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

Abstract

Rice inflorescence development determines yield and relies on the activity of axillary meristems (AMs); however, high-resolution analysis of its early development is lacking.Here, we have used high-throughput single-cell RNA sequencing to profile 37 571 rice inflorescence cells and constructed a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development. The differentiation trajectories of florets and AMs were reconstructed, and discrete cell types and groups of regulators in the highly heterogeneous young inflorescence were identified and then validated by in situ hybridization and with fluorescent marker lines.Our data demonstrate that a WOX transcription factor, DWARF TILLER1, regulates flower meristem activity, and provide evidence for the role of auxin in rice inflorescence branching by exploring the expression and biological role of the auxin importer OsAUX1.Our comprehensive transcriptomic atlas of early rice inflorescence development, supported by genetic evidence, provides single-cell-level insights into AM differentiation and floret development.

Genetic and molecular pathways controlling rice inflorescence architecture

“…By high-throughput single-cell RNA sequencing technology, auxin influx transporter gene OsAUX1 is identified to have enriched expression in BM. Consistent with its expression pattern, the loss-of-function mutant of OsAUX1 produces smaller inflorescence with reduced branch and spikelet number ( Zong et al., 2022 ).…”

Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication

“…In addition to the applications in Arabidopsis primary root tips, scRNA‐seq has been applied to study other dicots and monocots, as well as in leaves, inflorescences, and other tissues (Sun et al., 2022a; Zong et al., 2022). More recently, it was found that CYCLING DOF FACTOR 5 (CDF5) and REPRESSOR OF GA (RGA) have potential roles in the early development and function of leaf veins in cotyledons (Liu et al., 2022b).…”

Pushing the boundaries of organ identity: Homology of the grass lemma

“…New technologies can help define homologies: single‐cell RNA sequencing, which analyzes gene expression in thousands of cells across spatial and temporal gradients, has revealed genetic underpinnings of developmental trajectories in rice spikelets. Despite morphological similarity of lemmas and paleas in rice, lemma gene expression is similar to that of glumes, while palea gene expression is similar to that of lodicules and reproductive organs (Zong et al, 2022). This expression pattern again suggests that lemmas, with gene expression patterns more similar to bracts, may be homologous to bracts.…”