RNA-Seq Analysis of Prickled and Prickle-Free Epidermis Provides Insight into the Genetics of Prickle Development in Red Raspberry (Rubus ideaus L.)

Red raspberry (Rubus idaeus L.) is a globally commercialized specialty crop with growing demand worldwide. The presence of prickles on the stems, petioles and undersides of the leaves complicates both the field management and harvesting of raspberries. An RNA sequencing analysis was used to identify differentially expressed genes in the epidermal tissue of prickled “Caroline” and prickle-free “Joan J.” and their segregating progeny. Expression patterns of differentially expressed genes (DEGs) in prickle-free plants revealed the downregulation of some vital development-related transcription factors (TFs), including a MIXTA-like R2R3-MYB family member; MADS-box; APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and NAM, ATAF1/2 and CUC2 (NAC) in prickle-free epidermis tissue. The downregulation of these TFs was confirmed by qRT-PCR analysis, indicating a key regulatory role in prickle development. This study adds to the understanding of prickle development mechanisms in red raspberries needed for utilizing genetic engineering strategies for developing prickle-free raspberry cultivars and, possibly, other Rubus species, such as blackberry (Rubus sp.) and black raspberry (R. occidentalis L.).