Shanghai Jiaotong University Yuan Zheng's research group published a paper to analyze the dynamic panorama of single-cell early development of rice inflorescence

On February 4, 2022, NEW PHYTOLOGIST published online the title of "A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret.
and inflorescence meristems” research paper
.

The researchers used a single-cell sequencing system to map a dynamic panorama of early rice inflorescence development, reconstructing the developmental trajectories of rice spikelets, flowers, and various reproductive meristems

Rice is one of the important food crops for human beings and occupies an important position in China's food production
.

The morphological structure of rice inflorescence is one of the important agronomic traits that directly determines the final yield

In this study, two samples S1 (inflorescence length <2mm), S2 (inflorescence length 2-3mm) and flag leaves (control) covering the developmental process of each reproductive meristem transition and establishment of flower organ attributes in the early development of rice inflorescence were used.
performed single-cell sequencing (BD RhapsodyTM, Shanghai Liebing), obtained single-cell transcriptome data containing 37,571 high-quality cells, and divided these cells into four cell groups: spikelets, meristems, inflorescence rachis, and leaves ( Figure 1)
.

The researchers further performed cell taxonomic identification and comprehensive analysis of spikelet, flower, and meristem subsets, and verified the correctness of the classification by in situ hybridization, molecular marker transgenic plants, and mutant analysis

Figure 1.
Early developmental pattern and cell classification of rice inflorescence

(a) Diagram of the early developmental pattern of rice inflorescence
.

(b) Experimental workflow, showing the workflow of material collection, protoplast collection, cell capture, single-cell transcriptome sequencing, and bioinformatics analysis at two stages of early inflorescence development

In view of the fact that scholars have cloned many regulatory factors in rice spikelet and flower development in the early stage, it provides usable marker genes for cell grouping
.

The researchers first subdivided the spikelets and flower cells

Figure 2.

Rice flower cell type classification and dwt1 mutant phenotype

(a) UMAP map of rice flower showing 10 flower cell subgroups
.

The red and blue arrows indicate the two developmental trajectories of flower cells: reproductive organs (floral tissues such as FM, pa, lo, st, etc.

Through pseudo-chronological analysis, the researchers further constructed two pathways of flower development, and at the single-cell expressomic level proved that rice "true" flowers developed in the SIC–FM–pa/lo/st pattern, while rg, sl , le is the view of the bract-like organ (Fig.
3)
.

Verified by in situ results, the SIC cell population highly enriched in ROC/HDG family genes is located in the epidermis (L1) of SpM and FM, suggesting that floral meristem L1 plays an important role in the regulation of floral meristem activity and subsequent development; The researchers thus put forward the hypothesis that the ROC/HDG gene family may provide positional signals from the outer layer of the FM to activate rice spikelet and flower initiation (Fig.

Figure 3.

Pseudo-chronological analysis of rice flower cells and SIC-FM developmental model

(a) and (b) Pseudo-chronological analysis results of floral cells, showing that FM cells develop into floral organs, including palea, sera and stamens without leaf-attributed cells (a), and glume containing leaf-attributed cells , recessive bracts and border cells (b)
.
(c) Violin plot showing that ROC genes are enriched in floral SICs
.
(d) In situ hybridization of ROC1 (d1) and ROC3 (d2) mRNAs showed that SICs were inflorescence primordial epidermal cells
.
(e) Model plot of the relationship between SIC, SSC (supporting cell population), and FM in spikelets
.

The researchers then subdivided the reproductive meristem again, dividing the meristematic cell clusters into three types: inflorescence meristem, branch meristem, and spikelet meristem, and provided a new series of cells.
Type marker genes (Figure 4)
.
The study reconstructed the developmental pathways of various reproductive meristems by pseudo-chronological, and identified four types of regulators that control the transition of lateral meristems
.
The researchers also deeply analyzed the expression pattern and biological function of the second representative gene, OsAUX1, and confirmed that the Osaux1 mutant has a phenotype of smaller inflorescence, reduced number of branches and spikelets, which provides a direct link for auxin to regulate inflorescence development in rice.
Genetic evidence (Figure 4)
.

Figure 4.
Identification and pseudo-chronological analysis of rice inflorescence meristem cell types, and the phenotype of OsAUX1 regulating inflorescence branching

(a) UMAP map of inflorescence meristem cells divided into 3 cell types: IM, BM, and SM
.
(b) Pseudo-chronological analysis of meristem cells showing two differentiation trajectories from IM to BM and SM
.
(c) BEAM analysis of the red nodes in (b) shows that the contribution of transcription factors to meristem transformation falls into four categories
.
(d) Scatter plot of OsAUX1 gene BEAM analysis, indicating that OsAUX1 mainly affects the differentiation of IM to BM
.
(e) In situ hybridization results of OsAUX1 at the S1 stage, showing that OsAUX1 is expressed in BM and SM
.
(f) Osaux1-1;4 mutant inflorescences showed shorter branches and fewer spikelets compared to wild-type 9522
.
(g) The inflorescence length of the Osaux1-1;4 mutant was shortened compared to the wild type
.

These research results have systematically drawn a single-cell map of the early development of rice inflorescences, reconstructed the developmental trajectory of rice flowers and reproductive meristems, identified a series of important regulatory factors in the process of inflorescence development, and provided genetic evidence for future analysis.
The fine process and molecular mechanism of rice inflorescence development, and the high-yield breeding of rice have laid a good foundation
.

The project has been supported by the National Natural Science Foundation of China, the Open Project of the State Key Laboratory of Hybrid Rice, the Construction of the Shanghai Rice Industry Technology System, the Discipline Innovation and Talent Introducing Program of Higher Education Institutions, and the SMC Morning Star Program of Shanghai Jiaotong University
.

Paper link : https://nph.
onlinelibrary.
wiley.
com/doi/abs/10.
1111/nph.
18008