Modern tools for unveiling the genetic basis of prickliness in plants and their applications in plant breeding

Prickles, sharp projections of plant epidermis, serve as a defense mechanism against herbivory but present significant challenges in agricultural contexts, complicating cultivation, harvesting, and postharvest processes. We used advanced tools to uncover the genetic basis of prickle formation and its convergent loss across highly divergent plant lineages. Using interspecific mapping populations of eggplant (Solanum melongena) with introgressions of prickly wild relatives, we fine-mapped the locus designated prickleless (pl) and identified a LONELY GUY (LOG) gene, which regulates cytokinin biosynthesis, as a critical factor in prickle development. High-quality genome assemblies and sequencing of diverse Solanum accessions revealed 16 independent LOG mutations associated with prickle loss in cultivated and wild species, highlighting recurrent co-option of LOG paralogs during evolution. Beyond Solanum, mutations in LOG genes were identified in distant prickly taxa, such as roses (Rosa sp.), jujube (Ziziphus jujuba), and the giant spider-flower (Tarenaya hassleriana). LOG family genes are also involved in the prickly barbs of the awns of rice (Oryza sativa) and barley (Hordeum vulgare), underscoring a conserved genetic mechanism underlying this trait. Genome editing with CRISPR-Cas9 was utilized to knock-out the LOG gene to eliminate prickles in the scarlet eggplant (S. aethiopicum), in the foraged Australian desert raisin (S. cleistogamum), and in the forest nightshade (S. prinophyllum) without pleiotropic effects, demonstrating the practical application of our findings in crop improvement. These insights pave the way for breeding prickleless varieties in economically significant plants, improving safety and efficiency in cultivation and harvesting, as well as for domesticating wild prickly foraged plants. Our work also deepens the understanding of the convergent evolution of plant innovations, such as the development of prickles.