivar Development Inc Abbotsford British Columbia Canada

4. New Zealand Institute for Plant and Food Research Ltd Plant & Food Research Motueka New Zealand

5. Food Innovation Science Centre Plant & Food Research Palmerston North New Zealand

6. Pairwise Durham North Carolina USA

Abstract

AbstractRed raspberry is an economically important horticultural crop that is known for its fruit's sweet flavour 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.

Publisher

Wiley

Subject

Plant Science,Genetics,Agronomy and Crop Science

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