Plant genetics is the study of
gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s,
genetic variation
Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources ...
, and
heredity
Heredity, also called inheritance or biological inheritance, is the passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic infor ...
specifically in
plant
Plants are the eukaryotes that form the Kingdom (biology), kingdom Plantae; they are predominantly Photosynthesis, photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with c ...
s.
It is generally considered a field of
biology
Biology is the scientific study of life and living organisms. It is a broad natural science that encompasses a wide range of fields and unifying principles that explain the structure, function, growth, History of life, origin, evolution, and ...
and
botany
Botany, also called plant science, is the branch of natural science and biology studying plants, especially Plant anatomy, their anatomy, Plant taxonomy, taxonomy, and Plant ecology, ecology. A botanist or plant scientist is a scientist who s ...
, but it intersects with numerous life sciences, including molecular biology, evolutionary biology, and bioinformatics. Plants are used for genetic research in a multitude of disciplines. Understanding plant genetics is essential for improving crop yields, developing disease-resistant plants, advancing agricultural biotechnology and even making advancements in medicine. The study of plant genetics has significant economic and agricultural implications. Thus, there are many plant models that have been developed as well as genetic tools to study plants. Genetic research has led to the development of high-yield, pest-resistant, and climate-adapted crops. Advances in genetic modification (GMO Crops) and selective breeding continue to enhance global food security by improving nutritional value, resistance to environmental stress, and overall crop performance.
History
The earliest evidence of plant
domestication
Domestication is a multi-generational Mutualism (biology), mutualistic relationship in which an animal species, such as humans or leafcutter ants, takes over control and care of another species, such as sheep or fungi, to obtain from them a st ...
found has been dated to 11,000 years before present in ancestral wheat. While initially selection may have happened unintentionally, it is very likely that by 5,000 years ago farmers had a basic understanding of heredity and inheritance.
This selection over time gave rise to new crop species and varieties that are the basis of the crops we grow, eat and research today.

The field of plant genetics began with the work of
Gregor Johann Mendel
Gregor Johann Mendel OSA (; ; ; 20 July 1822 – 6 January 1884) was an Austrian biologist, meteorologist, mathematician, Augustinian friar and abbot of St. Thomas' Abbey in Brno (Brünn), Margraviate of Moravia. Mendel was born in a Ger ...
, who is often called the "father of genetics". He was an
Augustinian priest
A priest is a religious leader authorized to perform the sacred rituals of a religion, especially as a mediatory agent between humans and one or more deity, deities. They also have the authority or power to administer religious rites; in parti ...
and scientist born on 20 July 1822 in Austria-Hungary. He worked at the Abbey of St. Thomas in
Brünn
Brno ( , ; ) is a Statutory city (Czech Republic), city in the South Moravian Region of the Czech Republic. Located at the confluence of the Svitava (river), Svitava and Svratka (river), Svratka rivers, Brno has about 403,000 inhabitants, making ...
(now Brno, Czech Republic), where his organism of choice for studying
inheritance
Inheritance is the practice of receiving private property, titles, debts, entitlements, privileges, rights, and obligations upon the death of an individual. The rules of inheritance differ among societies and have changed over time. Offi ...
and
traits was the
pea plant. Mendel's work tracked many
phenotypic
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...
traits of pea plants, such as their height, flower color, and seed characteristics. Mendel showed that the inheritance of these traits follows two particular
laws
Law is a set of rules that are created and are law enforcement, enforceable by social or governmental institutions to regulate behavior, with its precise definition a matter of longstanding debate. It has been variously described as a Socia ...
, which were later named after him. His seminal work on genetics, "Versuche über Pflanzen-Hybriden" (Experiments on Plant Hybrids), was published in 1866, but went almost entirely unnoticed until 1900 when prominent botanists in the UK, like
Sir Gavin de Beer, recognized its importance and re-published an English translation. Mendel died in 1884. The significance of Mendel's work was not recognized until the turn of the 20th century. Its rediscovery prompted the foundation of modern genetics. His discoveries, deduction of
segregation ratios, and subsequent
laws
Law is a set of rules that are created and are law enforcement, enforceable by social or governmental institutions to regulate behavior, with its precise definition a matter of longstanding debate. It has been variously described as a Socia ...
have not only been used in research to gain a better understanding of plant genetics, but also play a large role in
plant breeding
Plant breeding is the science of changing the traits of plants in order to produce desired characteristics. It is used to improve the quality of plant products for use by humans and animals. The goals of plant breeding are to produce crop varie ...
.
Mendel's works along with the works of
Charles Darwin
Charles Robert Darwin ( ; 12 February 1809 – 19 April 1882) was an English Natural history#Before 1900, naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all speci ...
and
Alfred Wallace
Alfred Russel Wallace (8 January 1823 – 7 November 1913) was an English naturalist, explorer, geographer, anthropologist, biologist and illustrator. He independently conceived the theory of evolution through natural selection; his 1858 pap ...
on selection provided the basis for much of genetics as a discipline.
In the early 1900s, botanists and statisticians began to examine the segregation ratios put forth by Mendel. W.E. Castle discovered that while individual traits may segregate and change over time with selection, that when selection is stopped and environmental effects are taken into account, the genetic ratio stops changing and reach a sort of stasis, the foundation of
Population Genetics
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
. This was independently discovered by G. H. Hardy and W. Weinberg, which ultimately gave rise to the concept of
Hardy–Weinberg equilibrium published in 1908.
Around this same time, genetic and plant breeding experiments in
maize
Maize (; ''Zea mays''), also known as corn in North American English, is a tall stout grass that produces cereal grain. It was domesticated by indigenous peoples in southern Mexico about 9,000 years ago from wild teosinte. Native American ...
began. Maize that has been self-pollinated experiences a phenomenon called
inbreeding depression
Inbreeding depression is the reduced biological fitness caused by loss of genetic diversity as a consequence of inbreeding, the breeding of individuals closely related genetically. This loss of genetic diversity results from small population siz ...
. Researchers, like
Nils Heribert-Nilsson, recognized that by crossing plants and forming hybrids, they were not only able to combine traits from two desirable parents, but the crop also experienced
heterosis
Heterosis, hybrid vigor, or outbreeding enhancement is the improved or increased function of any biological quality in a hybrid offspring. An offspring is heterotic if its traits are enhanced as a result of mixing the genetic contributions o ...
or
hybrid vigor
Heterosis, hybrid vigor, or outbreeding enhancement is the improved or increased function of any biological quality in a Hybrid (biology), hybrid offspring. An offspring is heterotic if its trait (biology), traits are enhanced as a result of m ...
. This was the beginning of identifying gene interactions or
epistasis
Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is depe ...
. By the early 1920s,
Donald Forsha Jones had invented a method that led to the first hybrid maize seed that were available commercially. The large demand for hybrid seed in the U.S. Corn Belt by the mid 1930s led to a rapid growth in the seed production industry and ultimately seed research. The strict requirements for producing hybrid seed led to the development of careful population and inbred line maintenance, keeping plants isolated and unable to out-cross, which produced plants that better allowed researchers to tease out different genetic concepts. The structure of these populations allowed scientist such a
T. Dobzhansky,
S. Wright, and
R.A. Fisher to develop
evolutionary biology
Evolutionary biology is the subfield of biology that studies the evolutionary processes such as natural selection, common descent, and speciation that produced the diversity of life on Earth. In the 1930s, the discipline of evolutionary biolo ...
concepts as well as explore
speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
over time and the statistics underlying plant genetics. Their work laid the foundations for future genetic discoveries such as
linkage disequilibrium Linkage disequilibrium, often abbreviated to LD, is a term in population genetics referring to the association of genes, usually linked genes, in a population. It has become an important tool in medical genetics and other fields
In defining LD, it ...
in 1960.
While breeding experiments were taking place, other scientists such as
Nikolai Vavilov
Nikolai Ivanovich Vavilov ( rus, Никола́й Ива́нович Вави́лов, p=nʲɪkɐˈlaj ɪˈvanəvʲɪtɕ vɐˈvʲiləf, a=Ru-Nikolay_Ivanovich_Vavilov.ogg; – 26 January 1943) was a Russian and Soviet Union, Soviet agronom ...
were interested in wild
progenitor
In genealogy, a progenitor (rarer: primogenitor; or ''Ahnherr'') is the founder (sometimes one that is legendary) of a family, line of descent, gens, clan, tribe, noble house, or ethnic group.. Ebenda''Ahnherr:''"Stammvater eines Geschlec ...
species of modern crop plants. Botanists between the 1920s and 1960s often would travel to regions of high plant
diversity
Diversity, diversify, or diverse may refer to:
Business
*Diversity (business), the inclusion of people of different identities (ethnicity, gender, age) in the workforce
*Diversity marketing, marketing communication targeting diverse customers
* ...
and seek out wild species that had given rise to domesticated species after selection. Determining how crops changed over time with selection was initially based on morphological features. It developed over time to chromosomal analysis, then
genetic marker
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can ...
analysis, and eventual
genomic analysis. Identifying traits and their underlying genetics allowed for transferring useful genes and the traits they controlled from either wild or mutant plants to crop plants. Understanding and manipulating of plant genetics was in its heyday during the
Green Revolution
The Green Revolution, or the Third Agricultural Revolution, was a period during which technology transfer initiatives resulted in a significant increase in crop yields. These changes in agriculture initially emerged in Developed country , devel ...
brought about by
Norman Borlaug
Norman Ernest Borlaug (; March 25, 1914September 12, 2009) was an American agronomist who led initiatives worldwide that contributed to the extensive increases in agricultural production termed the Green Revolution. Borlaug was awarded multiple ...
. During this time, the molecule of heredity, DNA, was also discovered, which allowed scientists to actually examine and manipulate genetic information directly.
DNA
What is DNA?
Deoxyribonucleic acid
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of a ...
(DNA) is a
nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and
RNA
Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
molecules. The DNA segments that carry this genetic information are called genes, and their location within the genome are referred to as
genetic loci, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. DNA is the starting point for the central dogma of molecular biology and genetics, as it starts the flow of information from DNA, which is then transcribed into RNA and then RNA which is translated into functional proteins.
Geneticist
A geneticist is a biologist or physician who studies genetics, the science of genes, heredity, and variation of organisms. A geneticist can be employed as a scientist or a lecturer. Geneticists may perform general research on genetic process ...
s, including
plant geneticists, use this sequence of DNA to their advantage to better find and understand the role of different genes within a given genome. Through research and plant breeding, manipulation of different plant genes and loci encoded by the DNA sequence of the plant chromosomes by various methods can be done to produce different or desired
genotype
The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
s that result in different or desired
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...
s.
Discovery of DNA
Since the original discovery of DNA in 1869 by the Swiss physician Frederich Miescher as "nuclein" in white blood cells, it has been the subject of immense genetic research. This substance was found to be rich in phosphorus and nitrogen which made it widely distinguishable to proteins. Miescher laid the groundwork for distinguishing DNA as an entirely separate molecular entity however it wasn't until later in 1944 where Oswald Avery, Colin MacLeod, and Maclyn McCarty, clearly presented DNA as a hereditary material which allows for inheritance of genetic information. They ran extensive experiments involving purified bacterial components in order to undoubtedly demonstrate that it was not proteins but actually DNA which is responsible for bacterial transformation; which is the process by which bacteria can take up foreign DNA and incorporate it into their own genetic makeup. After the overall discovery of DNA was made, as well as its function, in 1953 thanks to the work of James Watson and Francis Crick the famous double helical structure of DNA was founded. Through careful analysis of prior X-ray diffraction data collected by Rosalind Franklin and Maurice Wilkin, Watson and Crick were able to model and outline its overall orientation. This structural discovery was pivotal for facilitating accurate DNA replication as well as properly transmitting genetic information. Further genetic research is continuously done and plants remain a beneficial model organism for such experiments, and these are the major benchmarks of discovery which have aided in major parts of our knowledge and understanding of what DNA is and what it does.
The Structure of DNA
DNA is a double helical structure which contains two antiparallel DNA strands made of nucleotide units. Each nucleotide contains a deoxyribose sugar, a phosphate group and one of the following nitrogenous bases (adenine, thymine, guanine or cytosine).
The specific sequences and orientations of these bases are what encode unique pieces of genetic information which is hereditary. Between antiparallel strands there is base pairing which is occurring between adenine and thymine, and between guanine and cytosine with the help of hydrogen bonds, which hold the strands together and create the unique double helical shape.
Plant DNA
Plants, like all other known living organisms, pass on their traits using
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. Plants however are unique from other living organisms in the fact that they have
chloroplast
A chloroplast () is a type of membrane-bound organelle, organelle known as a plastid that conducts photosynthesis mostly in plant cell, plant and algae, algal cells. Chloroplasts have a high concentration of chlorophyll pigments which captur ...
s. Like
mitochondria
A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...
, chloroplasts have their own
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
. Like animals, plants experience
somatic mutation
A somatic mutation is a change in the DNA sequence of a somatic cell of a multicellular organism with dedicated reproductive cells; that is, any mutation that occurs in a cell other than a gamete, germ cell, or gametocyte. Unlike germline muta ...
s regularly, but mutations within the
germ line can be passed to offspring, aiding in processes like natural selection and evolution of plant species.
Some plant species are capable of
self-fertilization
Autogamy or self-fertilization refers to the Cell fusion, fusion of two gametes that come from one individual. Autogamy is predominantly observed in the form of self-pollination, a Reproduction, reproductive mechanism employed by many flowering pl ...
, and some are nearly exclusively self-fertilizers. This means that a plant can be both mother and father to its offspring. Scientists and hobbyists attempting to make crosses between different plants must take special measures to prevent the plants from self-fertilizing. In
plant breeding
Plant breeding is the science of changing the traits of plants in order to produce desired characteristics. It is used to improve the quality of plant products for use by humans and animals. The goals of plant breeding are to produce crop varie ...
, people create
hybrids between plant species for economic and aesthetic reasons. For example, the yield of
Maize
Maize (; ''Zea mays''), also known as corn in North American English, is a tall stout grass that produces cereal grain. It was domesticated by indigenous peoples in southern Mexico about 9,000 years ago from wild teosinte. Native American ...
has increased nearly five-fold in the past century due in part to the discovery and proliferation of hybrid varieties.
Plants are generally more capable of surviving, and indeed flourishing, as
polyploid
Polyploidy is a condition in which the biological cell, cells of an organism have more than two paired sets of (Homologous chromosome, homologous) chromosomes. Most species whose cells have Cell nucleus, nuclei (eukaryotes) are diploid, meaning ...
s. Polyploid organisms have more than two sets of homologous chromosomes. For example, humans have two sets of homologous chromosomes, meaning that a typical human will have 2 copies each of 23 different chromosomes, for a total of 46.
Wheat
Wheat is a group of wild and crop domestication, domesticated Poaceae, grasses of the genus ''Triticum'' (). They are Agriculture, cultivated for their cereal grains, which are staple foods around the world. Well-known Taxonomy of wheat, whe ...
on the other hand, while having only 7 distinct chromosomes, is considered a hexaploid and has 6 copies of each chromosome, for a total of 42. In animals, inheritable germline polyploidy is less common, and spontaneous chromosome increases may not even survive past fertilization. In plants however this is less of a problem. Polyploid individuals are created frequently by a variety of processes; however, once created, they usually cannot cross back to the parental type. Polyploid individuals that are capable of self-fertilizing can give rise to a new, genetically distinct lineage, which can be the start of a new species. This is often called "instant
speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
". Polyploids generally have larger fruit, an economically desirable trait, and many human food crops, including wheat,
maize
Maize (; ''Zea mays''), also known as corn in North American English, is a tall stout grass that produces cereal grain. It was domesticated by indigenous peoples in southern Mexico about 9,000 years ago from wild teosinte. Native American ...
,
potatoes
The potato () is a starchy tuberous vegetable native to the Americas that is consumed as a staple food in many parts of the world. Potatoes are underground stem tubers of the plant ''Solanum tuberosum'', a perennial in the nightshade famil ...
,
peanut
The peanut (''Arachis hypogaea''), also known as the groundnut, goober (US), goober pea, pindar (US) or monkey nut (UK), is a legume crop grown mainly for its edible seeds. It is widely grown in the tropics and subtropics by small and large ...
s,
strawberries
The garden strawberry (or simply strawberry; ''Fragaria × ananassa'') is a widely grown hybrid plant cultivated worldwide for its fruit. The genus ''Fragaria'', the strawberries, is in the rose family, Rosaceae. The fruit is appreciated f ...
and
tobacco
Tobacco is the common name of several plants in the genus '' Nicotiana'' of the family Solanaceae, and the general term for any product prepared from the cured leaves of these plants. More than 70 species of tobacco are known, but the ...
, are either accidentally or deliberately created polyploids.
The main genetic components of plants include;
# Nuclear DNA (nDNA): This is linear DNA or genetic information which is found within the nucleus. This DNA holds instructions for the function and structure of the organism its self. This information is organized into chromosomes and the nucleus serves as a control center for the entire organisms behavior, growth, and reproduction. Nuclear DNA content is a very important area of study in order to determine things like plant taxonomy, evolution and its conservation over time.
This information is usually referred to as the organisms C-value and this data is remarkably variable among different plant species.
Overall the study of nuclear DNA among plants and plant C-values is crucial for insight into biodiversity, adaptation and ultimately evolution of organisms.
# Mitochondrial DNA (mtDNA): This is the DNA which is found within the mitochondria which are specialized organelles that produce ATP for important cellular functions and perform processing like metabolism, cellular signaling and apoptosis or programmed cell death.
This form of DNA is exclusively inherited from maternal genetic information and is smaller and more circular than nuclear DNA. Mitochondrial DNA encodes around 13 proteins and is heavily reliant on information from the nucleus and their own genome for proper functioning. Extensive studying of mitochondrial DNA is very important for evolutionary research, migration patterns and insight into genetic disease.
# Chloroplast DNA (cpDNA): This is genetic information found within the chloroplasts of plant cells. These specialized organelles perform photosynthesis for plants in order to convert light or photons into chemical/useful energy for plant growth and development.
These chloroplast genomes usually contain around 60-100 genes that are involved in photosynthesis and other essential metabolic functions. This form of DNA like mitochondrial DNA is also maternally inherited which is advantageous to studying phylogenetics and evolution.
Model Organisms
Model Organisms
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Mo ...
in the context of plant genetics are plant species that are well understood due to extensive research. This understanding of their genome and biological processes allows them to be used as a baseline to understand fundamental genetic, developmental, physiological and disease mechanisms. Discoveries from such research using a plant model organism is often able to apply its findings to other species including humans.
Plant model organisms are selected based on experimental advantages that vary depending on research objectives. Key factors influencing their selection include short life cycles, ease of genetic manipulation, and well-annotated genomes. Below, we review a few of the many plant model organisms that are widely used and their applications in plant genetics.
''Arabidopsis thaliana''

''In 2000,
Arabidopsis thaliana
''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...
'', also known as Thale Cress, became the first plant species to have its genome fully sequenced, solidifying its status as the most widely used plant model.
Even before its genome was sequenced, ''Arabidopsis'' was a popular model organism due to its small size, short generation time, and ability to self-pollinate. These traits not only made it ideal for genetic research but also facilitated its genome sequencing. By 2000, researchers had identified 25,498 coding genes and a genome size of 125 Mb.
However, while the genome sequence provided a complete list of genes, little was known about their specific functions. To address this, the Arabidopsis 2010 Project, launched by the National Science Foundation (NSF) which, aimed to characterize the function of every gene in Arabidopsis by 2010. The project was largely successful and significantly advanced the functional annotation of most genes. However, some genes remained uncharacterized due to their redundancy or subtle phenotypic effects. Since, research has continued to expand our understanding of the ''Arabidopsis'' genome. To date, 27,655 coding genes and 5,178 non-coding genes have been identified, with research continuing today.
''Arabidopsis'' is now the most well-known plant both genetically and in terms of function and has played a huge role in furthering molecular biology, medicine and genetic technology. One of the most notable applications of ''Arabidopsis'' is in Agrobacterium-mediated transformation, a technique widely used in plant biotechnology. Arabidopsis is particularly well-suited for this method, as its petals can be simply dipped in a liquid suspension of Agrobacterium, allowing for efficient genetic transformation. This approach has made ''Arabidopsis'' a cornerstone of genetic engineering since the petal dipping technique was refined in 2006. Since then, Agrobacterium-mediated transformation has contributed to advancements in many biological and medical contexts.
Due to extensive research conducted on ''Arabidopsis'' ''thaliana'', a comprehensive database called
The Arabidopsis Information Resource (TAIR) has been established as a central repository for various datasets and information on the species. TAIR houses a wide range of resources, including the complete genome sequence, gene structure and function, gene expression data, DNA and seed stocks, genome maps, genetic and physical markers, publications, and updates from the Arabidopsis research community. With ongoing discoveries and the expansion of resources like TAIR, ''Arabidopsis'' will continue to shape the future of genetic research and agricultural innovation.
''Zea mays''
''Zea mays'' (Maize), is one of the most widely studied crops in plant genetics due to its economic significance and its role as a model organism for studying genetic variation, plant breeding, and crop improvement. Furthermore, maize has been studied since before the 1940s notably for the discovery of transposable elements by Barbara McClintock.
In terms of Maize's use as a model organism, it has a very high genetic diversity, even higher than that of humans. This has been caused by its extensive domestication history, which began thousands of years ago. This makes it a good model organism its genetic diversity allows researchers to study a wide range of traits, including those related to yield, stress resistance, and adaptation to different environmental conditions.
The extensive variation present in maize enables scientists to investigate the underlying genetic mechanisms that control complex traits, making it an ideal system for functional genomics, quantitative trait locus (QTL) mapping, and genetic improvement of crops.
A major part of research involving Maize is for studying the mechanisms of
C4 photosynthesis, which involves a complex network of enzymes, transport proteins, and metabolic pathways. C4 photosynthesis is a highly efficient form of photosynthesis that allows plants to thrive in hot and dry environments. C4 plants, including Maize, are able to concentrate carbon dioxide in specialized leaf cells, reducing the loss of water through transpiration and increasing photosynthetic efficiency. This adaptation allows C4 plants to grow faster and more efficiently than C3 plants under conditions of high light intensity, heat, and drought. By studying C4 in Maize researchers are trying to develop crops (both Maize and other C4 crops) that are more resilient to environmental stress and better suited for future agricultural demands particularly in the face of climate change.
''Marchantia polymorpha''

''
Marchantia polymorpha
''Marchantia polymorpha'' is a species of large thalloid liverwort in the class Marchantiopsida. ''M. polymorpha'' is highly variable in appearance and contains several subspecies. This species is dioicous, having separate male and female plants. ...
'', a liverwort has more recently become an important model organism for studying plant biology, particularly in the context of evolution, development, and stress responses. The genome of ''Marchantia polymorpha'' was fully sequenced in 2017, revealing a compact genome of approximately 226 Mb with a relatively simple gene regulatory network.
Unlike many flowering plants, ''Marchantia'' has a haploid-dominant life cycle. This characteristic eliminates the production of heterozygous individuals, enabling more efficient and precise genetic manipulation and experimentation.
Subsequently, the presence of a single-copy genome with minimal gene redundancy makes Marchantia an attractive system for functional genomics.
As a member of the basal land plant lineage, ''Marchantia'' provides key insights into the evolutionary transition from aquatic to terrestrial plants. Liverworts like ''Marchantia'' are some of the oldest living land plants and thus, are essential to understanding the phylogenetics of plants. Using ''Marchantia'' researchers can and are reconstructing the genetic and physiological adaptations that enabled plants to colonize terrestrial habitats. This will allow us to have a better understanding of the origins of key traits such as desiccation tolerance, hormone signalling, and developmental plasticity which have many applications particularly in agricultural research.
Ultimately, ''Marchantia polymorpha'' with its unique evolutionary position, ease of genetic manipulation, and growing research tools, ''Marchantia'' continues to be a fundamental model for plant biology. Its contributions to developmental genetics, hormone signalling, and stress response research have expanded our understanding of early land plant evolution and offer potential applications in biotechnology.
''Oryza sativa''
Oryza sativa
''Oryza sativa'', having the common name Asian cultivated rice, is the much more common of the two rice species cultivated as a cereal, the other species being ''Oryza glaberrima, O. glaberrima'', African rice. It was History of rice cultivation ...
, commonly known as rice, is a cereal grain and one of the most important staple crops worldwide and is used as "a staple food for more than half of the world's population."
It is the primary source of food for a large portion of the population, particularly in Asia. Because of this agricultural importance, Rice has been extensively studied as a model organism in plant genetics.
When the rice genome was fully sequenced in 2002, it became the first major crop species to have its genome mapped.
Since then, th
Rice Genome Annotation Projectwas created in 2004 "to work from a common resource so that their results can be more easily interpreted by other scientists."
Between all the research combined in this database there has been 55,986 identified.
This database combined with the amount of investigation and research using Rice has opened new opportunities for functional genomics. Subsequently, allowing researchers to identify genes associated with important agronomic traits such as yield, drought resistance, and disease resistance.
''Brachypodium distachyon''
''
Brachypodium distachyon
''Brachypodium distachyon'', commonly called purple false brome or stiff brome, is a grass species native to southern Europe, northern Africa and southwestern Asia east to India. It is related to the major cereal grain species wheat, barley, oats ...
'' is an experimental model grass that has many attributes that make it an excellent model for temperate cereals. Unlike wheat, a tetra or
hexaploid
Polyploidy is a condition in which the cells of an organism have more than two paired sets of ( homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two complete sets of chromosomes, one fro ...
species, brachypodium is diploid with a relatively small genome (~355 Mbp) with a short life-cycle, making genomic studies on it simpler.
''Nicotiana benthamiana''
''
Nicotiana benthamiana
''Nicotiana benthamiana'', colloquially known as benth or benthi, is a species of ''Nicotiana'' indigenous to Australia. It is a close relative of tobacco.
A synonym for this species is ''Nicotiana suaveolens'' var. ''cordifolia'', a descripti ...
'' is a popular model organism for both plant-pathogen and transgenic studies. Because its broad leaves are easily transiently transformed with ''
Agrobacterium tumefaciens
''Agrobacterium tumefaciens'' (also known as ''Rhizobium radiobacter'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are cause ...
'', it is used to study both the
expression of pathogen genes introduced into a plant or test new genetic
cassette effects.
Other model plants
It is important to note that there are many more Plant Organisms that each have their own advantages and disadvantages depending on the area of study. Therefore, researchers must investigate their options and select a model organism for use that best fits the uses and applications of their study.
Genetically modified crops
Genetically modified (GM) foods are produced from
organism
An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...
s that have had changes introduced into their
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
using the methods of
genetic engineering
Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of Genetic engineering techniques, technologies used to change the genet ...
. Genetic engineering techniques allow for the introduction of new traits as well as greater control over traits than previous methods such as
selective breeding
Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant m ...
and
mutation breeding
Mutation breeding, sometimes referred to as "variation breeding", is the process of exposing seeds to chemicals, radiation, or enzymes in order to generate mutants with desirable traits to be bred with other cultivars. Plants created using mutagen ...
.
Genetically modifying plants is an important economic activity: in 2017, 89% of corn, 94% of soybeans, and 91% of cotton produced in the US were from genetically modified strains. Since the introduction of GM crops, yields have increased by 22%, and profits have increased to farmers, especially in the developing world, by 68%. An important side effect of GM crops has been decreased land requirements,
Commercial sale of genetically modified foods began in 1994, when
Calgene
The Monsanto Company () was an American agrochemical and agricultural biotechnology corporation founded in 1901 and headquartered in Creve Coeur, Missouri. Monsanto's best-known product is Roundup, a glyphosate-based herbicide, developed i ...
first marketed its unsuccessful
Flavr Savr
Flavr Savr (also known as CGN-89564-2; pronounced "flavor saver"), a genetically modified tomato, was the first commercially grown Genetic engineering, genetically engineered food to be granted a license for human consumption. It was developed by t ...
delayed-ripening tomato.
[Weasel, Lisa H. 2009. ''Food Fray.'' Amacom Publishing] Most food modifications have primarily focused on
cash crop
A cash crop, also called profit crop, is an Agriculture, agricultural crop which is grown to sell for profit. It is typically purchased by parties separate from a farm. The term is used to differentiate a marketed crop from a staple crop ("subsi ...
s in high demand by farmers such as
soybean
The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean. Soy is a staple crop, the world's most grown legume, and an important animal feed.
Soy is a key source o ...
,
corn
Maize (; ''Zea mays''), also known as corn in North American English, is a tall stout Poaceae, grass that produces cereal grain. It was domesticated by indigenous peoples of Mexico, indigenous peoples in southern Mexico about 9,000 years ago ...
,
canola
file:CanolaBlooms.JPG, Close-up of canola blooms
file:Canola Flower.jpg, Canola flower
Rapeseed oil is one of the oldest known vegetable oils. There are both Edible oil, edible and industrial forms produced from rapeseed, the seed of several ...
, and
cotton
Cotton (), first recorded in ancient India, is a soft, fluffy staple fiber that grows in a boll, or protective case, around the seeds of the cotton plants of the genus '' Gossypium'' in the mallow family Malvaceae. The fiber is almost pure ...
.
Genetically modified crops
Genetically modified crops (GM crops) are plants used in agriculture, the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of '' Agrobacterium'' for the delivery of ...
have been engineered for resistance to
pathogens
In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.
The term ...
and
herbicide
Herbicides (, ), also commonly known as weed killers, are substances used to control undesired plants, also known as weeds.EPA. February 201Pesticides Industry. Sales and Usage 2006 and 2007: Market Estimates. Summary in press releasMain page f ...
s and for better nutrient profiles. Other such crops include the economically important GM
papaya
The papaya (, ), papaw, () or pawpaw () is the plant species ''Carica papaya'', one of the 21 accepted species in the genus '' Carica'' of the family Caricaceae, and also the name of its fruit. It was first domesticated in Mesoamerica, within ...
which are resistant to the highly destructive
Papaya ringspot virus
''Papaya ringspot virus'' (PRSV) is a pathogenic plant virus in the genus ''Potyvirus'' and the virus family ''Potyviridae'' which primarily infects the papaya tree.
The virus is a non-enveloped, flexuous rod-shaped particle that is between 760& ...
, and the nutritionally improved
golden rice
Golden rice is a variety of rice ('' Oryza sativa'') produced through genetic engineering to biosynthesize beta-carotene, a precursor of vitamin A, in the edible parts of the rice. It is intended to produce a fortified food to be grown and ...
(it is however still in development).
There is a
scientific consensus
Scientific consensus is the generally held judgment, position, and opinion of the majority or the supermajority of scientists in a particular field of study at any particular time.
Consensus is achieved through scholarly communication at confer ...
that currently available food derived from GM crops poses no greater risk to human health than conventional food,
but that each GM food needs to be tested on a case-by-case basis before introduction.
Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe.
The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation.
There are still ongoing
public concerns related to food safety, regulation, labeling, environmental impact, research methods, and the fact that some GM seeds are subject to
intellectual property
Intellectual property (IP) is a category of property that includes intangible creations of the human intellect. There are many types of intellectual property, and some countries recognize more than others. The best-known types are patents, co ...
rights owned by corporations.
Methods of Genetically Modifying Plants
Beyond the traditional approach of inducing mutations through chemical or environmental agents, various techniques can directly introduce modified genetic material into a plant genome, allowing for more targeted genetics research. This targeted approach is essential to the development of plants with specific traits such as improved yield, pest resistance, or environmental resilience. These methods vary in effectiveness and the time required to achieve successful transformation. A major challenge, however, in genetic modification is overcoming the plant cell wall, which acts as a barrier to foreign molecules, such as DNA. To address this, techniques have been developed to either temporarily disrupt or bypass the cell wall. Completely removing the cell call poses the highest risk to the plant, as the cell may fail to regenerate. Additionally, even if transformation occurs, the inability to reform the cell wall renders the cell unusable. Therefore, alternative methods that maintain the integrity of the cell wall by bypassing it are typically preferred.
Microinjection
In this method, plant host cells are grown on a medium and then are injected with the DNA of interest using a very small needle. This approach allows DNA to be inserted into the plant cell without breaking or significantly disrupting the cell wall, effectively eliminating the need for cell wall regeneration, a process that is not always successful. Since the DNA is delivered using a needle, the injection site is highly specific, allowing a large amount of DNA to be inserted directly into a specific location such as the cytoplasm or nucleus. This precise delivery ensures targeted expression without the need for additional steps. Once the cells are successfully transfected, the cells can be reintegrated into the host. Despite the advantages of microinjection, the process is time consuming as each cell must be individually injected.
Electroporation
In Electroporation, plant cells are first grown in a medium that breaks down their cell walls, converting the plant cells into a
protoplast
Protoplast (), is a biology, biological term coined by Johannes von Hanstein, Hanstein in 1880 to refer to the entire cell, excluding the cell wall. Protoplasts can be generated by stripping the cell wall from plant, bacterium, bacterial, or f ...
.A protoplast is a plant cell that has had its cell wall removed, but retains all other typical components of a plant cell. Electric pulses are then applied to the medium to destabilize the membrane, allowing DNA to enter and integrate into the host genome. Afterward, the cells are removed from the medium and allowed to regenerate their cell walls before being reintroduced into the host organism. However, a major drawback is that many transformed cells fail to regrow their cell walls, rendering them unusable.
Particle Bombardment
Particle Bombardment, also known as
biolistics, involves small gold or tungsten particles being coated with the DNA intended for transformation. These DNA-coated particles are then placed in a vacuum chamber, with the target plant tissue positioned below. The particles are then accelerated at high velocity into the plant cells, where the DNA then dissociates from them. Gold and tungsten are preferred for this process because they do not readily react with other biological molecules or cellular components which could harm the plant and/or trigger toxic effects. Once inside the cell, the DNA may integrate into the host genome, resulting in stable expression, or it may remain temporarily before being degraded, leading to transient expression.
Agrobacterium-Mediated Transformation
''
Agrobacterium tumefaciens
''Agrobacterium tumefaciens'' (also known as ''Rhizobium radiobacter'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are cause ...
'' is a unique species of bacteria known for its ability to transfer a portion of its genetic material into the genome of certain plants. This natural phenomenon is facilitated by a specialized plasmid within the bacterium known as the tumour-inducing (Ti) plasmid. The Ti plasmid contains two essential components that work together to facilitate gene transfer.
The first major component is the transfer DNA (T-DNA) region, which is marked by defined left and right border sequences. These borders play a crucial role in ensuring that the T-DNA is excised and transferred to the plant cell. Additionally, the T-DNA carries several important genetic elements, including
oncogene
An oncogene is a gene that has the potential to cause cancer. In tumor cells, these genes are often mutated, or expressed at high levels. s. These are genes that, when expressed, drive uncontrolled cell division. This abnormal cell growth results in the formation of crown gall tumors on the plant, which are characteristic of infection by A. ''tumefaciens''.
The second essential element of the Ti plasmid is the virulence (''vir'') genes. These genes, once activated, are responsible for the excision of the T-DNA from the plasmid. They then mediate the complex process of transferring the T-DNA from the bacterial cell into the plant cell. Upon successful entry into the plant cell, the T-DNA is then further directed into the nucleus, where it becomes integrated into the plant’s genome, leading to stable genetic modification.
This natural gene transfer mechanism has been harnessed and re-utilized by researchers for genetic engineering purposes. By creating disarmed strains of A. ''tumefaciens'', strains that have had the tumor-causing oncogenes removed, researchers can safely leverage the bacterium’s natural transformation mechanisms to introduce genes of interest. In this process, a modified plasmid is constructed that includes the gene of interest, bordered by the left and right border sequences typically found in the Ti plasmid. The ''vir'' genes, which are still active on the Ti plasmid in the A. ''tumefaciens,'' recognize these borders, ensuring that the target gene is excised and transferred into the plant. Additionally, the newly created plasmid is engineered to contain both a plant-selectable marker and a bacterial-selectable marker. These markers are essential as they allow researchers to identify and cultivate only those plant cells that have successfully integrated the foreign DNA, ensuring the success of the genetic modification.
CRISPR-Cas9
CRISPR-Cas9 is a complex that edits the genome directly, allowing for greater specificity. Additionally, this method can be used in living cells, which is advantageous for assessing the impact of editing within an organism. While several types of CRISPR-Cas9 complexes exist, their overall structure is largely similar. The complex consists of two main components: guide RNA and Cas9. The guide RNA functions like a GPS, guiding the CRISPR-Cas9 complex to the correct target and enabling precise editing. It contains a single-stranded RNA component with the target DNA sequence, ensuring the complex binds to the intended location. Additionally, the guide RNA contains a double-stranded RNA component which is recognized and bound by the Cas9 protein, forming the complete complex. Cas9 is a nuclease that performs the actual cutting of the DNA. Genome editing via the CRISPR-Cas9 complex works by first recognizing the target DNA—the sequence you wish to edit. Cas9 then cuts the DNA, creating a double-stranded break. The cell then utilizes its own repair machinery to fix the break using one of two pathways:
Non-Homologous End Joining
Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. It is called "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair ...
(NHEJ) or
Homology-Directed Repair (HDR). In the former method, the break is repaired using a sister template strand, a process prone to errors that can introduce mutations to knock out a gene of interest. In the latter method, a DNA template containing the desired gene is provided to replace the original sequence during repair.
Current Plant Genetic Research and Applications
Advances in plant genetics are transforming the way scientists and breeders improve crops, offering tools that increase precision, efficiency, and responsiveness to environmental and market challenges. Current research focuses on multiple fronts, including molecular breeding, gene editing, transformation techniques, and synthetic biology, with the goal of building more sustainable, productive, and resilient agricultural systems.
Molecular Breeding and Genomic Selection
Molecular marker-assisted selection (MAS) and genomic selection (GS) have become central to modern crop improvement programs. These strategies enable breeders to predict and select plants with desirable genetic traits early in the breeding cycle, thus accelerating development. A key study demonstrated that using molecular marker-based methods like optimal cross selection results in higher long-term genetic gains and better maintenance of genetic diversity compared to traditional breeding methods.
Similarly, another scientific review emphasized that genomic selection—which combines genome-wide molecular markers with predictive models—can improve complex traits such as drought resistance, yield, and disease tolerance, even in crops with long generation times.
CRISPR and Genome Editing Technologies
One of the most significant breakthroughs in plant genetics is the application of CRISPR/Cas genome editing systems. These technologies allow precise, targeted changes to DNA sequences without introducing foreign genes. Recent reviews highlight the broad adoption of CRISPR for traits such as herbicide tolerance, improved nutritional content, and pathogen resistance. A 2023 review in ''IJMS'' further detailed how genome editing has been applied to improve crop architecture, flowering time, and stress responses across species like rice, maize, and wheat.
Gene Delivery and Plant Transformation
Efficient transformation techniques are essential for delivering genetic material into plant cells and regenerating whole plants. Classical approaches include Agrobacterium tumefaciens-mediated transformation, biolistic particle bombardment, and protoplast transformation. A 2023 review provided an overview of these technologies, noting challenges such as genotype dependency and low transformation efficiency in many crops.
To address these challenges, researchers have developed non-tissue culture-based transformation methods and novel delivery systems. A 2024 review highlighted the growing use of virus-based vectors, in planta techniques, and synthetic delivery systems that allow direct gene transfer into reproductive tissues, bypassing traditional tissue culture requirements.
Developmental Regulators
Recent work has shown that developmental regulators—genes that influence cell fate and regeneration—can significantly enhance transformation success. A study demonstrated that overexpressing the transcription factor PLETHORA5 (PLT5) improved transformation efficiency in both dicot and monocot species, such as tomato, cabbage, and snapdragon. These regulators promote stem cell identity and organogenesis, allowing more consistent transformation results across genotypes and species.
Synthetic Biology
Synthetic biology offers a new layer of control over plant traits by designing and engineering Synthetic biology is an expanding area of plant genetics that allows researchers to build novel genetic circuits and optimize metabolic pathways to precisely control traits in plants. One review describe how synthetic biology tools are enabling molecular farming—the use of plants to produce vaccines, biodegradable materials, and therapeutic proteins—thus transforming plants into efficient biofactories.
Additionally, an article published in Plant Communications emphasize the integration of artificial intelligence (AI) into synthetic biology platforms. AI tools are being used to model gene regulatory networks, design optimized gene circuits, and automate crop development pipelines. These approaches promise more efficient production of climate-resilient and nutritionally enhanced crops for global agriculture.
See also
*
Apomixis
In botany, apomixis is asexual development of seed or embryo without fertilization. However, other definitions include replacement of the seed by a plantlet or replacement of the flower by bulbils.
Apomictically produced offspring are geneti ...
*
Biological engineering
Biological engineering or
bioengineering is the application of principles of biology and the tools of engineering to create usable, tangible, economically viable products. Biological engineering employs knowledge and expertise from a number ...
*
Cloning
Cloning is the process of producing individual organisms with identical genomes, either by natural or artificial means. In nature, some organisms produce clones through asexual reproduction; this reproduction of an organism by itself without ...
*
DuPont
Dupont, DuPont, Du Pont, duPont, or du Pont may refer to:
People
* Dupont (surname) Dupont, also spelled as DuPont, duPont, Du Pont, or du Pont is a French surname meaning "of the bridge", historically indicating that the holder of the surname re ...
*
Experimental evolution
*
Gene flow
In population genetics, gene flow (also known as migration and allele flow) is the transfer of genetic variation, genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent ...
*
Gene pool
The gene pool is the set of all genes, or genetic information, in any population, usually of a particular species.
Description
A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survi ...
*
Genetic erosion
*
Genetic pollution
Genetic pollution is a term for uncontrolled gene flow into wild populations. It is defined as "the dispersal of contaminated altered genes from genetically engineered organisms to natural organisms, esp. by cross-pollination", but has come to be ...
*
Genetically modified organisms
A genetically modified organism (GMO) is any organism whose genetic material has been altered using genetic engineering techniques. The exact definition of a genetically modified organism and what constitutes genetic engineering varies, with ...
*
Ice-minus bacteria
*
Monsanto Company
The Monsanto Company () was an American agrochemical and agricultural biotechnology corporation founded in 1901 and headquartered in Creve Coeur, Missouri. Monsanto's best-known product is Roundup, a glyphosate-based herbicide, developed in ...
*
Paratransgenesis
References
External links
Ministry for the Environment NZ – Report of the Royal Commission on Genetic Modification, 2001
{{DEFAULTSORT:Plant Genetics