Genome-Wide Association Studies Reveal That the Abietane Diterpene Isopimaric Acid Promotes Rice Growth through Inhibition of Defense Pathways

Plants are an important source for the discovery of novel natural growth regulators. We used activity screening to demonstrate that treatment of Nipponbare seeds with 25 μg/mL isopimaric acid significantly increased the resulting shoot length, root length, and shoot weight of rice seedlings by 11.37 ± 5.05%, 12.96 ± 7.63%, and 27.98 ± 10.88% and that it has a higher activity than Gibberellin A3 (GA₃) at the same concentration. A total of 213 inbred lines of different rice lineages were screened, and we found that isopimaric acid had different growth promotional activities on rice seedlings of different varieties. After induction with 25 μg/mL isopimaric acid, 15.02% of the rice varieties tested showed increased growth, while 15.96% of the varieties showed decreased growth; the growth of the remaining 69.02% did not show any significant change from the control. In the rice varieties showing an increase in growth, the shoot length and shoot weight significantly increased, accounting for 21.88% and 31.25%. The root length and weight significantly increased, accounting for 6.25% and 3.13%. Using genome-wide association studies (GWASs), linkage disequilibrium block, and gene haplotype significance analysis, we identified single nucleotide polymorphism (SNP) signals that were significantly associated with the length and weight of shoots on chromosomes 2 and 8, respectively. After that, we obtained 17 candidate genes related to the length of shoots and 4 candidate genes related to the weight of shoots. Finally, from the gene annotation data and gene tissue-specific expression; two genes related to this isopimaric acid regulation phenotype were identified as <i>OsASC1</i> (<i>LOC_Os02g37080</i>) on chromosome 2 and <i>OsBUD13</i> (<i>LOC_Os08g08080</i>) on chromosome 8. Subcellular localization analysis indicated that OsASC1 was expressed in the plasma membrane and the nuclear membrane, while OsBUD13 was expressed in the nucleus. Further RT-qPCR analysis showed that the relative expression levels of the resistance gene <i>OsASC1</i> and the antibody protein gene <i>OsBUD13</i> decreased significantly following treatment with 25 μg/mL isopimaric acid. These results suggest that isopimaric acid may inhibit defense pathways in order to promote the growth of rice seedlings.