Figures (5)  Tables (2)

    • Figure 1. 

      Single-cell and spatial transcriptome sequencing and analysis pipeline.

    • Figure 2. 

      The number of publications utilizing single-cell and spatial transcriptome techniques for various types of plants, (a) from 2017 to 2025 (up to June 30th), and (b) in different families.

    • Figure 3. 

      Horticultural plants studied using single-cell and spatial transcriptomes from 2022 to 2025 (up to June 30th).

    • Figure 4. 

      Application prospects of single-cell and spatial transcriptome techniques in horticultural plants.

    • Figure 5. 

      Challenges and strategies for single-cell and spatial transcriptome applications in horticultural plants.

    • Plant type Species Family Key traits Number of publications
      Model plant Arabidopsis thaliana Brassicaceae Inflorescence; roots; calli; etc. 42
      Lotus japonicus Fabaceae Root nodules 2
      Marchantia polymorpha Marchantiaceae Dormant gemmae; developing thalli 1
      Medicago truncatula Fabaceae Root nodules 3
      Nicotiana attenuata Solanaceae Corolla limbs; throat cups 1
      Nicotiana tabacum Solanaceae Low-nitrogen resistance 1
      Physcomitrella patens Funariaceae Leaves 1
      Portulaca oleracea Portulacaceae Leaves 1
      Total 8 6 52
      Food crop plant Hordeum vulgare Poaceae Grains; embryos under ABA 2
      Manihot esculenta Euphorbiaceae Leaves; tuberous roots 2
      Oryza sativa Poaceae Leaves; roots; embryos; etc. 12
      Pisum sativum Fabaceae Shoot apices under boron deficiency 1
      Triticum aestivum Poaceae Root tips; grains under heat stress; grains; etc. 4
      Zea mays Poaceae Anthers; ears; endosperms; etc. 22
      Total 6 3 343
      Horticultural plant Allium sativum Amaryllidaceae Bulb basal plates; bulbs 2
      Amygdalus persica Rosaceae Flower buds 1
      Brassica campestris Brassicaceae Root tips under salt stress 1
      Brassica rapa Brassicaceae Heat resistance; young leaves; leaf vasculature 4
      Camellia sinensis Theaceae Leaves; root tips 2
      Camptotheca acuminata Nyssaceae Shoot apices 1
      Catharanthus roseus Apocynaceae Leaves 2
      Cucumis sativus Cucurbitaceae Inferior ovary 1
      Dendrobium devonianum Orchidaceae Flower buds 1
      Dimocarpus longan Sapindaceae Embryogenic callus 1
      Euryale ferox Nymphaeaceae Leaves 1
      Fragaria vesca Rosaceae Gray mold resistance 1
      Hylocereus undatus Cactaceae Pericarps senescence 1
      Ipomoea aquatica Convolvulaceae Root tips under Cd treatment 1
      Limonium bicolor Plumbaginaceae Young leaves 1
      Liriodendron chinense Magnoliaceae Stem-differentiating xylem 1
      Litchi chinensis Sapindaceae Undetermined resting buds; vegetative buds; floral buds 1
      Phalaenopsis Orchidaceae Inflorescences 1
      Phyllostachys edulis Poaceae Basal root tips 1
      Prunus mume Rosaceae Petals 1
      Rosa hybrida Rosaceae Gray mold resistance 1
      Solanum lycopersicum Solanaceae Root primordia; calli; ToCV resistance 3
      Spinacia oleracea Amaranthaceae Inflorescences 1
      Taxus mairei Taxaceae Leaves; young stems 2
      Tillandsia duratii Bromeliaceae Leaves 1
      Trochodendron aralioides Trochodendraceae Stem-differentiating xylem 1
      Vriesea erythrodactylon Bromeliaceae Roots 1
      Total 19 20 36
      Economic crop plant Arachis hypogaea Fabaceae Leaves; roots; peg/pod tips; etc. 7
      Bombax ceiba Malvaceae Ovary wall 1
      Camellia oleifera Theaceae Ovaries 1
      Cinnamomum camphora Lauraceae Leaves 1
      Glycine max Fabaceae Root nodules and various tissues 4
      Gossypium bickii Malvaceae Cotyledons 1
      Gossypium hirsutum Malvaceae Ovules; hypocotyls; anthers; etc. 12
      Hevea brasiliensis Euphorbiaceae Powdery mildew resistance 1
      Juglans regia Juglandaceae Fruit 1
      Saccharum spp. Poaceae Smut resistance 1
      Total 10 7 30
      Forest plants Eucalyptus grandis Myrtaceae Stem-differentiating xylem 1
      Picea abies Pinaceae Female cones 1
      Populus alba Salicaceae Bark; wood; apical buds 2
      Populus alba × Populus glandulosa Salicaceae Xylem; stems 3
      Populus alba × Populus tremula var. glandulosa Salicaceae Stem segments 1
      Populus euramericana Salicaceae Stem internodes 1
      Populus tremula Salicaceae Leaf buds 1
      Populus tremula × alba Salicaceae Shoot apices 1
      Populus trichocarpa Salicaceae Stems; stem-differentiating xylem 2
      Total 9 3 13

      Table 1. 

      Plant species studied using single-cell and spatial transcriptome techniques.

    • Species Tissue Cell types Ref.
      Allium sativum Bulb basal plates Xylem-type cells; stem cells; epidermis cells; sieve cells; proliferative cells; etc. Wang et al.[41]
      Allium sativum Bulbs Meristem cells; parenchyma cells; etc. Gao et al.[42]
      Amygdalus persica Flower buds Sepal; petal; stamen and filament; style; etc. Zhao et al.[43]
      Brassica campestris Root tips Root hair; epidermis; cortex; endodermis; stele; root cap; dividing cells; initial cells. Liu et al.[44]
      Brassica rapa Shoot apices and leaves Meristem cells; mesophyll cells; epidermal cells; guard cells; vascular cells; proliferating cells; etc. Sun et al.[45]
      Brassica rapa Young leaves Mesophyll cells; epidermis; vasculature; bundle sheath; guard cells; proliferating cells; phloem; xylem. Guo et al.[46]
      Brassica rapa Leaf vasculature Xylem parenchyma; tracheary elements; phloem parenchyma; companion cells; sieve elements; procambium cells; procambium cells with xylem features; unknown vascular cells. Guo et al.[47]
      Brassica rapa Young leaves Mesophyll cells; epidermal cells; guard cells; vascular cells; proliferating cells; etc. Zhang et al.[48]
      Camellia sinensis Leaves Epidermis cells; mesophyll cells; vascular bundle cells; proliferating cells; etc. Wang et al.[49]
      Camellia sinensis Root tips Xylem; epidermis; stem cell niche; cortex/endodermis; root cap; cambium; phloem; pericycle. Lin et al.[50]
      Camptotheca acuminata Shoot apices and leaves Shoot apices: mesophyll cells; epidermal cells; vascular cells; proliferating cells; central zone. Leaves: mesophyll cells; epidermal cells; vascular cells; proliferating cells. Wang et al.[51]
      Catharanthus roseus Leaves Mesophyll cells; epidermal cells (young); epidermal cells (mature); guard cells; vascular cells; proliferating cells; idioblast cells; internal phloem-associated parenchyma; etc. Sun et al.[38]
      Catharanthus roseus Leaves and roots Leaves: internal phloem-associated parenchyma; epidermis; idioblast; mesophyll; vasculature; guard cell; etc. Roots: Ground tissue; epidermis; stele; root cap; meristem; etc. Li et al.[39]
      Cucumis sativus Floral buds Floral primordia; placenta; ovule; stigma/transmitting tract; sepal; petal/stamen; floral intercalary meristem; receptacle-early; receptacle-late; conjunctive tissue; epidermis; trichome; provascular; phloem; mesocarp/endocarp; G1/S phase cells; G2/M phase cells. Dong et al.[52]
      Dendrobium devonianum Flower buds Epidermal cells; vascular bundle cells; mesophyll cells; xylem cells; phloem cells; ovule cells; anther cells; guard cells; proliferating cells. Wang et al.[53]
      Dimocarpus longan Embryogenic callus Proliferating cells; meristematic cells; vascular cells; epidermal cells; etc. Zhang et al.[54]
      Euryale ferox Leaves Proliferating cells; epidermis cells; mesophyll cells; procambium cells; phloem cells; xylem cells; bundle sheath cells; hydathode cells; etc. Liu et al.[55]
      Fragaria vesca Leaves Hydathode cells; mesophyll cells; bundle sheath cells; upper epidermal cells; phloem cells; lower epidermal cells; xylem parenchymal cells; meristem cells; xylem cells; etc. Bai et al.[35]
      Hylocereus undatus Pericarps Exocarp cells; mesocarp cells; endocarp cells; endocarp fiber cells; vascular bundle cells. Li et al.[56]
      Ipomoea aquatica Root tips Epidermis cells; cortex cells; endodermis cells; root cap cells; sub-cell type of stele; trichoblast cells; phloem cells; xylem cells; pericycle cells; procambium cells. Shen et al.[57]
      Limonium bicolor Young leaves Promeristem cells; epidermal cells; mesophyll cells; vascular tissue cells; salt gland-associated epidermal-cell subclusters. Zhao et al.[40]
      Liriodendron chinense Stem-differentiating xylem Ray organizer cells; ray precursor cells; ray parenchyma cells; fusiform organizer cells; fusiform early precursor cells; fusiform intermediate precursor cells; vessel elements; libriform fibers; tracheids. Tung et al.[58]
      Litchi chinensis Undetermined resting buds; vegetative buds; floral buds Mesophyll cells; epidermis cells; meristem cells; G1/S proliferating cells; G2/M proliferating cells; cortex cells; guard cells; floral meristem cells (Exists only in floral buds.); etc. Yang et al.[59]
      Phalaenopsis Inflorescences Inflorescence meristem cells; floral meristem cells; tepal cells; lip cells; column cells; pollinium cells; bract cells; primordium cells. Liu et al.[36]
      Phyllostachys edulis Basal root tips Root cap cells; epidermis cells; ground tissue cells; initial cells; transition cells; etc. Cheng et al.[60]
      Prunus mume Petals Epidermal cells; parenchyma cells; xylem parenchyma cells; phloem parenchyma cells; xylem vessels and fibers; sieve element-companion cell complex; etc. Guo et al.[61]
      Rosa hybrida Petals Epidermal cells; epidermis/Fra cells; xylem cells; phloem cells; petal mesophyll cells; guard cells; bundle sheath cells. Li et al.[62]
      Solanum lycopersicum Shoot-borne root primordia Phloem parenchyma cells; transition cells; root cap/initial cells; cambium cells; phloem companion cells; procambium cells; vasculature initials. Omary et al.[63]
      Solanum lycopersicum Calli Epidermis cells; vascular tissue cells; shoot primordia cells; inner callus cells; chlorenchyma cells. Song et al.[64]
      Solanum lycopersicum Leaves Mesophyll cells; epidermal cells; guard cells; vascular cells; trichome cells; proliferating cells. Yue et al.[65]
      Spinacia oleracea Inflorescences Vegetative shoot apical meristem cells; Inflorescence meristem/flower primordia cells; bract primordia/bract cells; epidermal cells; cortex cells; pith cells; pith rib meristem cells; basal bud cells. You et al.[66]
      Taxus mairei Leaves Bundle sheath cells; vein cells; mesophyll cells; stomatal complex cells; guard cells; epidermal cells; vascular cells; procambium cells; phloem cells; leaf pavement cells. Zhan et al.[67]
      Taxus mairei Young stems Xylem parenchyma cells; xylem cells; epidermal cells; photosynthetic/cork cells; vascular cells; xylem mother cells; companion cells & phloem cells; endodermal cells; cambium region and sieve element cells. Yu et al.[68]
      Tillandsia duratii Leaves Trichome cells; mesophyll cells; epidermal cells; vascular cells. Lyu et al.[37]
      Trochodendron aralioides Stem-differentiating xylem Ray organizer cells; ray precursor cells; ray parenchyma cells; fusiform organizer cells; fusiform early precursor cells; fusiform intermediate precursor cells; tracheids. Tung et al.[58]
      Vriesea erythrodactylon Roots Cortex cells; velamen cells; stele cells; meristem cells. Lyu et al.[37]

      Table 2. 

      Cell types of horticultural plant tissues.