Plant Genetics

Read this article in Spanish.

Featured Image: Forest Fungi Project (FFP) Lab, UW-Madison.
Uses passive analytical methods known as DNA barcoding to identify plants and fungi in volunteer collected samples for mapping interactions between trees, surrounding plants and mycorrhizal fungi.

https://forestfungi.russell.wisc.edu

Questions

Many have attempted to understand the ultimate composition of reality, or what stuff is really made out of. Ancient stories depicted humans as being constructed from clay or earth [1], other stories depicted our minds formed from condensed air [2], and ancient thinkers like Democritus postulated if we kept breaking things into pieces we would reach an indivisible particle, the atom [3].

Today’s model of the atom includes the configurations of electron clouds or orbitals, areas where there is greater than 10% probability of finding the super-positioned particle. The areas of lesser probability are of greater energy potential. The nucleus located at the center of the X-Y-Z axis consists of protons and neutrons.

Wikimedia Commons [1a]

Unlike objects like rocks and stones, life replicates mysteriously. One property of life which bewildered many gardeners and farmers was inheritance. The questions they asked were: ” How or why do the offspring of living beings look and function similar to their parents?” “How do the offspring of living beings become different than their parents?”

Before they knew about genetics, humans were breeding plants and animals, and seeing patterns in their appearances across generations and amongst populations. Characteristics like flower color, growth habit, and fruit size are known as traits.

Since fruit/vegetables don’t preserve well for archeologists, horticulturalists rely on depictions of fruit in art to compare changes in appearance[4]. A 1600’s depiction of watermelon reveals greater numbers of locules [5] and carpels which increases the mass of the rind or mesocarp [6][7].

Wikimieda Commons [2a]
Watermelons with thin rinds, internal vein-like structures, black seeds, and typical decorative serving styles depicted in Frida Kahlo’s last painting.

Text in center could be translated as:
“Long live life, Frida Kahlo, Coyoacán, 1954, México”
Frida Kahlo, 1954,

Google Arts & Culture [3a]

Nature

Many apple cultivars (cultivated variety) originate from randomly sexually produced specimens or chance seedlings [8]. However, most gardeners prefer to graft scions of their favorite fruit to the rootstock of more resilient less-tasty apple trees. By grafting their favorite cultivar, gardeners save time and preserve their favorite genetics [9].

Tree of 40 Fruit, an art installation by arborist Ronald Feldman, takes advantage of the graft compatibility between many species within the genus Prunus (ex: apricots, plums, peaches, cherries, etc.. ). Branches from each species are grafted together as seen by their varying flower colors. Not to be confused with natural mutations called bud sports.

Sam Van Aken.
Wikimedia Commons. [4a]
The 2011 harvest of the Tree of 40 Fruit demonstrates the diversity of stone fruits produced by each scion.

Sam Van Aken.
Wikimedia Commons. [5a]

Although there are many oaks across Europe and North America, an oak tree species in a swampy area in the hardier zones of North America will have uniquely adapted genetics, which make it more suitable to live in those conditions than any other oak. One example is the Swamp White Oak (Quercus bicolor) [10].

Nurture

Drip irrigation line provides small consistent amounts of water directly to this immature hops (Humulus lupulus). Unlike peas (Pisum sativum), which use tendrils to climb like grapevine (Vitis spp.), hops will twine up this two-string trellis by stem elongation [11].

USDA, 2004,
Wikimedia Commons [6a]

In a garden, we can dedicate our patience, our intellect and our attention to plants so they grow optimally.

The environment and interaction between plants and other organisms can control the outcome of its growth. Plants introduced from a different region can become invasive after it alters the soil microbiome to its favor [12][13]. Other plants can release allelopathic chemicals disrupting the life functions of certain plants around them [14].

These are all situations where the environment is the causal agent in determining the growth success of plants and not their genetics.

Inheritance

Before the concept of the gene and the discovery of DNA[15][16][17][18], humans slowly altered the characteristics of other organisms wittingly and unwittingly. Each generation of organisms inherited traits from the parent generation. During sexual reproduction traits are mixed. Therefore the patterns of inheritance can be complex and not as straightforward as a continuation of traits seen in clones or propagules in plants. Many other processes can influence inheritance patterns, which will be covered later in this article.

left: Dominant-recessive inheritance pattern, middle: intermediate, right: incomplete dominance.

Sciencia58.
Wikimedia Commons [7a]

Gregor Mendel, an Austrian monk, conducted thorough experiments showing how peas and other plants change when hybridized [19][20]. His research discovered the difference between dominant traits and recessive traits. His research showed how the ratio of traits in a generation depends on the configuration of traits in the parents and their dominance.

His research on the basic patterns of inheritance in peas was later rediscovered by scientists and has become fundamental in the field of genetics [21]. However, many scientists and breeders existed before him. We find many examples of breeders discussing the nature of inheritance in European literature. These writers between 1600s-1800s focused mostly on the breeding of cows, sheep, and dogs into new breeds through artificial selection [22].

Selection is a term used to describe how the environment places selective pressure on traits. For example, the camouflaged animals will survive and pass on their traits, but the colorful animals are spotted by predators and eaten. Plants with a waxy coating will survive water-stress better than the ones with an exposed epidermal layer on leaves, stems or flowers, and will then reproduce.

Artificial selection is when selection is guided by conscious intervention. Humans can force two organisms to procreate, or prevent organisms from procreating. Artificial selection changes the traits available to the next generation’s population.

These are simplified examples. In nature, traits are transient features of life. Similar traits can appear in two unrelated events and far away places, or new traits can appear seemingly out of nowhere.

The practice of artificial selection is ancient and was a major factor in designating regions as agricultural centers, like Mesopotamia, Indus Valley and Meso-America. Curiously, today some date palm farmers will say a prayer before artificially pollinating the trees, since they see it as an interference with God’s will.

In ancient Egypt, where gardening and farming was common, they ate sweet watermelon like we do today. Hieroglyphs show watermelon among other fruit in a platter and watermelon seeds have been found preserved [23]. Modern studies show how today’s watermelon is most related to other species of melon, which are bitter [24]. Scientists utilized modern techniques to show what mutations could have proliferated after artificial selection [25]. Scientists are also using these comparisons to solve the location of the watermelon’s ancestors, which are most similar to current populations in West Africa and near-east Africa [26].

Smaller watermelon cultivar is capable of hanging from its trellis, a cultivation technique in Japan.

MakinoKoji, Jun 6, 2021.
Wikimedia Commons [8a]

Genes

After people became interested in breeding and inheritance, they wondered, “How can we describe the process in a materialistic way?”. “What substance is traveling from the older generations to the newer generations?”

The word ‘gene’ stems from the Greek roots of the word ‘generation’, γενεά [27]. It is thought to have been first used in its modern context by the Danish botanist Wilhelm Ludvig Johannsen in 1909, who wrote the word in German, das Gen [28].

Genes were until the 1950’s only an idea. In the 1950’s scientists would begin to discover the cellular mechanisms responsible for storing instructions for the next generation.

Despite not knowing what genes truly were, the idea of the gene caused terrifying changes in our society. People became obsessed with controlling the inherited traits of our society.

Genetic determinism is the view, still commonly held, that genes are the material reason for differences in complex behavior in humans such as personality traits, abilities, addictions, behavior, intelligence and many other complex traits.

Eugenics (lit. true genes) and its followers, eugenicists, sought to find the reasons why genetic disorders exist and promote the success of the best genes in humanity. Eugenics has received scholarly criticism since its inception and has grown to become obscure [29].

Eugenicists have condoned the unethical treatment of people, as if their genes were the primary cause of their dysfunction. This has included people who do not look nor behave the way they want to. Although genetic disorders exist, they’ve promoted the idea of guiding society towards an optimal gene pool and target marginalized groups of people. They use their authority to justify their sensitivities, and normalize abuse and murder.

Left: Logo from 2nd International Eugenics Congress in 1921 reads: Eugenics is the self direction of human evolution.
Roots have written on them:
Anatomy, Physiology, Biology, Genetics, Psychology, Anthropometry, History, Geology, Archeology, Anthropology, Ethnology, Geography, Law, Statistics, Politics, Economics, Biography, Genealogy, Sociology, Education, Religion, Psychiatry, Surgery, & Medicine.
Below the roots: Like a tree eugenics draws its materials from many sources and organizes them into an harmonious entity.

Middle: International Hygiene Exhibition in Dresden, Germany, 1911

Right: Massachussets Dept. of Mental Diseases Exhibits Pictures of 50 Criminal Brains, 1920

Top speculative minds:
Madison Grant (1865–1937),
Francis Galton (18221911),
Charles Davenport (18661944).
Wikimedia Commons [9a]
“Also in Merseburg
Crimes against the sick and disabled. People
sterilized, medical abuse,
starved, murdered.
1940-1945

‘Stumbling doorstep’, a larger modification the ‘stumbling blocks’ used to commemorate the locations of deported Jewish people and other minorities during the Nazi Regime in Germany, who were murdered on the pretense of these ideas. The earliest atrocities by the regime, Action T4 (Tiergartenstraße 4), were inspired by eugenicists in the US, and developed by leading German doctors [30].

Stadtstreicher54,
Wikimedia Commons [10a]
Photos from Treblinka Extermination Camp, Poland, 19421943.
Jewish people were deported from the overcrowded and disease afflicted Warsaw Ghetto [31], where they were originally segregated by the German-occupation government (1940). Camp supervised by German doctors.

All over Europe and North Africa there were a total of 980 camps for slave labor, prisons and detention centers, exterminations and other uses [32][33]. All were under the authority of a government driven by eugenicist policies.

Wikimedia Commons [11a]

All of this occurred before we knew everything we know now about the cell.

After we review the mechanisms behind inheritance, we will revisit the gene and focus on how plant genetics helps us discover the ancient secrets of the world.

The Organelles

The most fundamental difference occurs in the cells, where differences emerge to create what we see on the outside. The greatest distinction is between prokaryotes[34], without a nucleus, and eukaryotes, with a nucleus. Prokaryotes are often unicellular and are microorganisms. We will focus on macroscopic eukaryotes.

The journey of emergent life:
(1) Nuclear envelope of the nucleus protects the nuclear DNA (nDNA) inside chromatin and other stuff.

(2) Nuclear pore, where gene products leave.

(5) Ribosomes in Rough Endoplasmic Reticulum (ER) and free ribosomes within the cytoplasm (white background) translate RNA into amino acids (building block of proteins).

Large black arrow shows the generalized trend of the simplest to most complex molecules, an emergent property of life.

Magnus Manske,
Wikimedia Commons [12a].

Not all eukaryotic cells are the same. Animal cells all share fundamental characteristics, despite whether they belong to a flea or an elephant. Animal cells are different than plant cells. For example, animal cells are covered by a membrane, whereas plant cells are covered by a more rigid cell wall. Plants and some other microbes have chloroplasts, whereas most animals don’t. Using sunlight, the chloroplast turns gases and water into energy-carrying molecules. A chloroplast is a type of plastid.

Both animal and plant cells have mitochondria inside of them, which help generate molecules used by the cells to store and transfer energy, including many other functions [35].

In plants, the nucleus, mitochondria, and plastids all have nucleic acids, which are the beginning step for protein production and creating more nucleic acid. Nucleic acid is a class of organic molecules. The two main nucleic acids are Deoxyribonucleic acid or DNA, and Ribonucleic acid or RNA.

Immuno-electron microscopic image shows Mitochondrial DNA or mtDNA labeled with gold (Au) infused Anti-DNA antibodies [36] seen as black dots near the edge of the mitochondrion in the microscopic image.

Iborra, FJ. Kumura, H. Cook, PR.
Wikimedia Commons [13a]
A higher magnification shows gold-filled mtDNA, the veiny structures are the remnants of the extracted cytoplasm.

Iborra, FJ. Kumura, H. Cook, PR.
Wikimedia Commons[13a]
Types of plastids, organelles unique to plants with their own circular DNA,

Mariana Ruiz Villareal,
Wikimedia Commons [14a]

The Chemistry and Structure

DNA’s infamous helical structure: nitrogenous bases (inside, blue), nucleoside (green), phosphate group (red/orange),

Richard Wheeler (Zephyris),
Wikimedia Commons [15a]

Deoxyribonucleic acid (DNA) is called an acid, because of the way the smallest atom, Hydrogen (H), is distributed around its molecule [37]. When paired with an electronegative atom like Oxygen (O), the electrons (e) from H will be attracted to the electronegative atom and will allow the proton (H+) to interact with other particles. H+ is also known as a Hydrogen ion.

Traditionally, ions dissolve in solutions like salt (NaCl) in water (H2O). The Na+ cation and the Cl anion will float around in the water until they interact with other strong inversely charged particles. H has so few electrons, and the smallest quantity of protons in its nucleus, it quickly and easily interacts with particles. For this reason, H ions dissolved in water (common occurrence) are known as H3O+. Hydrogen plays an important role in organic chemistry.

A skeletal formula[38] of the chemical components within nucleic acids show how extra structural changes, like Nitrogen with the Carbon rings (lines without letters), different nitrogenous bases, and the asymmetry of the molecules causes the helical shape,

Boris, Wikimedia Commons [16a]

When all of the DNA of a species is sequenced, the genome size is measure in base pairs (bp). Base pairs are the two bonded Purine and Pyrimidine bases. The sequence of bases is often called the nucleotide sequence.

Adenine (A) shares two Hydrogen-bonds with Thymine (T) to form one type of DNA base pair. Guanine (G) shares three H-bonds with Cytosine (C) for the other DNA base pair [39]. One strand is always mirroring the other strand’s chemical structure with its corresponding base.

Ribonucleic acid (RNA) has a different carbohydrate pentose structure and forms three-H bonds between A and Uracil (U), instead of T. The nucleotide sequence of RNA does not contain a T.

DNA nucleosides consists of gradations of Phosphorous (P) bonds.

The sequence of nucleotides are the building instructions for a sequence of amino acids. Amino acids form into chains or polymers called polypeptides [40]. Peptides are the building blocks of proteins and are defined by their peptide bonds (carboxyl group + amino group).

Proteins are a large class of complex molecules with 4 levels of structure:

ClassificationAbbv.Description
Primarysequence of amino acids known as a peptide
Secondaryα-helices and β-sheet geometrical structures or polypeptides
Tertiaryfolds into segments called domains
Quaternaryfunctional groups called sub-units
The structure of proteins [41][42][43].

Proteins have many forms and preform many functions, such as tissues and enzymes. Enzymes assist or catalyze biochemical reactions [44].

1° sequence of amino acids,
2° α-helices and β-sheet geometrical structures,
3° folds created by disulphide bridges,
4° functional groups called sub-units.

Thomas Shafee, CKRobinson & Hstuhlma.
Wikimedia Commons. [17a]

DNA is coiled around proteins called histones and into strands called chromatin. Long strands of chromatin float around the nucleus.

Replication

DNA must replicate whenever a cell divides for mitosis (growth replication) or meiosis (preparation for reproductive fusion). Before replication, chromatin condenses into a larger structure, the chromosome, in order to organize itself. This is part of the cell cycle.

A portion of a diagram showing how the helical DNA coils around protein structures or histones, which then condense during the process of cell replication into the popular X-like shape or submetacentric duplicated chromosome.

KES47, Wikimedia Commons [18a]

At first the chromosome is a single rod-like structure divided vertically into two segments. The X or Y chromosomes are the shapes of duplicated chromosomes [45] scientists observe in karyotype tests or karyograms. In this phase of the cell cycle, Metaphase, the chromosome duplicates but remains attached to the central point, the centromere. Even though most of it is duplicated, the entire structure is still referred to as the chromosome, whereas the duplicated parts are known as sister chromatids. Mitochondrial DNA and plastid DNA form into circular chromosomes.

Fluorescent microscopy series of dividing cell shows the condensation of genetic material before mitosis, asexual cell reproduction used by plants, primarily for growth. Alain Herzog & Jamani Caillet. Wikimedia Commons [19a]

One enzyme, helicase, unravels the strands by flattening the helical structure and another one, primase, generates a small bit of RNA to indicate the starting point to the other builder enzyme, DNA polymerase.

Skeletal formula of the ends of a double stranded nucleic acid (DNA, since Adenine is present). A diagram of a nucleotide shows why the ends of each strand has a 5′ (five prime) and 3′ (three prime) end. Arrows indicate the direction replication enzymes (polymerase) travel after the DNA is unwound by unwinding enzymes (helicase).

Madeleine Price Ball,
Wikimedia Commons [20a]

Strands are oriented based on the configuration of their ends: 5′ and 3′ (Read: Five prime and three prime). Because of these mechanics, strands are always read from 3′ to 5′ and replicated from 5′ to 3′. For this reason, the lagging strand unzips in the opposite direction and must replicate upstream in backwards intervals. Enzymes later fuse these fragments.

Diagram shows semi-discontinous replication of DNA on one half of the origin of replication. RNA Primers attach to the initiation site of the DNA strand.
Replication is continuous for the 3′-5′ strand in the direction of the unwinding (Leading strand, diagram: left side, up. not shown: right side, down).
In the Lagging Strand (diagram: left side, up. not shown: right side, down) replication is discontinuous. Pieces of DNA (Okazaki fragments) replicate on the 3′-5′ side going away from the unwinding. These are fused together by enzyme DNA Ligase.

César Jiménez Benito,
Wikimedia Commons [21a].
Diagram shows how both sides of the origin of replication work. The tan box shows how the one double-stranded nucleic acid and replicated strands eventually form two double-stranded nucleic acid molecules. [PRO]
Two diagrams of mtDNA show a simplistic depiction of condensed mtDNA and its replication. Plant’s Chloroplast DNA and mtDNA resembles the DNA in bacteria.

Catherinea228 & National Human Genome Research Institute.
Wikimedia Commons [22a]

Mitosis

Phases of mitosis. Not shown: Interphase – the phase where chromosomes are uncondensed. Shown: Prophase, Metaphase, Anaphase, Telophase and cytokinesis.

Originally from LadyofHats. Oct 7, 2020.
Wikimedia Commons [23a]
Stages of cell cycle. Interphase consists of stages G1, S, and G2. At M stage, cell is at Prophase.

Simon Caulton. Aug 14, 2013.
Wikimedia Commons [24a]
Mitosis in Onion (Allium sepa) root cells. Cell in center is in Anaphase, whereas most other cells are in Interphase.

Natalierussell77.
Wikimedia Commons [25a]

Meiosis

Phases of meiosis.

Originally from Xtabay. Sep 5, 2023.
Wikimedia Commons [26a]
Meiosis in Lily (Lillum) microgametophyte. Pollen mother cell is in Anaphase II.

Josef Reischig.
Wikimieda Commons [27a] (www.mantis.cz/mikrofotografie)

During meiosis, the coiled chromosome undergoes an extra division so there’s half of the normal information from potentially two different sources. During the first half of this extra division before fusion, the information from the parents of the organism can recombine or cross-over when the chromosomes are close to each other. Genetic recombination occurs during Meiosis I. The final product of meiosis is the production of a gamete. Gametes from two individuals fuse to form the zygote.

Diagram simplifies a plant’s life cycle and stages of ploidy, or the number of chromosome copies. Notice how meiosis divides genetic information, which prepares it for fusion. The bodies of mosses and many other non-vascular plants are gametophytes (See animation of moss cells). Where as, vascular land plants are enlarged and complex sporophytes.

Ehamberg, Wikimedia Commons [28a]
An animated montage of a moss, Plagiomnium affine, and its gametophytic leaves[46] in order of increasing magnification. Last photograph shows the chloroplasts within its haploid cells,

HermannSchachner & Kristian Peters,
Wikimedia Commons [29a]
Diagram shows more nuanced system featured in land plants [47]. See more.

Peter Coxhead.
Wikimedia Commons.[30a]

The abbreviations for haploid (1n) and diploid (2n), and so on, are used to describe their ploidy: the multiples of the number of chromosomes within a species’ cells . Some plants like mosses, liverworts and hornworts have most of their plant biomass dedicated to growing 1n cells. The sporophyte, the spore producing structures, are 2n. Most other terrestrial plants are the reverse of non-vascular plants. Most terrestrial plant bodies are composed of two or more copies of the chromosome number (≥ 2n), whereas the gametophyte (1n) is small.

The reduction of the gametophyte in plant taxa.

Translated and edited. March 17, 2021. MarceloTeles.
Wikimedia Commons [31a]

Botanists speculate that evolution of land plants favored the diversification of sporophyte structures into more complex bodies with vascular systems and other survival mechanisms. In mosses, the plant doesn’t mind spending its resources growing most of its tissues ready for fusion. In land plants, this process has been optimized. Angiosperm gametophytes have become between 2 and 8 cells large: pollen and the embryo sac.

Wikimedia Commons [32a]
Seedless watermelons *work in progress*,

Wikimedia Commons [33a]

For example, seedless watermelons are a cross between a 4n mutant cultivar and a normal 2n cultivar, which produces a 3n infertile cultivar. The cells are unable to divide reproductively which results in an ovary with no seeds. Therefore, these are more expensive because farmers must purchase seed from breeders who are constantly hybridizing the 4n and 2n watermelons.

One genetic signature of domestication by humans is when plants are found to have greater ploidy. In relatively recent years, ornamental plants have been mutated with mutagens which cause greater ploidy and sometimes results in gigantism.

Genes revisited

A gene is a discrete functional sequence of a nucleotide sequence (ex: GAATAACT) responsible for instructing enzymes how to produce proteins or RNA. A variation of a gene is known as an allele. The sum of all genes is the genome. The genes detected in a mixed sample of plants, fungi and other microbes is known as the meta-genome. The entire sequence of plastid genes found in the chloroplast is known as a plastome.

After a hundred years of inquiry and unjustified atrocities, comparative genetics has shown simpler organisms like grasses have more genes by way of chromosome count and by genome size.

For example, the genome size for humans is roughly 3.1Gbp (3,100,000,000bp). Despite lacking a central nervous system, opposable thumbs, a conscious brain, retinal eyes, and speech or language, the genome sizes of certain plants are much larger than humans [48][49]. For example, the genome sizes found in a research study of Ginkgo trees (Ginkgo biloba) was 11.75Gbp [50], Loblolly pine (Pinus taede) was 31Gbp [51], Chili peppers (Capsicum annuum) was around 3.48Gbp [52], Bread wheat (Triticum aestivum) was substantially more around 14Gbp [53] and Corn (Zea mays subsp. mays) was less than us at 307Mbp in one study [54]. Therefore, many scientists today agree that genes are not the main factor responsible for complex traits in social animals like humans.

An analysis of all the genetic components within the chloroplast or the plastome of Visser’s Hydnora, Hydnora vesseri, a strange plant with no leaves or chlorophyll and large red flower in Africa and southern Arabia [55],

Jan 9, 2017, Emmanuel Douzery,
Wikimedia Commons [34a].
The top of Visser’s Hydnora flower,

Namibia, Nov 13, 2013,
Wikimedia Commons [35a]
Plastome map of Arabidopsis thaliana,

Feb 2, 2018, Emmanuel Douzery,
Wikimedia Commons [36a]
Arabidopsis thaliana flowers, the plant model species used in microbiology,

Szczecin, West Pomeranian Voivodeship, Poland, Apr 27, 2019,
Salicyna, Wikimedia Commons [37a]

Transcription and Translation

In addition to replication, DNA forms RNA through the process known as transcription. This is the first step to produce a protein. RNA also has many functions of its own. Because RNA is single stranded, after it is created it can form many shapes by curving on itself. RNA has many functions within the cell (Messenger RNA or mRNA, Transfer RNA or tRNA, etc…).

Diagram showing the mechanics of one of the first steps in the protein synthesis, RNA transcription: the production of a new kind of single stranded nucleic acid. Similar to replication, the process is direction sensitive. In DNA, antisense strand and sense strands contain mirror sequences (G<->C, A<->T). The antisense strand is the template strand where the enzyme produces a new mirror sequence, except it contains Uracil (U) instead of Thymine (T).

National Human Genome Research Institute,
Wikimedia Commons. [38a]

RNA molecules are processed at small organelles, called Ribosomes, to begin the process of making proteins. Three bases correspond to the production of an amino acid. This process is known as translation.

Diagram of messenger RNA (mRNA) translating into polypeptides or chains of amino acids, the building blocks of proteins.

Cstreibert.
Wikimedia Commons [39a]

In summary, transcription is how the genes inside DNA produce the single stranded RNA, which is utilized in many ways and folds into many forms. Translation is how m-RNA is read to produce chains of amino acids.

1° sequence of amino acids,
2° α-helices and β-sheet geometrical structures,
3° folds created by disulphide bridges,
4° functional groups called sub-units.

Thomas Shafee, CKRobinson & Hstuhlma.
Wikimedia Commons. [17a]

These chains of amino acids, the product of translation, are the building blocks of proteins. Proteins are a large class of molecules with many functions.

Sex Determination

Meiosis in Lily (Lillum) microgametophyte. Pollen mother cell is in Anaphase II.

Josef Reischig.
Wikimieda Commons [27a] (www.mantis.cz/mikrofotografie)

We often see humans as divided into two sexes: men and women. The primary sex-determining chromosome pairs: XX – women, XY – men. These letters, X and Y, were chosen because they mimic the shapes of the duplicated chromosomes in a karyogram. All other chromosomes of an organism not involved in sex determination are called autosomal chromosomes. Statistically, most people have 23 pairs of chromosomes (46 chromosomes). However, some people have different combinations of sex chromosomes such as XXY or XO [56].

During primary sex determination, hormones linked to sex-chromosomes cause a bipotential gonad to form into either a testis (pl. testes) or ovary (pl. ovaries) gonad. In secondary sex-determination, these gonads develop tubes, the internal organs and external organs such as penises and vaginas. During this step-by-step process, there can be changes in hormonal interactions. Statistically, we categorize ourselves into men and women, however there exists many physical configurations in between these two categories, which occur during changes at any step of the sex-determination process. This is excluding the more complex characteristics of human behavior.

In other organisms, there are many different systems and processes which regulate sex determination. Birds, flies, and certain types of worms have their own system of assigning sex chromosomes and how they interact [57].

In plants, we observe a more complex interaction than in humans because humans are a single species of bipedal primates, whereas plants are a Kingdom of organisms consisting of more than 250,000 species [58].

The environmental stresses which determine the sex of the fern gametophyte. When there is less nutrients, less light, more competition, and the presence of the organic chemical Antheridiogen, fern spores are likely to mature into an Antheridium, the male gametophyte.

Nov 17, 2020. Jon Houseman.
Wikimedia Commons [40a]

Not all plants have flowers and fruit. Some produce cones with seeds, a variety of plants others produce no seeds and only spores.

Flowers, the structures that house the two reproductive structures or gametes: pollen and embryo sac.

Jul 11, 2019. Nefronus.
Wikimedia Commons [41a]

Plants can be monecious (both sexes on same individual), dioecious (sexes designated to separate individuals), have perfect flowers (flowers with both sexed organs), or imperfect flowers (flowers with only one of the two sexed organs)[59].

Seed producing plants have the same X and Y chromosome pair system as humans. 90% of all seed producing plants have perfect or hermaphroditic flowers. Of the other 10% of species, ~1/2 produce separately sexed flowers on the same plant (monoecious imperfect). Whereas the other half of that 10%, have designated sexes for each separate individuals (dioecious imperfect), analogous to humans [60]. As many gardeners and farmers find out, these are not set-in-stone categories. Similar to other organisms, plants can respond to stress and produce a different type of flower than originally expected. These changes occur, because plant hormones regulate primary and secondary sex determination [61].

In the case of the dioecious Ginkgo tree (Ginkgo biloba), landscapers prefer pollen-producing individuals since they won’t leave stinky fruit on sidewalks. In Cannabis flower production, cultivators watch for signs of pollen-producing plants before the mature and remove them from the population to ensure the narcotic resinous female inflorescence doesn’t spend its energy on seed production. In the case of Asparagus, unless you want seed for a future crop, sex determination isn’t decided at the time of harvest and therefore not important for growers.

Self-incompatibility

Plants differ in their ability to fertilize themselves. Unlike most animals, some plants can fertilize themselves. However, most plants want to fertilize other individuals with a different genetic configuration or genotype to ensure a chance at survival.

Diagram shows more nuanced system featured in land plants. See more.

Peter Coxhead.
Wikimedia Commons.[30a]

During sexual reproduction, gametes fuse combining the DNA of two individuals into a new unique individual. A new genotype can introduce new mutations for a better chance of survival. Plants can recognize if the pollen (microgametophyte) is from the same genotype and reject it.

For certain cultivated plants that have been grafted, growers are required to have two cultivars of the plant to be able to produce fruit. For example, most cultivars of apples are a clones of an original mutant, so apple growers need two cultivars or two varieties of apples for them to create fruit. In the case of apples, one variety could be a wild undesired variety and the other the cultivated variety (cultivar). The fruit growing on the branches of the grafted cultivar will be the one you want. However, the seed from that desired fruit will produce a tree with an apple that is a random mix of both varieties. Pollen can travel long distances, which some farmers utilize when designing their operations.

Galls and other changes caused by insects

Galls, large tumor-like formations on leaves and bark, form from changes in the expression of DNA caused by insects, which secrete mutagenic compounds. These compounds are studied by biologists to understand the mechanism behind mutagenesis. One example is oak gall, which was used by writers to create a dark ink, which was later infused with iron to produce the iron gall ink, which became a very popular ink.

Simple Examples

Notice the differences in the structure of the stems and leaves of the beans in the foreground to the plant in the background. These are genetic differences.
A few plants can produce enough seeds to double the original population.
In this case, the variation of color in the bean pods results from the its age, which was caused by changes in water from the mother plant and increased stress from environment. In this case, this is not an inherited trait.
After aging the difference in coloration is diminished.
Each pod contains many seeds. Fruits differ in how many seeds they contain. Not all plants have fruit. A legume is a type of dehiscent/dry fruit.
If seeds are stored well and meet the germination requirements, they will produce a new plant.
After germination, the plant produces bulky leaves known as cotyledons. The next set of leaves are known as the true leaves. Environmental conditions such as low light can cause stem elongation or etiolated stems.
Growing plant indoors requires nurture. Each species has a different growing requirement. Too much water or too little water (and so on with nutrients,light, pruning, etc…) can cause the plant to become stressed and die.

“It’s not rocket science. It’s just as easy to do it right than it is to do it wrong. That’s what makes it difficult.” – Dr. J talking about plant propagation and pruning.
The environment controls the growth of the plant. These beans were grown outside. They true leaves are much larger and their stems are much shorter.
Given the right environment a plant can thrive, and its genes are instructing it where and how to grow.
Same beans grown outdoors. Consider why it is important for gardeners and landscapers to distinguish the two growth habits: bush and climbing
(See https://www.gardendesign.com/vegetables/beans.html )

Modern Breeding

In the 1980s a biotechnology company filed a patent on the first genetically engineered bacteria used to clean up oil spills[62]. Since then, the world of the life sciences industry has dramatically changed.

Supporters of genetic engineered (GE) organisms will often cite artificial selection as a type of genetically modified organism (GMO)[63]. For this reason we use the term GE. GE refers to the direct change to the genome using some microbiological technique. Many GE organisms can also be called transgenic organisms, which technically are instances where genes are transferred from one organism to another. When most people talk about GMO, they are referring to GE crops. These arguments, and the technical definitions used by scientists, pundits, and governments can create confusion.

Recombinant or transgenic bacterial plasmids have inserted DNA from another organism.

The DNA is included into the plasmid during recombination, a naturally occurring event. Therefore not all recombinant DNA is transgenic. The subtle differences between the categorizations, recombinant and transgenic, are used to obscure human activity.

Recombinant bacterial cells are used to produce hard to find compounds like Insulin at an industrial scale or to produce enzymes used in Genetic Engineering (GE) techniques.

Wikimedia Commons [41a]

Prior to GE techniques, breeders have used many methods to induce random mutations. Chemical mutagens have been used [64]. After the discovery of radioactive substances, many breeders radiated seeds to produce mutations. Some of these mutations, which were random and not engineered, have made their way into common corn varieties through hybridization of archived seed from US Navy experiments [65]. Some used ultraviolet (UV) radiation [66], the same type as the solar radiation which can give you a sunburn.

Besides causing mutations to artificially increase diversity, there are many strategies to breed plants. Another advanced method has been to find a naturally existent or artificially placed genetic marker associated with a desired to trait, and to breed with the help of computer simulations and increased precision [67].

Comparison of DNA repair mechanism pathway with CRISPR-Cas nuclease induced pathway.

Wikimedia Commons [43a].

GE techniques are many. Today the most popular is the use of the CRISPR cas method [68], which utilizes a cell repair mechanism and a unique GE bacterium. There exists other methods in the past such as TALEN and Zinc-Finger nuclease techniques [69].

These methods have been used by biotech companies to control plant responses. One of the most common GE traits is Bt [70] and glyphosate-resistance [71]. Bacillus thuringensis (Bt) is an insecticidal bacterium, which produces crystal proteins which disrupts the guts of a different types of insects (beetles, flies, moths, mosquitos) depending on the strain of Bt. GE crops with the Bt sequence produce the insecticidal compounds within their tissues and prevent herbivore damage from insect larvae [72]. Glyphosate (Trademark: Round Up) is an herbicide used in industrial agriculture to inhibit the growth of weeds. Glyphosate disrupts plants’ ability to produce vital proteins. Glyphosate-resistance sequences in GE crops allows them to be sprayed with the chemical and survive, while the surrounding weeds die [73].

Communication barriers.

One of the failures of anti-GE advocates has been appealing to people’s emotions. Confusion about the proper nomenclature and processes create divisions between educated and concerned individuals.

Scientists will criticize the public and suggest they lack an understanding of the mechanisms governing their technology and are irrationally fearful.

Therefore, without becoming scientists themselves and peer-reviewing GE research, dissenters cannot convince those who believe their work conforms to the ideal of the scientific process.

Ecofestiv’ 2015, Verney Park, Chambéry, France.
Wikimedia Commons [44a]

The 1980s ruling on the GE bacteria patent later allowed non-GE breeders to patent their cultivars. If breeders can demonstrate the process they used to breed a crop is unique, in the USA they are allowed to patent it. Plant nurseries need to pay for a license every time they sell a patented cultivar. Another way plant retailers make money is creating a trademark name (Read more about it here).

In reaction to the trends of GE and patents, breeders have mimicked the Open-Source software movement led by Richard Stallman and the GNU operating system. The Open Source Seed Initiative (OSSI) creates a platform and a community for breeders to have access to sources and obligates them to return their innovations to the community [74]. They are restricted from using GE techniques. These expectations help farmers have access to what nature has given to us free-of-charge.

Seeds

In addition, libraries around the USA provide seeds for local gardeners to use in their gardens with the expectation that they will return some for the next generation.

Seed Library, Sequoya Public Library, Madison, WI

Seed banks around the world protect the world’s genetic diversity and prevent extinction. Many of these places are centers for research to increase genetic diversity of domesticated crops which have been removed from their centers of origin and greatest diversity. One example of genetics in agriculture is the common cultivation of Russet potatoes across the USA, only one genotype. Whereas in South America, where potatoes were orignally cultivated, farmers cultivate a greater variety of potatoes and thus have less risk of crop failure from disease and greater nutritional diversity.

It’s not just seeds. Germplasm banks contain any plant material necessary for reproducing a plant. Thousands of vital and rare varieties are maintained by biologists in lab conditions and specialized growers in the field, who grow crops isolated from each other to sustain the contents of the germplasm directory.

Bioversity International’s Musa Germplasm International Transit Centre (ITC), Catholic University of Leuven, Belgium. Jan 1, 2016.
WIkimedia Commons [45a]
(Musa is the genus for Banana or Plantain)

Consequences

All breeding can have a desired and an undesired consequence, whether it is using new GE techniques or old classical breeding techniques. An example of a GE consequence was the unintentional poisoning of Monarch Butterflies by an older Bt-gene corn variant [75]. Many classically bred crops are annual crops which require yearly human intervention, and which can promote ecological disturbances from the need to till, weed and grow in mono-culture.

The desired consequences of these techniques suite our short-term and long-term needs. For example, some microbiologists wish to promote a GE yellow-colored rice, which in theory will be able to save millions from starvation [76]. The quickness of GE methods make them quicker solutions than traditional breeding methods. Traditional breeding is necessary for the continuation of a large diversity of crops. Without farmers planting potato seeds (potato tubers destined for re-planting) yearly, such rare cultivated varieties would cease to exist.

The journey of emergent life:
(1) Nuclear envelope of the nucleus protects the nuclear DNA (nDNA) inside chromatin and other stuff.

(2) Nuclear pore, where gene products leave.

(5) Ribosomes in Rough Endoplasmic Reticulum (ER) and free ribosomes within the cytoplasm (white background) translate RNA into amino acids (building block of proteins).

Large black arrow shows the generalized trend of the simplest to most complex molecules, an emergent property of life.

Magnus Manske,
Wikimedia Commons [12a].

Given our overview of the emergent properties of life, GE technologies appear to be a more consequential technology, because it alters cellular activity. Cellular activity is the first stage and one of the most sensitive of lifeforms’ functions. Mutation breeding can also introduce detrimental and undesirable mutations. Even marker assisted breeding could potentially limit future generations to a very-specific genotype. All of these consequences are inheritable and functionally irreversible.

Natural diversity is abundant and still not unexplored. In a market-led agricultural ecosystem, the decision by farmers, companies, and governments can have consequences on the genetic make-up and ecology of life on Earth.

Our Philosophy

PlantResearchOrg and its author are outliers in the scientific community, because we are against GE technology/GE crops and any breeding not guided by ethics, moral principles, peer-review, and the scientific method.

Many in the scientific community are experts in their field and have defended themselves and their work by suggesting that opponents of GE crops do not understand its mechanisms. They claim the dissenters of GE are purely political and emotional. We implore all opponents of GE to educate themselves so we can avoid catastrophic consequences.

Books, media, pundits, blogs (such as this one), and all the other influences on our value system (depicted by a scale) influence how and where we search for answers.

Therefore, there should be one step before building a hypothesis which is governed by irrationality. Example of this is Dmitri Mendeleyev’s dream [77], which revealed to him the pattern of the periodic table.

Wikimedia Commons [46a]
The scientific method has helped us create a process to discover and refute the truth. Before this method was popularized, the truth was argued between many and controlled by those who used violence. The scientific process helps us learn about recurring patterns or the cause-and-effects in the Universe.

The scientific method cannot be applied to phenomena that are not causal and materialistic. Therefore, most scientists agree there are no phenomena outside of the influence of our causal natural laws.

In an ideal world, each step of the scientific method is critiqued and preformed by other scientists to ensure its validity.

Wikimedia Commons [47a]

There is a fuzzy area between academic culture, people’s traditions, and the scientific method. We observe that the scientific method is strictly a technique to study mechanistic phenomena, which is open to intelligent criticism through experimentation and peer-review. It is unpopular to suggest that the scientific community is guided by faith in what is perceived to be the most-acceptable. However, it seems as if waves of skepticism come only after waves of support for scientific advancements.

In science, the word ‘law’ and ‘theory’ have specific meanings. The scientific method governs the discovery and refutation of these fundamental concepts. These help us discern the causal behavior of the Universe.

Wikimedia Commons [48a]
The distinction between basic and applied research does not imply anything else except for the reason for research. Applied research does not imply a positive or a negative consequence. Searching for a specific technique to organically grow fruits and vegetables would be a kind of applied research activity.

There is also a difference between observing the environment and creating technology to alter the environment. While some scientists wish to understand the mechanisms that govern natural behavior (basic research), other scientists wish to uncover those mechanisms for their use in applied research. Sometimes these two overlap. We implore people to be aware of the consequences.

Observation

Plant genetics is not only useful for breeding. The study of plant genetics has allowed us to re-look at nature like never before. Today many changes are occurring to the taxonomic system due to discoveries of genetic similarities between plants we never thought would be related. Today the Angiosperm Phylogeny Group (APG) works to determine the classifications of plants.

Some gardeners are frustrated that so much of what they thought was true is changing and are expecting more to change.

Around the year 2000, many phylogenetic studies showed that Maple trees (Acer spp.) did not belong to their own family as previously believed. Instead they are genetically related to the members of the Sapindaceae family, such as the Horse Chestnut trees (Aesculus spp.) and other soap nuts used as natural detergents for washing. Today, the genus Acer belongs in the family Sapindaceae [78].

Sugar Maple (Acer saccharum) and its tiny flowers within its drooping inflorescence in Spring,

Dendrological Garden in Glinna, Poland. Apr 22, 2023.
Kenraiz Krzysztof Ziarnek.
Wikimedia Commons [49a]
The fungal pathogen Rhytisma acerinum causing tar spot on A. saccharum leaf, a common disease on maples and identification tool [79] .

Hamilton, Ontario, Canada. Oct 19, 2007.
Saforrest. Wikimedia Commons [50a]
A. saccharum fruit are known as schizocarps, a double-winged type of samara . The wings are the dispersal mechanism of the fruit. The seeds are inside the hard fleshy mass.

Morton Arboretum, Lisle, Illinois. Sept 2, 2006.
Quercus1981. Wikimedia Commons [51a]

European Horsechestnut (Aesculus hippocastanum) inflorescence.

Rakowice, Poland. May 7, 2008.
Jan Mehlich. Wikimedia Commons [52a]
Fruits or conkers of A. hippocastanum.

Feeringbury Manor in Feering, Braintree, Essex, England. Oct 2, 2015.
Acabashi. Wikimedia Commons [53a]
The fruit of A. hippocastanum are a type of capsule fruit, technically not a nut. When crushed and washed they release saponins, which froth the water and can be used as a soap.

Sept 22, 2004. Andrew Dunn © Photography.
Wikimedia Commons [54a]
Inflorescence of Soapnut tree (Sapindus mukorossi), a tree popular across Central and Eastern Asia and known for its fruit, which are processed into a detergent.

Thane, India. June 4, 2008. Dinesh Valke.
Wikimedia Commons [55a]
Immature soapnuts.

Oct 1, 2022. Hitachiota, Ibariki, Japan. 小石川人晃 ( Koishikawa Hito Akira ).
Wikimedia Commons [56a]
Soapnut capsules.

Clemenspool. Wikimedia Commons [57a]

Hackberry tree (Celtis occidentalis) is a tree native to North America and now commonly used in landscaping and parks. It has small purple hard fruits which are purported to have thin edible skins [80]. Recently it has been classified as belonging to the Cannabaceae family, the family of Cannabis [81][82][83]. Ancient common ancestors between these very different looking plants once existed in Central Asia.

Hackberry tree (Celtis occidentalis) and its ridged bark, an identification feature.

Onandaga County, New York. Sept 15, 2010. R. A. Nonenmacher.
Wikimedia Commons [58a]
Hackberry tree inflorescence.

Arhus Botanical Gardens, Arhus, Denmark. May 23, 2008.
Sten Porse. Wikimedia Commons [59a]
Overwintered hackberries in Spring.

Arhus Botanical Gardens, Denmark. Feb 26, 2007.
Sten Porse. Wikimedia Commons [60a]
Cannabis or Hemp or Marijuana (Cannabis sativa) male inflorescence. Cannabis is a dioecious plant: a female flower plant and male flower plant.

Thimphu, Bhutan. Oct 7, 2019.
Vinayaraj. Wikimedia Commons [61a]
Female cannabis inflorescence.

Viote Alpine Botanical Garden near Trent, Italy. Sept 2, 2017.
Nicollò Caranti. Wikimedia Commons [62a]
Fruit of female Hemp plant (See archived article for more about Hemp).

Cultiva (International Hemp Fair) in Vienna, Austria. Oct 11, 2008.
D-Kuru. Wikimedia Commons. [63a]
Male inflorescence of Hops (Humulus lupulus) .

Valais, Switzerland. Aug 15, 2010. Robert Flogaus-Faust.
Wikimedia Commons [64a]
Hops female inflorescences.

Daxlanden, Karlsruhe, Germany. Aug 15, 2009.
Wikimedia Commons. [65a]
Hops’ dissected immature infructescence or assembly of fruits. Seeds would be located where yellow material is located in image.

Tennanger Hopfen.
Wikimedia Commons [66a]

Genetics has become an extremely powerful forensic tool to help us observe the connectivity in nature. Researchers have mapped genomes and now observe field samples (soil, roots, leaf tissue) to determine the composition of fungal communities associated with plant communities.

The term genetic barcoding refers to a search method for functional sequences of type of plant, fungi, or any other organism in order to identify them within a community. This research is helping ecologists understand how the microbiome and macrobiome in forests work together and will help guide preservation efforts.

One opportunity which PlantResearchOrg is excited about is the use of these forensic techniques to identify unknown domesticated plants living returned to the wild after changes in human history. We are also interested in using plant genetics as a forensic tool for many other types of historical, criminal and ecological investigations.

Summary

The world of plant genetics is part of the foundation of field of human and animal genetics. This affirms the plant sciences’ influence over discoveries and observations, such as the discovery of cells in the bark of Cork Oak (Quercus suber) and the discovery of viruses in Tobacco (Nicotina tabacum), a species originally from the Americas but commercially grown and studied in the Netherlands [84].

It is daunting and overwhelming. It is complex and critically important. It is sensitive and dangerous. We should be strongly opposed to reckless human activity.

Process tree. Top parameter is source of all lower parameters. Relationships between parameters and the number of parameters in nature are many and complicated.

Wikimedia Commons [67a]

Remember, genes are instructions for producing proteins and RNA (ribonucleic acid). While genes are the first step for all biological functions, they are not the main factor influencing the complicated functions. Think of it like a process tree. Genes are near the base (the source), and the complex processes are at the very end. Complex processes are more influenced by the mechanism at each fork in the process tree than the initial cause.

We should have hope. There is hope that this information will help us solve great mysteries and help us on our journey forward to a more just and peaceful world.

Author: Gustavo Meneses
Published: 2022-09-23
Revised: 2024-03-25

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