Abscisic Acid (ABA)

A plant hormone that regulates growth and promotes leaf abscission (shedding or falling off) and dormancy.

Acclimation

An organism’s adjustment of its physiology, morphology or behavior to lessen the effect and stress of an environmental change.

Adaptation

A physiological, morphological or behavioral trait with an underlying genetic basis that enhances the survival and reproduction of its bearers in their environment. Organisms that possess heritable traits which enable them to better adapt to their environment compared to other members of their species will be more likely to survive, reproduce and pass more of their genes on to the next generation.

Allele

One or more alternative forms of a gene that occur at a given locus (location) on a chromosome. Differing alleles produce variations of a genetic trait that can be genetically inherited. Alleles are represented with variation on the same symbol (such as G or g, H or h) based on dominance.

Allelic Diversity

The average number of alleles per locus, used as a metric to characterize the extent of genetic diversity.

Allotetraploid

Hybrids created as a result of both chromosome sets of each parent of an organism being present. An allotetraploid has four sets of chromosomes derived from two different diploid species. For example, Coffea arabica is likely an allotetraploid derived from a cross of the two diploid species Coffea canephora and Coffea eugenioides.

Amphidiploid

A polyploid cell or organism produced by the hybridization of two species from the union of two separate diploid chromosome sets.

Angiosperms

Flowering plants, which make up one of the most diverse major plant groups in existence, with at least 260,000 living species classified into more than 400 families.

Anther

The pollen-bearing structure on the top of the stamen (male sex organ), which is part of the flower.

Assimilation Rate

The rate at which a plant or leaves on that plant assimilate carbon via photosynthesis.

Autotetraploid

A polyploid cell or organism that results from the multiplication of chromosome sets from a single species, resulting in four copies of a single genome.

Autotrophy

The ability of plants to self-nourish by building their own nutrients via photosynthesis.

Axil

The angle between the leaf petiole with its supporting stem or branch and the main stem.

Back Crossing

Crossing an individual with a parent in order to bring out a certain gene or trait.

Bacteria

A domain name for many single-celled microorganisms. Present in most natural systems in the world, including soil, water, plant materials and even extreme environments such as hot springs, inside the earth’s crust and deep in the ocean.

Berry

A fleshy fruit produced from a single ovary, with one or more seeds inside, the pericarp not differentiated by a hardened endocarp. Examples of true berries include grapes, currants, cranberries and tomatoes. In the coffee industry, it is sometimes colloquially used to desribe the coffee fruit. Compare to cherry, drupe.

Bottleneck

A period of reduced population size that constricts the genetic pool of a group of organisms, affecting the group’s ability to adapt to new conditions after the recovery of more individuals.

Bracts

Leaf-like scales located at the base of a flower.

Bud

The beginning of a leaf cluster or flower on a stem, which is not fully open.

C3 Photosynthesis

A method of photosynthesis most plants use to fix carbon from carbon dioxide in the air. This process takes place mostly in the mesophyll (surface) leaf cells and utilizes enzymes to convert carbon into sugars for energy. Coffea arabica is a C3 plant as it utilizes this metabolic pathway. Grasses and cacti, among other plants, often utilize an alternative pathway, name C4 photosynthesis.

Cherry

A fruit characterized by a drupe. In biology this term is primarily utilized for fruit of the genus Prunus (which includes plums, cherries, apricots and peaches, among others). In the coffee industry it is sometimes used to describe the coffee fruit.

Chromosome

Nucleoprotein bodies (compounds including a protein and a nucleotide, which make up DNA and RNA) that are observed in cells during division. Each carries a linear array of genes, made up of DNA.

Cisgenic

Organisms that have been altered by introducing one or more DNA sequences from another individual within their species into them by artificial means. Compare to transgenic.

Clone

All identical individuals carrying a particular DNA sequence derived from another organism. In plants, all individuals derived from vegetative propagation [plant embryogenesis (where a new embryo is formed via the differentiation of undifferentiated cells), cuttings, or another method].

Coffea

The botanical genus colloquially referred to as the “coffee genus,” which is comprised of more than 120 individual species. These are generally opposite-leaved, evergreen shrubs or small understory trees with a horizontal branching pattern. They contain a pair of seeds, flat on one side and convex on the other, with a groove on the flat side (i.e., “coffee beans”). The preferred habitat of most plants in the Coffea genus is tropical forests.

Coffea Arabica

The botanical genus and species name for Arabica coffee. Originated in the forests of Ethiopia and South Sudan, then famously spread throughout the world for the production of its seeds.

Coffea Eugenioides

The botanical genus and species name for Eugenioides coffee. Indigenous to the highlands of East Africa, including the Democratic Republic of Congo, Rwanda, Uganda, Kenya and western Tanzania. Famously known to be one of the two diploid parent plants of Coffea arabica. it has a lower caffeine content than Coffea arabica.

Coffea Canephora

The botanical genus and species name of Robusta coffee, described more than 100 years after Coffea arabica. One of the two diploid parent plants of Coffea arabica. Originated in western and central sub-Saharan Africa. A largely productive commercial crop distinct from Arabica by physical and chemical attributes, including higher productivity and caffeine content.

Cotyledon

A leaf of the embryo of a seed plant, which upon germination emerges and becomes the first green leaf or leaves of a plant.

Cross

The deliberate breeding of two different individuals resulting in offspring that carry a portion of the genetic material of both the parent individuals. The parent individuals involved in the cross may be from species that are closely related or from different varieties.

Cultivar

Cultivated variants of a species originating through human influence. These could be selected from existing cultivated stock or from wild populations. It is a systematic group of cultivated plants that is clearly distinct, uniform and stable in its characteristics and which, when propagated with the appropriate methods, retain the same characteristics. Compare to variety.

Cytokinins

A class of plant growth substances (phytohormores) that promote cell division, or cytokinesis, in plant roots and shoots. Concentrations are highest in meristematic regions (in which cells have the ability to divide and differentiate) and areas of continuous growth potential such as roots, young leaves, developing fruits and seeds.

Deleterious Alleles

A version of a gene (allele) that, on average, decreases the fitness of the organism carrying it.

Diploid

A cell or organism having a double complement of chromosomes (generally a paternal and a maternal set). Exceptions to diploidy include polyploid species (particularly in plants).

DNA (Deoxyribonucleic Acid)

A large biological molecule composed of subunits known as nucleotides strung together in long chains. These chains carry genetic material and the information that make up genes.

Dominant

Describes the relationship between variants of a gene. When a dominant gene is present it masks the expression of alternative alleles. Compare to recessive.

Drupe

A type of fruit with a fleshy mesocarp and a hard, stone-like endocarp with a seed inside. Many plants within the Coffea genus, including Coffea arabica, produce drupe fruits.

Endocarp

The hard inner layer of the pericarp of many fruits, such as the pit or stone of a cherry, peach or olive. This layer protects the seed. In the coffee industry this layer is commonly known as parchment.

Endosperm

A nutritive tissue, largely made up of starch, which surrounds and nourishes the embryo in the seed of a flowering plant.

Enzyme

A protein that accelerates a specific chemical reaction in a living organism.

Epidermis

The outermost cellular layer covering the whole plant structure, including leaves, flowers, roots and stems. it forms a boundary between the plant and the external environment.

Evolution

The process that consists of changes in the heritable traits of a population of organisms as successive generations replace one another. Populations of organisms evolve, not indidivual organisms.

Ex Situ

A Latin phrase that translates roughly to “off site.” in Biology, it is used to refer to the examination of a plant or phenomenon away from its original location. Compare with in situ.

Exocarp

Also known as epicarp. Refers to the outermost shell of a fruit or the protective layer that contains oil glands and pigments. Often called skin.

F1 Hybrid

A colloquial term used by many breeders in the coffee industry to refer to recently developed crosses between established cultivated varieties and landraces/traditional varieties from Ethiopia.

First Filial (F1) Generation

Otherwise known as “F1.” The first generation of descent from a given mating. Compare with F1 Hybrid.

Fitness

The ability for an individual to both survive and reproduce in a particular environment, as made possible due to that individual’s genotype and resulting phenotype.

Fruit

The developed ovary of a seed plant with its contents, commonly fleshy, which contains the seed. Can often be eaten as food. Many fruits have evolved specific secondary purposes, such as to attract animals as a mode of transportation.

Gene

A hereditary determinant of a specific biological function. A segment of DNA located in a fixed position on the chromosome.

Genetic Diversity

The measure of differences in the genetic makeup of a population or species. Genetic diversity is an important mechanism for populations to adapt to changing environments. With greater diversity, it is more likely that some individuals in a populations will posses variations of alleles that are suited for the new environment. Those individuals are more likely to survive to produce offspring bearing that allele.

Genetic Drift

A mechanism of evolution referring to random fluctuations in alleles from generation to generation due to chance events. Genetic drift can cause traits to be dominant or disappear from a population. The effects of genetic drift are most pronounced in small populations.

Genetic Marker

A DNA sequence with a known physical location on a chromosome that can be associated with specific traits. The placement of and distance between these markers are used by scientists to measure the amount of diversity between organisms.

Genetic Selection

The exposure of an organism to environmental conditions in which it can survive only if it carries a specific gene or genetic element. This gives rise to a population selection based upon that genetic advantage.

Genetic Variation

A measure of genetic differences in or between populations, species or larger units, such as ecosystems and other geographic and political boundaries.

Genome

The complete set of an organism’s chromosomes, inherited from the parents or parent of that organism.

Genotype

The genetic constitution of an organism.

Genotype Frequency

The proportion of a specific genotype in a population.

Germplasm

An individual, group of individuals, or clone representing a genotype, variety or species, held in an in situ or ex situ collection. For plants, the germplasm may be stored in a seed collection, garden or other nursery.

Gibberellin

One type of naturally occurring, growth-promoting hormone found in plants. It is responsible in part for promoting growth in the embryo of a seed.

Haploid

A cell or an organism having a single set of unpaired chromosomes.

Heterozygosity

Having multiple/differing alleles at the same gene locus. The term can also refer to population-level genetic diversity.

Homologous Chromosome

Chromosome pairs (one from each parent) of approximately the same length, position and pattern, with genes for the same characteristics at corresponding loci.

Hybridization

Also known as hibrido in Spanish. The interbreeding of species, races, varieties and so on. A process of forming a hybrid by cross-pollinating plants of different types. Some consider hybrids only crosses between different species (compared with crosses within individuals of the same species). For example, the Hibrido de Timor (or Timor Hybrid) is a cross between Coffea canephora and Coffea arabica (Typica).

In Situ

A Latin phrase that translates literally to “in position.” In biology, it is used to refer to the examination of a phenomenon in the place where it occurs (i.e., in nature). Compare with ex situ.

Inbreeding

Repeated self-fertilization or mating between closely related organisms.

Inbreeding Depression

The progression of inbred populations weakening in fitness relative to non-inbred lines due to the presence of deleterious alleles.

Inbred

An organism that is the result of many generations of inbreeding.

Inflorescence

A cluster of flowers where all flowers arise from a main stem. The stem holding the whole inflorescence is called a peduncle.

Internode

The section of a plant stem between the nodes from which leaves emerge. The length of the internode is commonly used to differentiate species or varieties.

Interspecific

Between different species. Compared with Intraspecific.

Intraspecific

Within the same species. Compare with Interspecific.

Lateral Roots

Secondary roots that extend horizontally or diagonally from the primary root and serve to anchor the plant.

Leguminous

Referring to the plant family Leguminosae (also known as Fabaceae) that produces fruits in a pod, including peas, beans, clover, alfalfa and other plants. Many have interactions with fungi in the soil that enable them to fix nitrogen, making them high-value intercrops.

Locus/Loci

A segment of a chromosome that may code for a gene or have a regulatory function.

Meristem

A concentrated region of cells capable of division and growth in plants. Plants have various meristems including the apical meristem, shoot apical meristem, root meristem and the floral meristem.

Mesocarp

The botanical term for the fleshy middle layer of a fruit, between the exocarp and the endocarp. it is usually the part of the fruit that is eaten.

Microorganism/Microbe

A live microscopic organism such as a bacterium, archaeon, protist, alga or gunfus, which is made of up of one or more cells. Microorganisms use a variety of energy sources to interact with and later the environment and are critical to nutrient cycling in ecosystems, particularly the nitrogen cycle. They live in every part of the biosphere and participate in many of biological processes.

Model Plant

A plant species that is extensively studied to understand particular biological phemena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. For plants, a commonly studied model plant is Arabidopsis thaliana, a mustard relative preferred due to its short generation time and small stature.

Morphology

The form and structure of an organism or one of its parts. this includes aspects of the outward appearance such as shape, structure, color or pattern, as well as the form and structure of the internal parts like cells or organs. Compare to physiology.

Mutation

A change in the sequence of one or more nucleotides in DNA at a particular locus in an organism. Changes can alter an organism’s traits to have a greater or lesser chance of survival and reproduction relative to other members of its species.

Natural Selection

Differential survival and reproduction in nature that favors individuals that are better adapted to their environment, leading to the elimination of less fit organisms.

Nitrification

The chemical reaction that oxidizes an ammonia compound into any nitrate or nitrite, specifically due to the action of bacteria. An integral step in the nitrogen cycle which turns nitrogen into plant-available forms.

Nitrogen Fixation

A process by which nitrogen in the air is converted into ammonia, which plants and other organisms can assimilate. This conversion occurs naturally via enzymes produced by certain soil microorganisms, as well as by the energy made available by lighting.

Node

The point on a plant stem where a leaf is or has been attached. Each plant has many nodes and the number of leaves that come out of a node depends on the species. Internodes are the spaces between those nodes.

Non-Vascular Plant

Any plants that lack vascular tissue. Land plants known as bryophytes are non-vascular; this group includes mosses liverworts and hornworts. They do not possess true roots, stems, leaves, flowers or seeds, although the plant body is differentiated into leaf-like and stem-like parts. Compare to vascular plant.

Ovule

The structure that gives rise to and contains the female reproductive cells, which develops into a seed when fertilized.

Parchment

See endocarp.

Pectin

A class of plant cell wall polysaccharide that helps fruit maintain firmness, eventually breaking down into simple sugars and certain acids as fruit becomes overripe.

Pectinase

A natural enzyme that degrades pectin, commonly referred to as pectic enzymes. Commercially available pectic enzymes have been used during coffee processing to expedite the fermentation step.

Pericarp

The fruit wall, containing the endocarp, mesocarp and exocarp that make up the form, texture and structure of the fruit body.

Perisperm

The segment of some plant seeds that feeds the developing embryo.

Petiole

The small stalk that connects a leaf to a stem.

Phenology

Refers to recurring plant and animal life stages. The study of phenology also addresses the relationship between these periodic biological phenomena (such as flowering, fruiting and senescence) and climatic, seasonal and other environmental conditions.

Phenotype

The observable traits that manifest from an organism’s genotype.

Phenotypic Plasticity

The capacity of a single genotype to exhibit variable phenotypes when exposed to different environments or conditions.

Phloem

The live vascular tissue in plants that conducts sugars and other nutrients from the leaves to all other parts of the plant, based on growth and development.

Photosynthesis

A process by which a plant produces its food using energy from sunlight, carbon dioxide from the air and water from the soil. Energy for photosynthesis is captured by light-absorbing pigments, such as chlorophyll. Photosynthesis directly affects the health and growth of a plant, and can be limited by light, water, nutrients and carbon dioxide.

Physiology

The functions of living organisms and their parts. In plants, a subdiscipline of botany concerned with the functioning, or physiology, of plants and their organs. Compare to morphology.

Pistil

The female reproductive part of a flower. The pistil consists of three parts: a swollen base called the ovary, which contains the potential seeds; the style, arising from the ovary; and a pollen-receptive tip, the stigma, which takes various shapes and is often sticky.

Polyploid

A cell or organism that contains more than two haploid sets of chromosomes, meaning that the chromosome number is some multiple greater than the content of diploid cells. (Diploid organisms include humans and most animals.) For example, triploid and tetraploid cells are polyploid. Polploigy is a heritable condition and is common among plants, as well as among certain groups of fish and amphibians.

Protein

A large molecule consisting of a chain of molecules called amino acids. The sequence of amino acids and the molecule’s three-dimensional structure are coded by DNA and determine a protein’s specific function in cells or organisms.

Pure Line

A selected line of plants that is bred and evaluated over time until a uniform breeding population is established, with many generations of plants presenting the same basic phenotype. These lines are relatively similar genetically and can be planted from seed with assurance that they will grow to have a specific set of traits.

Recessive

Describes the relationship between variants of a gene. If the alleles are different, the dominant allele will be expressed, while the expression of the other allele, called recessive, is masked.

Seed

A flowering plant’s reproductive organ capable of developing into another such plant. Formed by sexual reproduction of gymnosperms and angiosperms, consisting of a protective layer that encloses a fertilized embryo and energy reserves. The coffee seed is colloquially referred to as the coffee bean.

Selection

An act of choosing an individual. In plant breeding, the term selection is used to define plants which have been chosen by humans to be bred together. Selection can happen inadvertently or with strong purpose based on an individual’s traits and phenotype.

Senescence

The death of and falling off of plant leaves or other organs.

Silverskin

A thin coating of a seed, known in biology as the integument and known to the coffee industry as chaff.

Species

In sexually reproducing organisms, species consist of individuals that can breed with each other to produce viable offspring.

Spore

Reproductive cells formed by certain organisms that can be highly resistant to external stressors in order to survive under various unfavorable conditions. They are similar to a seed in their purpose as a reproductive unit. Some spore-producing organisms include non-flowering plants, bacteria, fungi and algae.

Stipule

A small pair of outgrowths at the base of a leaf or leaf stalk (petiole).

Stoma (Plural: Stomata)

A “pore” in the epidermal layer of leaf tissue that allows for gas exchange. Stomata are made up of special types of cells that allow the “pore” to open and close to varying degrees depending on the climate of the plant’s energy balance.

Tetraploid

A cell or organism containing four sets of chromosomes.

Trait

A measurable physical or behavioral characteristic of an organism, determined by DNA.

Transgenic

Organisms that have been altered by introducing one or more DNA sequences from another species into them by artificial means. Transgenic plants can be made by introducing foreign DNA into a variety of different tissues. Compare to cisgenic.

Variety

A botanical variety is a rank in the taxonomic hierarchy below the rank of species and subspecies and above the rank of form (form / variety / subspecies / species / genus / etc.). It will have an appearance distinct from other varieties, but will hybridize freely with those other varieties. Another meaning, as used by plant breeders and in legal texts, is synonymous with cultivar and can have legal implications. Compare to cultivar.

Vascular Plant

A large group of land plants that have tissues for conducting water and nutrients throughout the plant. They appeared in the fossil record more than 400 million years ago. They are also called “higher plants” and make up most of the plants around the globe today. All Coffea species are vascular plants. Compare to non-vascular plants.

Wilting Point

The water content of oil when plants wilt and fall to recover upon rewetting. Most plants show signs of wilting long before this point is reached in soil.

Xylem

A type of vascular tissue in plants that is primarily involved in transporting water and nutrients from roots throughout the plant via transpiration forces. It also provides structural support. Compare to phloem.