The control of prickle formation in Rubus

Abstract Prickles on blackberry and raspberry canes make pruning, harvesting, and handling more difficult and can increase labor costs for growers. The trait has been challenging to improve in these clonal crops because it is recessive and linked to undesirable agronomic traits. In blackberry and red raspberry, breeding programs have used recessive mutants at the S locus to generate prickleless cultivars for the last century. In this study, we identified independent loss-of-function mutations in a WUSCHEL-LIKE HOMEOBOX transcription factor, WOX1, as the genetic basis of the prickleless S locus in both blackberry and red raspberry. We mapped the S locus using integrated genome-wide association, bulked segregant analysis, and identity-by-descent analyses informed by breeding pedigrees. Additionally, we generated a genome sequence from Luther Burbank’s prickleless blackberry variety Burbank Thornless that contained an additional allele of WOX1. To verify the gene’s role, we used gene editing to knock out WOX1 in an elite prickled commercial blackberry line. All edited plants were prickleless and lacked glandular trichomes, confirming that WOX1 controls a joint developmental pathway. Other plant traits were unchanged, indicating WOX1 is a specific and safe target for improvement. Gene editing can enable breeders to remove prickles directly from elite varieties, reducing the need for extensive breeding cycles and delivering safer, easier-to-harvest cultivars to growers. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵* Joint first authors bstaubin{at}pairwise.com tpoorten{at}pairwise.com afister{at}pairwise.com cochsenfeld{at}pairwise.com jreiner{at}pairwise.com acastillo{at}pairwise.com reseearyal{at}gmail.com olga.dudchenko{at}utmb.edu sargentdj{at}gmail.com d.g.r.mead{at}gmail.com matteo.buti{at}unifi.it easilva{at}uark.edu melanie_pham{at}ymail.com David.Weisz{at}bcm.edu nahla.bassil{at}usda.gov hamidashrafi{at}ncsu.edu erez{at}erez.com ngraham{at}pairwise.com dchauhan{at}pairwise.com edean{at}pairwise.com wlowry{at}pairwise.com lredpath{at}pairwise.com pmarri{at}pairwise.com Author list and affiliations updated, Bibliography style changed