Integrating single nuclei and bulk RNA sequencing in rice shoot apical meristems uncovers candidate early floral transition gene networks.

We describe transcriptional dynamics at the rice shoot apex by integrating time resolved single nuclei RNA-seq with bulk RNA-seq data. In rice, short days trigger floral transition and the transcriptional reprogramming of the shoot apex to become reproductive. We integrated time-resolved bulk RNA-seq with single nuclei RNA-seq analysis to gain a refined understanding of the transcriptional programs induced at the shoot apex during floral transition. Our analyses highlighted technological and conceptual differences between single nuclei RNA-seq and bulk RNA-seq data and described previously uncharacterized transcriptional programs associated with the early steps of floral induction in rice.