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During this phase, the process of morphological differentiation begins, leading to the formation and development of the nascent organ. The initiation of organogenesis is characterized by a distinct shift in polarity, followed by the establishment of radial symmetry and subsequent growth along the newly defined axis, ultimately forming the structural bulge that marks organ initiation.{{cn|date=June 2025}}
The sequential development of organogenesis can be observed in species such as ''Pinus oocarpa Schiede'', where shoot buds are regenerated directly from cotyledons through direct organogenesis. However, the specific developmental patterns may vary across different plant species grown in vitro. The progression of organ formation includes distinct morphological changes, beginning with alterations in surface texture, the emergence of meristemoids, and the expansion of the [[Meristem|meristematic]] region either vertically or horizontally. This is followed by the protrusion of the meristematic region beyond the epidermal layer, the formation of a structured meristem with visible leaf primordia, and eventually, the full development of an adventitious bud.{{cn|date=June 2025}}
A notable characteristic of in vitro organogenic cultures is the simultaneous formation of multiple meristemoids on a single explant, with varying degrees of differentiation. Within the same explant, buds may exist in different developmental stages, ranging from early initiation to fully developed structures. Once the elongated shoots surpass a length of 1 cm, they are transferred to either in vitro or ex vitro rooting substrates, allowing for the completion of plantlet regeneration and the establishment of a fully formed plant.{{cn|date=June 2025}}
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In the process of direct organogenesis, axillary shoots are generated directly from pre-existing meristems located at the shoot tips and nodes, offering a high rate of multiplication. One of the key advantages of this method is the low likelihood of mutations occurring in the organized shoot meristems, ensuring that the resulting plants maintain genetic consistency. This technique is particularly valuable for the production and conservation of economically and environmentally significant plants, as it allows for the efficient generation of multiple shoots from a single explant, maintaining uniformity across the propagated plants. Furthermore, all plants produced via direct organogenesis are true-to-type, meaning they are genetic clones of the original plant.{{cn|date=June 2025}}
However, there are some limitations to organogenesis. Somaclonal variation, which can result in unwanted genetic diversity, is a potential issue, particularly in the indirect organogenesis process. Additionally, this technique may not be suitable for recalcitrant plant species, which are those that do not respond well to in vitro culture or regeneration protocols. These limitations highlight the need for ongoing research and optimization of methods for different plant species to overcome these challenges in [[plant propagation]] and conservation.{{cn|date=June 2025}}
===Cell elongation===
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[[File:Growth of a Plant.svg|thumb|This image shows the development of a normal plant. It resembles the different growth processes for a leaf, a stem, etc. On top of the gradual growth of the plant, the image reveals the true meaning of phototropism and cell elongation, meaning the light energy from the sun is causing the growing plant to bend towards the light aka elongate.]]
Plant growth and development are mediated by specific [[plant hormone]]s and plant growth regulators (PGRs) (Ross et al. 1983).<ref name="ross">Ross, S.D.; Pharis, R.P.; Binder, W.D. 1983. Growth regulators and conifers: their physiology and potential uses in forestry. p. 35–78 ''in'' Nickell, L.G. (Ed.), Plant growth regulating chemicals. Vol. 2, CRC Press, Boca Raton FL.</ref> Endogenous hormone levels are influenced by plant age, cold hardiness, dormancy, and other metabolic conditions; [[Photoperiodism|photoperiod]], drought, temperature, and other external environmental conditions; and exogenous sources of PGRs, e.g., externally applied and of [[Rhizosphere|rhizospheric]] origin.{{cn|date=June 2025}}
=== Morphological variation during growth ===
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===Adventitious structures===
Plant structures, including, [[Root|roots]], [[Bud|buds]], and [[Shoot (botany)|shoots]], that develop in unusual locations are called ''adventitious''.{{cn|date=June 2025}}
Adventitious roots and buds usually develop near the existing vascular tissues so that they can connect to the [[xylem]] and [[phloem]]. However, the exact ___location varies greatly. In young stems, adventitious roots often form from [[Ground tissue#Parenchyma|parenchyma]] between the [[vascular bundle]]s. In stems with secondary growth, adventitious roots often originate in phloem parenchyma near the [[vascular cambium]]. In stem cuttings, adventitious roots sometimes also originate in the [[Callus (cell biology)|callus]] cells that form at the cut surface. Leaf cuttings of the ''[[Crassula]]'' form adventitious roots in the epidermis.<ref>McVeigh, I. 1938. Regeneration in ''Crassula multicava''. ''American Journal of Botany'' 25: 7-11. [https://www.jstor.org/stable/2436624]</ref>
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Some leaves develop adventitious buds, which then form adventitious roots, as part of [[vegetative reproduction]]; e.g. piggyback plant (''[[Tolmiea menziesii]]'') and mother-of-thousands (''[[Kalanchoe daigremontiana]]''). The adventitious plantlets then drop off the parent plant and develop as separate [[Cloning|clone]]s of the parent.{{cn|date=June 2024}}
[[Coppicing]] is the practice of cutting [[tree]] stems to the ground to promote rapid growth of adventitious shoots. It is traditionally used to produce poles, fence material or firewood. It is also practiced for [[biomass]] crops grown for fuel, such as [[Populus|poplar]] or [[willow]].
{{anchor |adventitious root}}
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[[File:Adventitious roots on Odontonema aka Firespike.jpg|thumb|Roots forming above ground on a cutting of ''[[Odontonema]]'', also known as firespike]]
Adventitious rooting may be a stress-avoidance acclimation for some species, driven by such inputs as [[hypoxia (environmental)|hypoxia]]<ref>{{cite journal | url=https://doi.org/10.1007%2FBF00384595 | doi=10.1007/BF00384595 | title=Ethylene-promoted adventitious rooting and development of cortical air spaces (Aerenchyma) in roots may be adaptive responses to flooding in Zea mays L | year=1979 | last1=Drew | first1=M. C. | last2=Jackson | first2=M. B. | last3=Giffard | first3=S. | journal=Planta | volume=147 | issue=1 | pages=83–88 | pmid=24310899 | s2cid=7232582 | url-access=subscription }}</ref> or nutrient deficiency. Another ecologically important function of adventitious rooting is the vegetative reproduction of tree species such as ''[[Willow|Salix]]'' and ''[[Sequoia sempervirens|Sequoia]]'' in [[riparian]] settings.<ref>{{cite journal | url=https://www.jstor.org/pss/2952507 | jstor=2952507 | title=The Ecology of Interfaces: Riparian Zones | last1=Naiman | first1=Robert J. | last2=Decamps | first2=Henri | journal=Annual Review of Ecology and Systematics | year=1997 | volume=28 | pages=621–658 | doi=10.1146/annurev.ecolsys.28.1.621 | s2cid=86570563 | url-access=subscription }}</ref>
The ability of plant stems to form adventitious roots is utilised in commercial propagation by [[Cutting (plant)|cutting]]s. Understanding of the physiological mechanisms behind adventitious rooting has allowed some progress to be made in improving the rooting of cuttings by the application of synthetic auxins as rooting powders and by the use of selective basal wounding.<ref>{{cite journal | url=https://doi.org/10.1007%2Fs11627-999-0076-z | doi=10.1007/s11627-999-0076-z | title=Review the formation of adventitious roots: New concepts, new possibilities | year=1999 | last1=De Klerk | first1=Geert-Jan | last2=Van Der Krieken | first2=Wim | last3=De Jong | first3=Joke C. | journal=In Vitro Cellular & Developmental Biology - Plant | volume=35 | issue=3 | pages=189–199 | s2cid=44027145 | url-access=subscription }}</ref> Further progress can be made in future years by applying research into other regulatory mechanisms to commercial propagation and by the comparative analysis of molecular and ecophysiological control of adventitious rooting in 'hard to root' vs. 'easy to root' species.{{cn|date=June 2024}}
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==Leaf development==
The genetics behind leaf shape development in ''[[Arabidopsis thaliana]]'' has been broken down into three stages: The initiation of the [[leaf primordium]], the establishment of [[dorsiventrality]], and the development of a marginal [[meristem]]. Leaf primordium is initiated by the suppression of the genes and proteins of the class I ''[[Evolutionary history of plants|KNOX]]'' family (such as ''SHOOT APICAL MERISTEMLESS''). These class I KNOX proteins directly suppress [[gibberellin]] biosynthesis in the leaf primodium. Many genetic factors were found to be involved in the suppression of these genes in leaf primordia (such as ''ASYMMETRIC LEAVES1,'' ''BLADE-ON-PETIOLE1'', ''SAWTOOTH1'', etc.). Thus, with this suppression, the levels of gibberellin increase and leaf primorium initiates growth.{{cn|date=June 2024}}
==Flower development==
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