GWAS identifies candidate regulators of in planta regeneration in Populus trichocarpa

Plant regeneration is an element of natural and horticultural plant propagation, and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. To shed light on the causes of variation in natural regeneration capacity, we undertook a GWAS of shoot regeneration from dormant cut stems in Populus trichocarpa. Using estimates of callus and shoot regeneration provided by a novel computer vision system, and using a variety of GWAS pipelines and statistical approaches, our analyses revealed over 200 candidate genes. The candidates each explained small fractions of the total genetic variance and many appeared to be members of genetic regulatory networks, showing regeneration to be a highly polygenic trait. The top candidates included regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. These candidates provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species. ### Competing Interest Statement The authors have declared no competing interest.