Dwarfism in Pinus taeda originates from independent somatic mutations co-localized in a shared genomic region

Somatic mutations in long-lived conifers are rarely characterized yet offer a unique window into the spontaneous genetic forces that shape variation in plants. In Pinus taeda, dwarf phenotypes originate from abnormal branches, colloquially known as "witches' brooms", where progeny derived from the affected branch segregate for dwarfism in an apparent Mendelian 1:1 ratio. In this study, we genotyped six unrelated wind-pollinated families segregating for dwarfism using single-nucleotide polymorphism markers that had been previously positioned on a linkage map. Trait-loci association analyses identified a genomic region on linkage group eight (spanning 98-155 cM) that was strongly associated with dwarfism across unrelated families. This finding suggests that independent, de novo somatic mutations within a common genomic region are the basis for stable dwarf phenotypes in P. taeda. The implicated region is quite large and it remains to be determined if the same growth regulation gene or genes are responsible, but the shared region is evidence for disruption of a common pathway. To more formally describe the witches' broom phenomenon and distinguish mutants from pathogen-induced brooms, we propose the Latin name Ramus nanus mutatus. We discuss the contribution of somatic mutations to variation in forest trees, the potential utility of the dwarfing mutation for rootstocks in forestry seed orchards, and the next steps toward characterizing the pathways underlying dwarfism and their homology in other conifer species.