TABLE 1.
Regulatory elements of the PmLEC1 locus and associated transcription factors most relevant to embryo development and somatic embryogenesis (SE)
| Cis‐element | Transcription factor | Source organism | Gene ontology—biological process |
|---|---|---|---|
| AGAMOUS | AGAMOUS | A. thaliana | Flower development. |
| MADS box; MIK3 | AGL3 | A. thaliana | Plant ovule, carpel, petal, sepal, stamen development; cell differentiation; maintenance of floral meristem identity; multicellular organism development. |
| MADS box; MIK3 | AGL6 | A. thaliana | Cell differentiation; floral organ development; vegetative to reproductive phase transition of meristem; multicellular organism and plant ovule development. |
| MADS box; MIK3 | AGL15 | A. thaliana | SE; cellular response to auxin stimulus; embryo development ending in seed dormancy; GA catabolic process; multicellular organism development; seed maturation, short‐day photoperiodism. |
| MADS box; MIK3 | FLOWERING LOCUS C (FLC) | A. thaliana | Cell differentiation; multicellular organism development; regulation of circadian rhythm; response to temperature stimulus; vernalization response. |
| AP2; B3; RAV | RAV1 | A. thaliana | Cellular response to hypoxia, brassinosteroids; ethylene‐activated signaling pathway; lateral root development; leaf development. |
| AP2; ERF | ABI4 | A. thaliana | ABA‐activated, ethylene‐activated, and sugar‐mediated signaling pathways; defense response; response to glucose, osmotic stress, sucrose, trehalose, water deprivation; root meristem growth; seed development; starch catabolism. |
|
B3; RY element |
ABI3 |
A. thaliana; B. napus |
ABA‐activated signaling pathway; embryo development ending in seed dormancy; response to ABA; response to auxin. |
| B3 | LEC2 | A. thaliana | SE; embryo development ending in seed dormancy; seed maturation; seed oilbody biogenesis; auxin biosynthetic process. |
| B3 | FUS3 | A. thaliana | SE; embryo development ending in seed dormancy; plant organ development; regulation of ABA and GA biosynthetic processes; regulation of ABA‐activated signaling pathway, cell population proliferation, embryonic development; response to auxin; vegetative to reproductive phase transition of meristem. |
|
SPH CORE; RY REPEAT4 |
VP1 |
Z. mays; T. aestivum; O. sativa |
Expression of the maturation program in seed development; potentiation of seed‐specific hormone response. |
| WOX |
WUSCHEL (WUS) |
A. thaliana | Anther development; axillary shoot meristem initiation; cell differentiation; stem cell population maintenance. |
| HD‐ZIP | MERISTEM L1 | A. thaliana | Cotyledon development; plant epidermal cell differentiation; seed germination; cell specification and pattern formation during embryogenesis. |
| MYB‐related | CCA1 | A. thaliana | Circadian rhythm; long‐day photoperiodism, flowering; response to ABA, auxin, cadmium ion, cold, ethylene, jasmonic acid, GA, organonitrogen compound, salicylic acid, salt stress. |
| Myb/SANT; MYB; G2‐like | KANADI 1 (KAN1) | A. thaliana | Abaxial cell fate specification; adaxial/abaxial axis specification; plant organ morphogenesis; plant ovule development; radial pattern formation; xylem and phloem pattern formation; polarity specification of adaxial/abaxial axis. |
| Cold Shock Domain | CSD protein 4 (CSP4) | A. thaliana | Embryo development ending in seed dormancy; response to cold. Regulates seed development, particularly at late stages of embryo development. |
| Myb/SANT; ARR‐B | Two‐component response regulator ARR1 | A. thaliana | Maintenance of shoot apical meristem identity; regulation of root meristem growth, seed growth; response to cytokinin, water deprivation; root development; shoot system development. |
| NAC; NAM |
NAC TF 29 (NAC029) |
A. thaliana | Embryo development ending in seed dormancy; multidimensional cell growth; flower development; fruit ripening; leaf senescence. |
| YABBY | Axial regulator YABBY 1 | A. thaliana | Abaxial cell fate specification; cell fate commitment; meristem structural organization; regulation of shoot apical meristem development; specification of plant organ position. |
| YABBY | CRABS CLAW | A. thaliana | Cell fate commitment; floral meristem determinacy; meristem determinacy; polarity specification of adaxial/abaxial axis. |
| AP2; ERF | Ethylene‐responsive TF RAP2‐6 | A. thaliana | Cellular response to heat; chloroplast organization; defense response; ethylene‐activated signaling pathway; response to ABA, cold, jasmonic acid, osmotic stress, salicylic acid, salt stress, water deprivation, wounding. |
| ARID | ARID6 | A. thaliana | Chromatin silencing; glucosinolate metabolic process. |
| bHLH | HBI1 | A. thaliana | Brassinosteroid‐ and GA3‐mediated signaling pathways; regulation of growth. |
| Dof | CDF5 | A. thaliana | Flower development; negative regulation of long‐day photoperiodism, flowering; negative regulation of short‐day; photoperiodism, flowering. |
| C3H | Splicing factor U2AF35B | A. thaliana | Photoperiodism; flowering; mRNA splicing via spliceosome. |
| Myb/SANT | MYB33 | A. thaliana | Pollen sperm cell differentiation; ABA‐activated and GA3‐mediated signaling pathways; regulation of cell proliferation, growth, programmed cell death; protein storage vacuole organization; responses to cytokinin, ethylene, GA. |
| Myb/SANT; MYB | MYB44 | A. thaliana | ABA‐activated signaling pathway; defense responses to bacteria and fungi; responses to ABA, auxin, cadmium ion, chitin, ethylene, GA, jasmonic acid, salicylic acid, salt stress, water deprivation. |
| Myb/SANT | MYB 65 | A. thaliana | Cell differentiation; regulation of auxin mediated signaling pathway, protein storage vacuole organization, cell population proliferation, growth, programmed cell death; pollen sperm cell differentiation; response to ethylene, salicylic acid. |
| Myb/SANT; MYB | MYB 88 | A. thaliana | Embryo sac development; guard cell and guard mother cell differentiation; megasporogenesis; responses to salt stress, ABA, water deprivation, gravity; water homeostasis; regulation of cell cycle G1/S phase transition. |
| Myb/SANT | MYB111 | A. thaliana | Cell differentiation; flavanol biosynthetic process; responses to UV‐B and light. |
| Myb/SANT; MYB | MYB 118 | A. thaliana | SE; regulation of embryo and endosperm development, seed maturation, fatty acid biosynthesis; vegetative to reproductive phase transition of meristem. |
| Myb/SANT; MYB‐related |
REVEILLE 4 RVE4 |
A. thaliana | Circadian rhythm; response to ABA, auxin, cadmium ion, ethylene, GA, jasmonic acid, salicylic acid, salt stress. |
| Myb/SANT; MYB‐related | REVEILLE 8 (RVE8) | A. thaliana | Circadian regulation of gene expression; photoperiod; response to ABA, auxin, cadmium ion, ethylene, GA, jasmonic acid, salicylic acid, salt stress. |
| Myb/SANT; MYB‐related | LHY | A. thaliana | Circadian rhythm; long‐day photoperiodism, flowering; response to ABA, auxin, cadmium ion, cold, ethylene, GA, jasmonic acid, salicylic acid, salt stress. |
| Myb/SANT | KUA1 | A. thaliana |
Auxin homeostasis; postembryonic plant organ morphogenesis; response to ABA, absence of light, auxin, cadmium ion, ethylene, GA, salt stress, sucrose, jasmonic acid, salicylic acid; hypocotyl elongation in response to darkness. |
| Myb/SANT; MYB‐related | Telomere repeat‐binding factor 2 | A. thaliana | Nucleosome assembly; response to ABA, auxin, cadmium ion, ethylene, GA, jasmonic acid, salicylic acid, salt stress. |
| WRKY | WRKY46 | A. thaliana | Brassinosteroid‐mediated signaling pathway; cellular response to hypoxia; response to water deprivation, bacteria, chitin, and salicylic acid. |
| WRKY | WRKY57 | A. thaliana | Response to osmotic stress, salt stress, water deprivation. |
| ZF‐HD | ZHD1 | A. thaliana | Seed maturation; regulation of GA biosynthetic process. |
| ZF‐HD | ZHD10 | A. thaliana | GA3‐mediated signaling pathway; response to blue light, GA. |
| VOZ | VOZ2 | A. thaliana | Long‐day photoperiodism, flowering; positive regulation of long‐day photoperiodism; red, far‐red light phototransduction; response to salt stress. |
| Dehydrin | Protein COLD‐REGULATED 15A (COR15A) | A. thaliana | Circadian rhythm; cold acclimation; drought recovery; heat acclimation; leaf senescence; red or far‐red light signaling pathway; response to ABA, cold, freezing, light, osmotic stress, salt stress, water deprivation. |
| Others | RD29A (Desiccation‐responsive protein 29A) | A. thaliana | Circadian rhythm; hyperosmotic salinity response; leaf senescence; regulation of root development; response to abscisic acid, cold, mannitol, osmotic stress, reactive oxygen species, salt, salt stress, symbiotic bacterium, water deprivation, wounding; responses to abiotic stresses. |
| bHLH | PIF1 | A. thaliana | Chlorophyll biosynthetic process; GA3‐mediated signaling pathway; regulation of photomorphogenesis, seed germination; red light signaling pathway. |
| bHLH | PIF3 | A. thaliana | De‐etiolation; GA3‐mediated signaling pathway; red, far‐red light phototransduction; red or far‐red light signaling pathway and response. |
| PYRIMIDINE BOX; NF‐YC | NF‐YC9 |
O. sativa; H. vulgare |
ABA‐activated signaling; GA3‐mediated signaling pathway; positive regulation of photomorphogenesis; regulation of seed germination. |
| Myb/SANT; MYB; NF‐YC | CDC5 | A. thaliana | Cell cycle; defense response signaling pathway; defense responses to bacteria and fungi; DNA repair; innate immune response; RNA splicing. |