Comparative study of meristem specific functions of the rice transcription factor RFL for vegetative and reproductive development

Abstract

In model laboratory plant Arabidopsis thaliana, LEAFY (a plant specific transcription factor) is reported to act as a floral organ identity gene. Whereas its ortholog (RFL) in rice, is reported to be involved in regulating plant shoot architecture, floral morphology and flowering time. In our study, using CRISPR-Cas9 I have raised rfl mutant lines with partial loss-of-function and one null allele. These new alleles reveal previously unreported functions of RFL in regulating the root system architecture and tiller bud outgrowth in addition to the previously reported phenotypes. Further, to get molecular insights on RFL function in these meristems, RFL RNA ¬in situ hybridization and immunohistochemistry studies using affinity purified anti-RFL antibody suggest that RFL function in the rice plant architecture including crown root primordia development is likely cell-autonomous. Combining genomics tools of ChIP-seq (with anti-RFL antibody) and the RNA-seq (using different developmental pools of tissues from the stable line with rfl weak allele) we have identified the novel pathways regulated by RFL in young vegetative meristems (seedling culm at 21 DAG with the shoot meristem, incipient axillary meristems and crown root primordia embedded in the ground tissue surrounding the pith) and in young inflorescence meristems (<0.1-0.25cm with growing primary and secondary panicle branch primordia and early developing floral meristems). Our work reveals that RFL acts by directly and indirectly regulating the auxin distribution pattern in the various meristems of rice seedling tissue to regulate the crown root development and axillary bud outgrowth in rice plants. Our transcriptome studies also show, how RFL regulates the same sets of genes targets in meristem specific manner to control to overall plant architecture (both vegetative and reproductive) and reproductive transition.