Transcriptome Analysis of Auxin Drives Cone Size Regulation in Fokienia hodginsii

As the reproductive organ of the endangered species Fokienia hodginsii, the size of the cones is a constraint on the reproductive renewal of the population. In this study, the molecular basis of the influence of cone size on F. hodginsii was elucidated by comparing the phenotype, biochemistry, and transcriptome of two cultivars of F. hodginsii ('FJ431' and 'FJ415'). The two cultivars differed significantly in cone size, with FJ431 having a significantly larger cone size and weight than FJ415, 1.32 and 1.90 times that of FJ415, respectively. RNA-Seq analysis of both cultivars retrieved 75,940 genes whose approximate functions were classified as the pathway of response to endogenous stimulus and response to hormone and showed significant differences in the auxin-activated signaling pathway, particularly the MAPK signaling pathway-plant. Furthermore, the endogenous IAA content was significantly higher in FJ431 than in FJ415, and 1.58 and 1.29 times more IAA was present in immature and mature cones, respectively. Moreover, exogenous IAA treatment significantly induced the expression of the MAPK pathway-related gene TRINITY_DN10564_c0_g1 and significantly inhibited the expression of the MAPK pathwayrelated gene TRINITY _DN17056_c0_g1. Our work suggests that IAA can affect the cone size of F. hodginsii, most probably through the MAPK pathway. This has high theoretical and practical significance for the improvement of genetic breeding and the further cultivation of quality germplasm resources of F. hodginsii.