About Single Cell Multi-omics in Rice
Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the major crop plants. We simultaneously profiled chromatin accessibility and RNA expression in 116,564 cells from eight organs. We annotated the majority of cell types and identified cell-type expression programs, and found a high correlation between RNA and chromatin accessibility across cells. We constructed single-cell gene regulatory networks and co-expression networks, which allowed us to identify the cell type-specific regulators RSR1, F3H and LTPL120 in rice development. Furthermore, our analysis revealed a correlation between cell type and agronomic traits of rice, and the conserved and divergent functions of cell type during evolution. In summary, this study not only offers a valuable single-cell multiomics resource, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.
Tissues
Crown root
In crown root tissue, there are Cortex, Endodermis, Epidermis, Exodermis, Meristem, Root cap, Sclerenchyma, Vascular and other cell types.
Culm
In culm tissue, there are Cortex, Epidermis, Parenchyma cell, Procambium, Vascular and other cell types.
Leaf
In leaf tissue, there are Epidermis, Fiber, Guard cell, Mesophyll, Parenchyma cell and Vascular cell types.
Flag leaf
In flag leaf tissue, there are Epidermis, Fiber, Guard cell, Mesophyll and Vascular cell types.
Shoot apex
In shoot apex tissue, there are Epidermis, Guard cell, Meristem, Parenchyma cell, Proliferating cell, Vascular and other cell types.
Tiller bud
In tiller bud tissue, there are Bud axis, Bud primordium, Epidermis, Parenchyma cell, Root meristem, Shoot apical meristem, Vascular and other cell types.
Panicle
In panicle tissue, there are Epidermis, Filament, Lodicule, Pollen mother cell, Rachilla, Style ovary, Tapetum, and Vascular cell types.
Seed
In seed tissue, there are Epidermis, Plumule, Scutellum, Vascular and other cell types.
Crown root
Crown roots in rice are adventitious roots that emerge from the base of the stem near the soil surface. They provide additional support and help in nutrient absorption for the plant. Crown roots contribute to the stability of the rice plant and aid in its ability to withstand environmental stresses.
Culm
The culm of a rice plant is the main, above-ground stem that grows vertically. It provides structural support and facilitates the transport of water, nutrients, and sugars between different parts of the plant. The culm has a hollow structure that allows for efficient nutrient and water flow within the plant.
Leaf
Rice leaves are green, flat structures that emerge from the culm. They play a vital role in photosynthesis, converting sunlight into energy. Rice leaves contain chlorophyll, which captures sunlight, and a network of veins that transport water, nutrients, and sugars throughout the plant. Leaves are essential for the growth and development of the rice plant.
Flag leaf
The flag leaf in rice refers to the topmost leaf on the culm, located just below the panicle. It is larger and more prominent than other leaves. The flag leaf is crucial for photosynthesis during the grain-filling stage. It captures sunlight and produces carbohydrates, which are essential for the development and filling of rice grains.
Shoot apex
The shoot apex is the actively growing tip of the culm in rice. It is responsible for producing new leaves, stems, and reproductive structures. The shoot apex ensures the continuous upward growth of the plant and contributes to its overall development.
Tiller bud
Tiller buds in rice are lateral shoots that arise from the base of the main culm. They contribute to the plant's productivity by producing additional stems and panicles. Tiller buds enable efficient resource utilization and the production of multiple panicles per plant, increasing the potential grain yield.
Panicle
The young panicle is the developing reproductive structure of a rice plant. It emerges from the tip of the culm and consists of multiple branches called spikelets. The young panicle undergoes further development and maturation before it reaches the stage of pollination and grain filling.
Seed
Seeds are the basic units of the rice panicle. They contain the florets, which are the potential rice grains. Each spikelet consists of several floral organs, including the stamens and pistil. Spikelets are the site of pollination and fertilization, leading to the formation of filled grains and the eventual harvest of the rice crop.
Locus
You can search for the expression or chromatin accessibility status of each locus in each tissue or the whole plant.
Network
The WGCNA (Weighted Gene Co-expression Network Analysis) module provides a comprehensive analysis framework for identifying gene co-expression networks and exploring their biological relevance in complex biological systems.
