# Genetics/Botany

Botany is the scientific study of plant life. As a branch of biology, it is also called plant science(s) or plant biology. Botany covers a wide range of scientific disciplines that study plants including: structure, growth, reproduction, metabolism, development and diseases of plants, chemical properties and evolutionary relationships between different plant groups. The study of plants and botany began with tribal lore, used to identify edible, medicinal and poisonous plants, making botany one of the oldest sciences. From this ancient interest in plants, the scope of botany has increased to include the study of over 550,000 kinds or species of living organisms.
Traditionally, botany included the study of fungi, algae and viruses. Botany covers a wide range of scientific disciplines including structure, growth, reproduction, metabolism, morphogenesis, development, phytopathology, diseases, chemical properties, and evolutionary relationships among taxonomic groups. Botany began with early human efforts to identify edible, medicinal and poisonous plants, making it one of the oldest branches of science. There are about 410,000 species of Embryophytes (land plants) of which some 391,000 species are vascular plants (including ca 369,000 species of flowering plants), and ca 20,000 are bryophytes.
To propose a definition for say a plant whose flowers open at dawn on a warm day to be pollinated during the day time using the word "thing", "entity", "object", or "body" seems too general and is.

## Biology

On the right is a drawing of the archaean Haloquadratum walsbyi.
Biology is the study of living organisms, divided into many specialized fields that cover their morphology, physiology, anatomy, behavior, origin, and distribution. The study of biology is important in many ways. On the most basic level, one can satiate their curiosity on the mechanisms of life. One can also utilize biology within different closely related fields, such as agriculture, medicine, engineering and more. Biology solves problems, either tending to an illness, or promoting food growth, it is essential in our daily lives. By understanding the interaction of living organisms, it enables us to make most of the planet's resources and minimizing our imprint onto it, allowing us to be responsible caretakers of our home. Biology is also a basic subject in all primary and secondary education institutions, one may also seek to specialize themselves in the many branches of biology. Biology is a nigh endless journey of exploration and discovery, making its place as a natural science utmost deserving.
Def. the "study of all life or living matter" is called a biology.

## Colors

Cells contain chlorophyll a and b.
The magnesium center of chlorophyll uniquely defines the structure as a chlorophyll molecule. The porphyrin ring of bacteriochlorophyll is saturated, and lacking alternation of double and single bonds causing variation in absorption of light.
Chlorophyll a absorbs most energy from wavelengths of violet-blue and orange-red light. It also reflects green-yellow light, and as such contributes to the observed green color of most plants. This photosynthetic pigment is essential for photosynthesis in eukaryotes, cyanobacteria and prochlorophytes because of its role as primary electron donor in the electron transport chain. Chlorophyll a also transfers resonance energy in the antenna complex, ending in the reaction center where specific chlorophylls P680 and P700 are located.
* Structure of chlorophyll a molecule showing the long hydrocarbon tail |
Side chains attached to the chlorin ring characterize each type of chlorophyll molecule, and alter the absorption spectrum of light. For instance, the only difference between chlorophyll a and chlorophyll b is that chlorophyll b has an aldehyde instead of a methyl group at the C-7 position.
The systematic name for chlorophyll a is magnesium [methyl (3S,4S,21R)-14-ethyl-4,8,13,18-tetramethyl-20-oxo-3-(3-oxo-3-{[(2E,7R,11R)-3,7,11,15-tetramethyl-2-hexadecen-1-yl]oxy}propyl)-9-vinyl-21-phorbinecarboxylatato(2−)-κ$^2$N,N′].

## Theoretical botany

Def. the "scientific study of plants, ... [typically] those disciplines that involve the whole plant" is called botany.
Usage notes:
"The scientific definition of what organisms should be considered plants changed dramatically during the 20th century. Bacteria, algae, and fungi are no longer considered plants by those who study them. Many textbooks do not reflect the most current thinking on classification."

## Plants

The study of plants is vital because they underpin almost all animal life on Earth by generating a large proportion of the oxygen and food that provide humans and other organisms with aerobic respiration with the chemical energy they need to exist. Plants, algae and cyanobacteria are the major groups of organisms that carry out photosynthesis, a process that uses the energy of sunlight to convert water and carbon dioxide into sugars that can be used both as a source of chemical energy and of organic molecules that are used in the structural components of cells. As a by-product of photosynthesis, plants release oxygen into the atmosphere, a gas that is required by anaerobic organisms to carry out cellular respiration. In addition, they are influential in the global carbon cycle and water cycles and plant roots bind and stabilise soils, preventing soil erosion. Plants are crucial to the future of human society as they provide food, oxygen, medicine, and products for people, as well as creating and preserving soil.
Historically, all living things were classified as either animals or plants and botany covered the study of all organisms not considered animals. Botanists examine both the internal functions and processes within plant organelles, cells, tissues, whole plants, plant populations and plant communities. At each of these levels, a botanist may be concerned with the classification (taxonomy), phylogeny and evolution, structure (anatomy and morphology), or function (physiology) of plant life.
The strictest definition of "plant" includes only the "land plants" or embryophytes, such as seed plants (gymnosperms: Pinophyta, pines, and flowering plants) and the free-sporing cryptogams including ferns, Lycopodiopsida clubmosses, Marchantiophyta liverworts, hornworts and mosses. Embryophytes are multicellular eukaryotes descended from an ancestor that obtained its energy from sunlight by photosynthesis. They have life cycles with alternation of generations haploid and diploid phases. The sexual haploid phase of embryophytes, known as the gametophyte, nurtures the developing diploid embryo sporophyte within its tissues for at least part of its life, even in the seed plants, where the gametophyte itself is nurtured by its parent sporophyte. Other groups of organisms that were previously studied by botanists include bacteria (now studied in bacteriology), fungi (mycology) – including lichen-forming fungi (lichenology), non-chlorophyte algae (phycology), and viruses (virology). However, attention is still given to these groups by botanists, and fungi (including lichens) and photosynthetic protists are usually covered in introductory botany courses.
Palaeobotanists study ancient plants in the fossil record to provide information about the evolutionary history of plants. Cyanobacteria, the first oxygen-releasing photosynthetic organisms on Earth, are thought to have given rise to the ancestor of plants by entering into an endosymbiotic relationship with an early eukaryote, ultimately becoming the chloroplasts in plant cells. The new photosynthetic plants (along with their algal relatives) accelerated the rise in atmospheric oxygen started by the cyanobacteria, great oxygenation event, changing the ancient oxygen-free, reducing, atmosphere to one in which free oxygen has been abundant for more than 2 billion years.
Among the important botanical questions of the 21st century are the role of plants as primary producers in the global cycling of life's basic ingredients: energy, carbon, oxygen, nitrogen and water, and ways that our plant stewardship can help address the global environmental issues of resource management, conservation, human food security, biologically invasive organisms, carbon sequestration, climate change, and sustainability.
Def. an "organism of the kingdom Plantae; now specifically, a living organism of the Embryophyta (land plants) or of the Chlorophyta (green algae), a eukaryote that includes double-membraned chloroplasts in its cells containing chlorophyll a and b, or any organism closely related to such an organism" is called a plant.

## Agriculture

Agriculture is the science, art, or practice of farming, including cultivation of the soil for the growing of crops and the rearing of animals to provide food, wool, and other products.
At right are farm buildings with trees surrounded by fields on a fair weather day.
Def. "[t]he art or science of cultivating the ground, including the harvesting of crops, and the rearing and management of livestock; tillage; husbandry; farming" is called agriculture.

## Agronomy

Def. "[t]he science of utilizing plants, animals and soils for food, fuel, feed, and fiber and more" is called agronomy.
"Annual broadleaf weeds (17 species) were clearly the dominant group under all tillage treatments, compared with the perennials (6 species) and annual grassy (4 species) weeds."
"Regardless of year or treatment combination, values for each parameter (except ASI$_p$) were nearly always lower for the dominated relative to intermediate and dominant plant group(s). For all parameters but ASI$_p$, the application of either 165 or 330 kg N ha$^{-1}$ often decreased the dominant group/dominanted group mean ratio in both years for either plant density."
"In all, 75.6% of the trees fall into the dominant group which has only 12 species, far more than that of park and institutional forests (Table 2)."

## Angiosperms

Def. a "member of the plant group characterized by having ovules enclosed in an ovary" is called an angiosperm.
"Flowering plants, or angiosperms, are presently the most dominant group of terrestrial autotrophs."
From 1880 is the following: “The Plant life of this Period was of a very varied and luxuriant character, and the Angiosperms had now become the dominant group.”
"Today, with approximately 300,000 species distributed worldwide, the angiosperms are the dominant group of vascular plants in terrestrial ecosystems."

### Brassicales

A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a relatively small genome of approximately 135 megabase pairs (Mbp).
"The minimum DNA-binding elements are 6-bp CGCG box, (A/C/G)CGCG(C/G/T)."
"AtSR1 [Arabidopsis thaliana signal-responsive genes] targets the nucleus and specifically recognizes a novel 6-bp CGCG box (A/C/G)CGCG(G/T/C). The multiple CGCG cis-elements are found in promoters of genes such as those involved in ethylene signaling, abscisic acid signaling, and light signal perception. The DNA-binding domain in AtSR1 is located on the N-terminal 146 bp where all AtSR1-related proteins share high similarity but have no similarity to other known DNA-binding proteins. The calmodulin-binding nuclear proteins isolated from wounded leaves exhibit specific CGCG box DNA binding activities. These results suggest that the AtSR gene family encodes a family of calmodulin-binding/DNA-binding proteins involved in multiple signal transduction pathways in plants."
"Ca$^{2+}$-mediated signaling is involved in the transduction of physical signals such as temperature, wind, touch, light, and gravity; oxidative signals such as those arising from pathogen attacks; and hormone signals such as ethylene, abscisic acid (ABA),$^1$ gibberellins, and auxin (2-7). All these signals have been shown to trigger changes in amplitude or oscillation in cytosolic free Ca$^{2+}$ level. Recently, the signal-induced nuclear free calcium changes were also observed (8). Free Ca$^{2+}$ changes are sensed by a number of Ca$^{2+}$-binding proteins that usually contain a common structural motif, the “EF-hand,” a helix-loop-helix structure (9). One of the best characterized Ca$^{2+}$-binding proteins is calmodulin (CaM), a highly conserved and multifunctional regulatory protein in eukaryotes. Its regulatory activities are triggered by its ability to modulate the activity of a certain set of CaM-binding proteins after binding to Ca$^{2+}$, and thereby generating physiological responses to various stimuli (10-15)."
"The CaM-regulated basic helix-loop-helix family of transcription factors was reported in mammals, where CaM inhibits the protein-DNA interaction by competing with the DNA-binding domain in certain proteins (16)."
"cis-acting elements ACGCGG/CCGCGT were present in the promoter regions of about 130 genes (more than two copies) in Arabidopsis genome."
"The promoter regions are assumed to be within ∼1 kb upstream of the starting transcription site (for the known genes) or the first ATG (for the predicted genes). These genes are related to ethylene signaling (EIN3) and ABA signaling (a putative ABA responsive protein), light perception (phytochrome A, phyA), stress responsive such as the DNA repairing protein, heat shock protein, touch protein (TCH 4), and CaM-regulated ion channel. CaM genes (CaM2 andCaM3) and AtSR6 also contains CGCGcis-elements in their promoter regions."

### Poales

"The pyrimidine box is another promoter element that is observed in cereal GA-responsive promoters examined thus far (Huang et al., 1990). Mutations on the pyrimidine box caused the reduction of the GA induction with a lesser magnitude than those of GARE in the GA-treated aleurone (Gubler and Jacobsen, 1992; Rogers and Rogers, 1992). The pyrimidine box alone could not confer the hormone responsiveness to the minimal promoter of the cauliflower mosaic virus 35S (CaMV35S), suggesting accessory roles of the pyrimidine box on the transcription response to GA (Skriver et al., 1991)."
"[A]leurone proteins that recognized the pyrimidine box sequence [are] from barley (BPBF; Mena et al., 2002) and rice (Oryza sativa; OsDOF3; Washio, 2001)."
"A member of Dof proteins, prolamine box-binding factors PBF that were originally identified to be transcription factors regulating the expression of genes for stored proteins in developing seeds (Vicente-Carbajosa et al., 1997; Mena et al., 1998), BPBF and OsDOF3 are likely to be a pyrimidine box-binding protein in the germinated aleurone."
"OsDOF3, binding the pyrimidine box, affected the DNA binding of GAMYB to GARE".
"Functional promoter analysis using transgenic rice seeds has confirmed that the 5'-regulatory region extending from -232 (nucleotide position relative to the site for transcription initiation) to +31 is sufficient for hormonal regulation by GA (Itoh et al., 1995), along which are found the distal (Pyr-1, -312) and proximal pyrimidine boxes (Pyr-2, -214), GARE (-148), and three potential sites for the Dof binding (D-1, -191; D-2, -109; D-3, -78; [on the diagram in the GA responsive complexes section above]; Huang et al., 1990)."
"The upstream portion from the RAmy1A promoter (-380 to +27) had a stimulatory effect on the GA-induced expression of the reporter gene in transfected aleurone cells."
"The drastic loss of the GA induction associated with a mutation on GARE (M4) further verifies the importance of this motif in the GA-regulated expression of genes. Other mutations of the proximal pyrimidine box (M2) and one site for the Dof binding (M5) also reduced the GA-induced activities to 48% and 54% of the wild-type sequence, respectively, but the effects were not as marked as seen when GARE was mutated."
"Sequence analysis shows that the OsDof3 cDNA encodes a 371-amino acid polypeptide related to the PBF factors of cereal plants. The predicted amino acid sequence of OsDOF3 aligns well with those of maize (Zea mays; Vicente-Carbajosa et al., 1997), wheat (Triticum aestivum), and barley PBF proteins (Mena et al., 1998; [...]). The N-terminal sequence of OsDOF3 contains four Cys residues reminiscent of the Dof zinc finger and shows around 80% sequence identities with PBFs, whereas the C-terminal parts are divergent showing several insertions and deletions."
"Pentanucleotide sequence from the pyrimidine box (CTTTT; Huang et al., 1990) and D-3 (AAAAG) is capable of matching a favored substrate selected by in vitro DNA binding of maize Dof proteins (CTTTT or AAAAG; Yanagisawa and Schmidt, 1999). These results indicate preferential binding of OsDOF3 to two pyrimidine box and D-3 motifs in the RAmy1A promoter context."

## Archaeaology

"This path has attracted 'archaeaologists' with great tenacity and drive, impressive creativity and dynamic thinking, and a capacity to expand a mental comfort zone to broker remarkable observations, often in view of reluctant acceptance."
Def. the scientific study of the archaea is called archaeaology.
The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.
In the archaean from the Dead Sea imaged at the right, "We have completely fragmented their DNA. I mean we have completely destroyed it by bombarding it with [radiation]. And they can reassemble their entire chromosome and put it back into working order within several hours."

## Bacteriology

Def. the "scientific study of bacteria, especially in relation to disease and agriculture" is called bacteriology.

## Biochemistry

Biochemistry, sometimes called biological chemistry, is the study of chemical processes within, and relating to, living organisms.
Organic phosphates are important in biochemistry and biogeochemistry or ecology.
In biological systems, phosphorus is found as a free phosphate ion in solution and is called inorganic phosphate, to distinguish it from phosphates bound in various phosphate esters. Inorganic phosphate is generally denoted P$_i$ and at physiological (neutral) pH primarily consists of a mixture of HPO$_4$$^{2-}$ and H$_2$PO$_4$$^-$ ions.

## Bryology

Def. "[t]he study of bryophytes (non-vascular plants including mosses and liverworts)" is called bryology.
Bryophytes are an informal group consisting of three divisions of non-vascular land plants (embryophytes): the Marchantiophyta (liverworts), Anthocerotophyta (hornworts) and mosses. They are characteristically limited in size and prefer moist habitats although they can survive in drier environments. The bryophytes consist of about 20,000 plant species.
"The Lejeuneaceae, with about 1000 species in about 90 genera, is the largest family of liverworts (Marchantiophyta) (Wilson et al., 2007) and the most dominant group of the epiphyllous flora (Gradstein, 1997; Zhu & So, 2001)."
"Liverworts were the dominant group in all localities and habitats, accounting for about two-thirds of the species."
"Yet it is these leafy members which make up the dominant group of the Hepaticae, since they comprise more than 85 per cent of the total (8500 species)."

## Coals

Def. a "black rock formed from prehistoric plant remains, composed largely of carbon and burned as a fuel" is called a coal.
Def. the process by which plant remains become coal is called coalification.
The chart on the right is an idealized classification of coals from peat through anthracite using total water content (%), energy content (kJ/Kg), volatiles, and surface reflectivity.
Coal is formed if dead plant matter decays into peat and over millions of years the heat and pressure of deep burial converts the peat into coal.
Coalification starts with dead plant matter decaying into peat; then over millions of years the heat and pressure of deep burial causes the loss of water, methane and carbon dioxide and an increase in the proportion of carbon. Thus first lignite (also called "brown coal"), then sub-bituminous coal, bituminous coal, and lastly anthracite (also called "hard coal" or "black coal") may be formed.
Coal is known from Precambrian strata, which predate land plants—this coal is presumed to have originated from residues of algae.

## Dendrology

Def. "the study of trees and other woody plants" is called dendrology.
Notation: let the symbol ECG stand for ecological-coenotic groups.
"We have suggested assigning a dominant group in ground vegetation according to the regional probabilistic tables of correspondence between forest site index and dominant ECG (constructed for different dominant tree species)."
"In terms of trophism index the dominant group are plants of rich soils (279 species)."

## Dominant groups

"[I]n any limited country, the species which is most common, that is abound most in individuals, and the species which are most widely diffused within their country (and this is a different consideration from wide range, and to a certain extent from commonness), often give rise to varieties sufficiently well-marked to have been recorded in botanical works. Hence it is the most flourishing, or as they may be called, the dominant species -- those which range widely over the world, are the most diffused in their own country, and are the most numerous in individuals, -- which oftenest produce well-marked varieties, or, as I consider them, incipient species."

## Ecology

"It is no surprise that the data show the grass family (Poaceae) to be the dominant group, with nearly 200 exotic species in the western U.S. and 73 in the Sonoran Desert province. It is notable that species of Mediterranean origin are dominant in biomass in the Sonoran region (even though fewer in species than European or Eurasian weeds)."

## Economic botany

"We recognized three types of crusts based on texture and the dominant group of organism."
"The farmers consisted of four ethnic groups, and among the herders the Fulani people were the dominant group[.]"

## Embryophytology

The Embryophyta are a clade within the Phragmoplastophyta, a green algae group, as sister of the Zygnematophyceae/Mesotaeniaceae and consists of the Bryophytes and the Polysporangiophyta.

## Ethnobotany

Def. the "scientific study of the relationships between people and plants" is called ethnobotany.
"Our results showed that: (1) Dai people of Xishuangbanna used a wide range of wetland plants, including 46 families and 102 species, of which hygrophytes (helophytes) are the dominant group."
"Ethnocide is when a dominant political group attempts to purposely put an end to a people’s traditional way of life. Linguicide (linguistic genocide) is when such a dominant group tries to extinguish the language of a minority group, say by punishing anyone caught speaking it." "What about the “science” of these tiny undiscovered endangered languages? Does that kind of “primitive” ethnoscience have anything to teach us? The main examples that are quoted in the responses to this question have to do with ethnobotany and ethnomedicine."
"The coconut family is the dominant group of palms in South America, with specialized tribal and generic characters, and hundreds of wild species, but is not represented in the Old World tropics."

## Evolution

The chloroplasts of plants have a number of biochemical, structural and genetic similarities to cyanobacteria, (commonly but incorrectly known as "blue-green algae") and are thought to be derived from an ancient endosymbiotic relationship between an ancestral eukaryotic cell and a cyanobacterial resident.
The algae are a polyphyletic group and are placed in various divisions, some more closely related to plants than others. There are many differences between them in features such as cell wall composition, biochemistry, pigmentation, chloroplast structure and nutrient reserves. The algal division Charophyta, sister to the green algal division Chlorophyta, is considered to contain the ancestor of true plants. The Charophyte class Charophyceae and the land plant sub-kingdom Embryophyta together form the monophyletic group or clade Streptophytina.
Nonvascular land plants are embryophytes that lack the vascular tissues xylem and phloem. They include mosses, Marchantiophyta (liverworts) and (hornworts). Pteridophytic vascular plants with true xylem and phloem that reproduced by spores germinating into free-living gametophytes evolved during the Silurian period and diversified into several lineages during the late Silurian and early Devonian. Representatives of the lycopods have survived to the present day. By the end of the Devonian period, several groups, including the Lycopodiophyta (lycopods), Sphenophyllales (sphenophylls) and progymnosperms, had independently evolved "megaspory" – their spores were of two distinct sizes, larger megaspores and smaller microspores. Their reduced gametophytes developed from megaspores retained within the sporangium (spore-producing organs), (megasporangia) of the sporophyte, a condition known as endospory. Seeds consist of an endosporic megasporangium surrounded by one or two sheathing layers (integuments). The young sporophyte develops within the seed, which on germination splits to release it. The earliest known seed plants date from the latest Devonian Famennian stage. Following the evolution of the seed habit, Spermatophyte (seed plants) diversified, giving rise to a number of now-extinct groups, including Pteridospermatophyta (seed ferns), as well as the modern gymnosperms and angiosperms. Gymnosperms produce "naked seeds" not fully enclosed in an ovary; modern representatives include Pinophyta (conifers), cycads, Ginkgo, and Gnetophyta (Gnetales). Angiosperms produce seeds enclosed in a structure such as a Gynoecium (carpel) or an ovary. Ongoing research on the molecular phylogenetics of living plants appears to show that the angiosperms are a sister clade to the gymnosperms.

## Farming

"These three false-color images [on the right] demonstrate some of the applications of remote sensing in precision farming. The goal of precision farming is to improve farmers’ profits and harvest yields while reducing the negative impacts of farming on the environment that come from over-application of chemicals. The images were acquired by the Daedalus sensor aboard a NASA aircraft flying over the Maricopa Agricultural Center in Arizona."
"The top image shows the color variations determined by crop density (also referred to as #147;Normalized Difference Vegetation Index”, or NDVI), where dark blues and greens indicate lush vegetation and reds show areas of bare soil."
"The middle image is a map of water deficit, derived from the Daedalus’ reflectance and temperature measurements. Greens and blues indicate wet soil and reds are dry soil."
"The bottom image shows where crops are under serious stress, as is particularly the case in Fields 120 and 119 (indicated by red and yellow pixels). These fields were due to be irrigated the following day."

## Forestry

Def. the science or practice of planting, managing, and caring for forests is called forestry.
"Gap-opportunistic species were the dominant ecological group in low forest, bamboo forest, and high forest, while shade tolerant canopy species formed the dominant group in mature forest."
"Hydrophobic acids, which constitute the dominant group of dissolved organic compounds in the humic layer, are effectively retained as water percolates through E and B horizons of podzol profiles (Easthouse et al., 1992)."
"The opportunist functional group is the dominant group at low disturbance treatments and its relative abundance becomes suppressed as disturbance increases."
"Continuous cover forestry (CCF) is not a new idea in forest management but there has been renewed interest in it for the potential it has to meet the sustainability requirements which are part of the Rio/Helsinki process and certification. Broadly speaking CCF includes those silvicultural systems which involve continuous and uninterrupted maintenance of forest cover and which avoid clearcutting."

## Gardening

Def. "the process or action of cultivating of the soil particularly in" an "outdoor area containing one or more types of plants" is called gardening.

## Genetics

"The way in which these genes interact with the dominant group 2 genes has yet to be determined."
"From about 41 million ha represented (with a total of about 1,200 cultivars on the official list), about 145 cultivars (12%) belong to the dominant group (occupying at least 50% of the barley acreage)."
"Bacteria are the most dominant group of this diversity which produce a wide range of products of industrial significance."
Transposons or "jumping genes" were discovered by Barbara McClintock while she was studying maize.
Species boundaries in plants may be weaker than in animals, and cross species hybrids are often possible. A familiar example is peppermint, Mentha × piperita, a sterile hybrid between Mentha aquatica and spearmint, Mentha spicata. The many cultivated varieties of wheat are the result of multiple inter- and intra-species, specific crosses between wild species and their hybrids. Angiosperms with monoecious flowers often have self-incompatibility mechanisms that operate between the pollen and stigma so that the pollen either fails to reach the stigma or fails to germinate and produce male gametes. This is one of several methods used by plants to promote plant reproductive morphology (outcrossing). In many land plants the male and female gametes are produced by separate individuals. These species are said to be dioecious when referring to vascular plant sporophytes and dioicous when referring to bryophyte gametophytes.
Apomixis can also happen in a seed, producing a seed that contains an embryo genetically identical to the parent.
Both autopolyploid and allopolyploid plants can often reproduce normally, but may be unable to cross-breed successfully with the parent population because there is a mismatch in chromosome numbers. These plants that are reproductively isolated from the parent species but live within the same geographical area, may be sufficiently successful to form a new sympatric species. Some otherwise sterile plant polyploids can still reproduce vegetatively or by seed apomixis, forming clonal populations of identical individuals.
Chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants.

## Horticulture

Def. the "art or science of cultivating gardens" is called horticulture.
"The results reveal that a dominant group I rDNA lineage appears in these three provinces."
"Thus the NZ industry is one of the dominant group of apple exporters, which includes the EU, the USA, Chile, South Africa and Argentina."
"Alcohols, however, were the dominant group of volatiles present in each sample, and linalool was highest within each profile."

## Human nutrition

Virtually all staple foods come either directly from primary production by plants, or indirectly from animals that eat them. Plants and other photosynthetic organisms are at the base of most food chains because they use the energy from the sun and nutrients from the soil and atmosphere, converting them into a form that can be used by animals. This is what ecologists call the first trophic level. The modern forms of the major staple foods, such as maize, rice, wheat and other cereal grasses, Pulses or legumes, bananas and plantains, as well as flax and cotton grown for their fibres, are the outcome of prehistoric selection over thousands of years from among Neolithic founder crops, or wild ancestral plants with the most desirable characteristics.
Botanists study how plants produce food and how to increase yields, for example through plant breeding, making their work important to mankind's ability to feed the world and provide food security for future generations. Botanists also study weeds, which are a considerable problem in agriculture, and the biology and control of plant pathogens in agriculture and natural ecosystems. Ethnobotany is the study of the relationships between plants and people. When applied to the investigation of historical plant–people relationships ethnobotany may be referred to as archaeobotany or palaeoethnobotany. Some of the earliest plant-people relationships arose between the indigenous peoples of the Americas, including Canada, in identifying edible plants from inedible plants. This relationship the indigenous people had with plants was recorded by ethnobotanists.

## Lichenology

Def. "the scientific study of lichens" is called lichenology.
"Although free-living cyanobacteria are the dominant group in biological crusts covering the inselbergs, the number of cyanobacterial lichens is relatively high and their distribution is homogenous over long distances and macro-climatic gradients."
"Alectorioid lichens are the dominant group of epiphytic lichens in boreal forests."
"The dominant group of lichens in tropical rain forests are crustose microlichens, a highly diverse assemblage that lacks detailed taxonomic and ecological studies, among them the families Graphidaceae and Thelotremataceae (Wirth and Hale 1963, 1978; Hale 1974, 1978"

## Medicines

The pain killer aspirin is the acetyl ester of salicylic acid, originally isolated from the bark of willow trees, and a wide range of opiate analgesics (painkillers) like diamorphine (heroin) are obtained by chemical modification of morphine obtained from the opium poppy.
Popular stimulants come from plants, such as caffeine from coffee, tea and chocolate, and nicotine from tobacco. Most alcoholic beverages come from fermentation of carbohydrate-rich plant products such as barley (beer), rice (sake) and grapes (wine). Native Americans have used various plants as ways of treating illness or disease for thousands of years. This knowledge Native Americans have on plants has been recorded by enthnobotanists and then in turn has been used by pharmaceutical companies as a way of drug discovery.

## Mycology

Mycology is the branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicine (e.g., penicillin), food (e.g., beer, wine, cheese, edible mushrooms), and entheogens, as well as their dangers, such as poisoning or infection.
Species of the filamentous fungal genus Trichoderma are considered as one of the most important biological control agents as an alternative to chemical based products for effective crop diseases management.

### Saccharomycetales

Shown in the image on the right are the C box (3'-AGUAGU-5') and the D box (3'-AGUCUG-5'). Substituting T for U yields C box = 3'-AGTAGT-5' and D box = 3'-AGTCTG-5' in the transcription direction on the template strand.
"Members of the box C/D snoRNA family, which are the subject of the present report, possess characteristic sequence elements known as box C (UGAUGA) and box D (GUCUGA)."

## Paleobotany

Paleobotany is the study of plant or plant-like fossils.
The image at the right shows fronds impressed onto shale in a specimen on display at the Paläontologische Museum München. The fossil is from Scalby Ness, Scarborough, England.
Neuropteris, a fern, leaf impressions and fossils occur in bituminous coal such as in the image on the right. These coal seams and strata are dated to the Carboniferous period.
The Lepidodendrales, quillwort-like large tree-like plants from the Carboniferous also left fossils in bituminous coal as on the left.
Def. the "branch of paleontology that deals with the study of plant fossils" is called paleobotany.
"The groups could then be arranged from the dominant group (first rank) to the least common group (fifth rank)."
"The dominant group in the Palaeozoic microplankton is the Acritarcha."
"Pteridophyta is the second dominant group."
"The angiosperms are both the dominant group of land plants and by far the most important plants for human use."
"Statistical analyses indicate that the Phanerozoic history of vascular land plants (tracheophytes) may be interpreted in terms of the successive radiations of four major plant groups, each characterized by a common morphological and/or reproductive grade. Following initial invasion of the land, the diversification of each group coincides with a decline in species numbers of the previously dominant group."

## Palynology

Def. the "scientific study of spores, pollen and particulate organic matter in rocks" is called palynology.
Although regarded as a separate field of its own, in a real sense palynology is the micropaleontological equivalent of paleobotany that involves the study of fossil pollen and spores.
The image at right contains a spore tetrad (in green) of genus Scylaspora and trilete spores (blue, ~30-35μm diameter) from a late Silurian sporangium (Burgsvik beds, Sweden).
"A palynological study on Miocene–Pleistocene sediments exposed at Surai Khola in central Nepal yields new information on vegetation and climate change over the last ∼11.5 Ma. [...] Pollen assemblages from the Surai Khola section suggest complex vegetation changes, of which the shift to C$_4$ grass dominance was only one. [...] Grassland taxa (Gramineae and others) characterize this zone as the dominant group."
The "palynological record from two shallow core holes (6611/09-U-01 and -02) from the Trøndelag Platform offshore mid-Norway [consist] of 750 m of Upper Permian and Lower Triassic sediments. The relatively homogeneous assemblages recovered from the Upper Permian deposits are dominated by gymnosperm pollen, mainly pteridosperms. At the base of the Griesbachian, numerous spore species appear in the record, leading to an increased diversity. The change at this boundary is also marked by the massive reduction of one group of pteridosperm pollen (Vittatina). Together with other typical Permian elements (e.g., Lueckisporites virkkiae), this group is rare but consistently present in the lower part of the Griesbachian, and it gradually disappears in its upper part. The distribution of other groups such as taeniate and non-taeniate bisaccate gymnosperm pollen (pteridosperms and conifers) shows no significant change across the boundary, whereas spores and other gymnosperm pollen increase in diversity and abundance. These changes coincide with the formational change between the Schuchert Dal Formation (Upper Permian) and the Wordie Creek Formation (Griesbachian) equivalents."
"In contrast to the common claim that marine and terrestrial biota both suffered a mass extinction related to the Permian-Triassic boundary event, the studied material from the Norwegian midlatitudinal sites shows no evidence for destruction of plant ecosystems. The presence of diverse microfloras of Griesbachian age supports the idea that the climate in this area allowed most plants to survive the Permian-Triassic boundary event."
"According to the data from mid-Norway as well as the previous records from East Greenland and the Barents Shelf, the widely accepted image of the lowermost Triassic flora, after which herbaceous lycopsids invaded the devastated terrestrial ecosystems and became the globally dominant group, has to be revised."

## Peats

Def. soil "formed of dead but not fully decayed plants found in bog areas" is called peat.
Def. a brown, soil-like material characteristic of boggy, acid ground, consisting of partly decomposed vegetable matter, is called a peat.

## Phycology

Def. the "scientific study of algae" is called phycology.

## Phytochemistry

Phytochemistry is a branch of plant biochemistry primarily concerned with the chemical substances produced by plants during secondary metabolism.
Def. the "scientific study of the chemicals found in plants" or the "collection of chemicals and chemical processes found in a particular plant" is called phytochemistry.
The broadest definition of natural product is anything that is produced by life.
"Natural products include a large and diverse group of substances from a variety of sources. They are produced by marine organisms, bacteria, fungi, and plants. The term encompasses complex extracts from these producers, but also the isolated compounds derived from those extracts. It also includes vitamins, minerals and probiotics." and includes the likes of biotic materials (e.g. wood, silk), bio-based materials (e.g. bioplastics, cornstarch), bodily fluids (e.g. milk, plant exudates), and other natural materials (e.g. soil, coal). A more restrictive definition of a natural product is an organic compound that is synthesized by a living organism.
"Natural products are organic compounds that are formed by living systems."
Natural products may be classified according to their biological function, biosynthetic pathway, or source. One estimate of the number of natural product molecules is about 326,000.

### Alcohols

Def. "any of a class of organic compounds (such as ethanol) containing a hydroxyl functional group (-OH)" is called an alcohol.

### Alkaloids

Def. any "of many organic (often heterocyclic) bases that occur in nature and often have medicinal properties" is called an alkaloid.

### Oils

Def. "liquid fat" or "petroleum-based liquid used as fuel or lubricant" is called an oil.
Def. "a volatile oil, used to make perfumes and flavourings, especially one having the characteristic odour of the plant from which it is obtained" is called an essential oil.

### Polyphenols

Def. "any of a large class of organic compounds, of plant origin, having more than one phenol group; they tend to be colourful and to have antioxidant properties" is called a polyphenol.

### Terpenoids

Def. "a very large class of naturally occurring and synthetic organic compounds formally derived from the hydrocarbon isoprene; they include many volatile compounds used in perfume and food flavours, turpentine, the steroids, the carotene pigments and rubber" is called a terpenoid.
| Terpenoids | Analogue terpenes | Number of isoprene units | Number of carbon atoms | General formula | Examples |
| Hemiterpenoids | Isoprene | 1 | 5 | C$_5$H$_8$ | Dimethylallyl pyrophosphate (DMAPP), isopentenyl pyrophosphate, isoprenol, isovaleramide, isovaleric acid, (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), prenol |
| Monoterpenoids | Monoterpenes | 2 | 10 | C$_{10}$H$_{16}$ | Bornyl acetate, camphor, carvone, citral, citronellal, citronellol, geraniol, eucalyptol, hinokitiol, iridoids, linalool, menthol, thymol |
| Sesquiterpenoids | Sesquiterpenes | 3 | 15 | C$_{15}$H$_{24}$ | Farnesol, geosmin, humulone |
| Diterpenoids | Diterpenes | 4 | 20 | C$_{20}$H$_{32}$ | Abietic acid, ginkgolides, paclitaxel, retinol, salvinorin A, sclareol, steviol |
| Sesterterpenoids | Sesterterpenes | 5 | 25 | C$_{25}$H$_{40}$ | Andrastin A, manoalide |
| Triterpenoids | Triterpenes | 6 | 30 | C$_{30}$H$_{48}$ | Amyrin, betulinic acid, limonoids, oleanolic acid, sterols, squalene, ursolic acid |
| Tetraterpenoids | Tetraterpenes | 8 | 40 | C$_{40}$H$_{64}$ | Carotenoids |
| Polyterpenoid | Polyterpenes | >8 | >40 | (C$_5$H$_8$)$_n$ | Gutta-percha, natural rubber |

### Vitamins

Def. any "of a specific group of organic compounds essential in small quantities for healthy human growth, metabolism, development, and body function; found in minute amounts in plant and animal foods or sometimes produced synthetically" is called a vitamin.

### Waxes

Def. any "oily, water-resistant, [solid or semisolid] substance; normally long-chain hydrocarbons, alcohols or esters" is called a wax.

## Phytomorphology

Plant morphology is the study of their external form.
Phytomorphology is the study of the physical form and external structure of plants.
Plant morphology "represents a study of the development, form, and [external] structure of plants, and, by implication, an attempt to interpret these on the basis of similarity of plan and origin."

## Phytotomy

Plant anatomy is the study of the structure of plant cells and tissues.
Def. the "art of studying the different parts of any organized body, to discover their situation, structure, and economy" is called anatomy, or for plants, phytotomy.
"To date about 33 species belonging to 17 genera of fossil wood have been recorded from the Jurassic in China (Fig. 3, Table 1). They are mainly preserved as silicified type, which is predominant group of fossil preservation."
"Coniferales: this is the dominant fossil wood group in the Jurassic of China ranging in age from Early to Late Jurassic."
"Growth rings are well developed in these woods with wider early wood and narrow late wood, normally 1-2 tracheids wide and maximum 5-6 tracheids. These anatomical features may imply that the climate in western Liaoning was warm and humid during the Early Jurassic with seasonal variations: long spring and summer seasons and a shorter winter season. The megaplant assemblages in the Beipiao Formation (Zhang and Zheng, 1987) show that ferns are the dominant group in the assemblages, with diverse Cladophlebis foliages of larger fronds. The ferns were growing under the canopy of an arborescent forest dominated by conifers and ginkgoaleans, which are tolerant of a warm and humid climate. The fossil woods in the Beipiao Formation were dominated by conifers, which are the coal-forming plants during the Early Jurassic."

## Soils

"In soil, estimates are that 80 to 99% of the microorganisms remain unidentified (1)."
"The soil at the Arlington site is a Plano silt-loam. The 20-cm-deep A horizon is a silt-loam and contains 4.4% organic matter. The loess mantel is >1.25 m deep. Four 2.5-cm-diameter soil cores were taken from the top 10 cm of a clover-grass pasture at the Arlington Agricultural Research Station. The soil samples were immediately placed on dry ice, mixed, and then stored at -70°C prior to DNA extraction. Soil analysis was done by the Soil Testing Laboratory of the University of Wisconsin—Madison as described by Schulte et al. (40). The soil sample contained 13% sand, 70% silt, 17% clay, 4.4% organic matter, 0.3% total N, 400 ppm of K$^+$, and 98 ppm of P. The soil pH was 6.5. The site is well drained, with groundwater more than 25 m below the surface. Two-thirds of the 79-cm annual rainfall occurs from April to October. The site has an average of 165 frost-free days."
In the image on the right, A, B, and C represent the soil profile: A is the topsoil; B is a regolith; C is a saprolite, a less-weathered regolith; the bottom-most layer represents the bedrock.

## Taxonomy

Scientific classification in botany is a method by which botanists group and categorize organisms by biological type, such as genus or species. Biological classification is a form of scientific taxonomy. Modern taxonomy is rooted in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings have since been revised to improve consistency with the Darwinian principle of common descent. While scientists do not always agree on how to classify organisms, molecular phylogenetics, which uses DNA sequences as data, has driven many recent revisions along more efficient, evolutionary lines and is likely to continue to do so. Botanical classification belongs to the science of plant systematics. The dominant classification system is called the Linnaean taxonomy. It includes ranks and binomial nomenclature. The classification, taxonomy, and nomenclature of botanical organisms is administered by the International Code of Nomenclature for algae, fungi, and plants (ICN). Bold added.
Superregnum: Eukaryota Regnum: Plantae Divisiones (8): "Algae" (first four)
* Charophyta
* Chlorophyta
* Glaucophyta
* Rhodophyta
* Anthocerotophyta
* Bryophyta
* Marchantiophyta
* Tracheophyta

## Virology

Virology is the study of viruses – submicroscopic, parasitic particles of genetic material contained in a protein coat – and virus-like agents.
Def. the "branch of microbiology that deals with the study of viruses and viral diseases" is called virology.

## Hypotheses

* Plant classification before genomics may not agree with classification after application of genomics.