Layer-specific genetic variation unlocks secondary metabolite diversity in long-lived clonal peppermint
Somatic mutations can generate novel clonal variants with commercially valuable traits. Periclinal chimeras, which carry genetically-differentiated meristematic layers, are common in clonally-propagated crops and can be highly stable. Given their economic and evolutionary impact, it is critical to understand the potential of layer-specific breeding in long-lived vegetatively-propagated crops. Peppermint clones are polyploid hybrids, sterile, and a source of essential oils. Using ionizing radiation, we induced large indels in an elite peppermint cultivar. We produced a haplotype-aware, high continuity assembly of this clone and used it to characterize the induced genetic variation in this mutant population. We detected, on average, 6 large indels per individual. The vast majority of these mutants are genetic chimeras in which the indels are confined to either the outer, L1-derived layer, responsible for mint oil production and accumulation, or derived from the inner L2/3 layers. These results highlight new opportunities for mint oil improvement and demonstrate the potential of layer-specific variation for breeding of clonally propagated crops that suffer from genetic diversity bottlenecks.The development and characterization of the gamma mutant population was supported by Mars Wrigley. The development of the genome assembly for Black Mitcham was supported by the National Science Foundation - Division of Integrative Organismal Systems grant 1956429 RESEARCH-PGR: Variants and Recombinants without Meiosis. The sequencing was carried out by the DNA Technologies and Expression Analysis Core at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01.