It is a debate whether trunk twisting belongs to environmental
alteration or genetic variation. Through a diallel cross experiment, we
first determined that trunk twisting of Yunnan pines was controlled by
recessive genes. Anatomical analysis identified that straight and twisty
types differed in xylem and phloem. RNA-seq of materials enriched by
laser microdissection revealed three genes involved in auxin signal
transduction, photosynthesis, and sucrose metabolism, namely ARF,
POR, and CBH. These genes were co-expressed at different
growth stages of twisty types, and among them, ARF is crucial
regulating trunk twisting formation. The enzyme activities involved in
sucrose metabolism, carbon fixation, and glycolysis were significantly
increased after exogenous auxin was added to twisty types. When auxin
signal transduction inhibitor (auxinole) and transport inhibitor (TIBA)
were added, the plant height and related pathways were more obviously
reduced in straight types. ARF can not only downregulate
POR to block chlorophyll synthesis but also allows abundant
sucrose to synthesize cellulose. Nevertheless, due to downregulated
CBH expression and abnormal cellulolysis, cellulose accumulates
and the lignin content decreases, eventually making the trunk highly
prone to twisted growth. This study suggests that ARF can be
vital in trunk shape screening during the early growth of Yunnan pines.