A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

We have used high-throughput single-cell RNA sequencing to profile rice inflorescence cells, and construct a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development. Two replicate inflorescence samples were staged by length — stage 1 (S1) was <2 mm, while stage 2 (S2) was 2–3 mm — to coincide with commencement of branching, spikelet, and floret meristem development . A single young flag leaf (L) covering the inflorescence was used as the control, as bracts could not be removed from the inflorescence . Each replication contains around 100 young inflorescences or leaves.