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Glossary
A B C D E F G H I L M O P Q R S T U V Y
Abiotic
Not associated or derived from living organisms. Abiotic factors in an environment include such items as sunlight, temperature, wind patterns, and precipitation. Drought and low temperatures are both examples of abiotic stress.
Acids
Chemical compounds in grapes, and other fruits, that lower the pH and are responsible for a sour taste. The major acids in grapes are malic and tartaric acid.
Adaptive Trait
A genetic (inheritable) trait that helps an organism to maximize its reproductive success.
Allele
One of a number of possible versions of the same gene, or more broadly, the same gene locus.
Allele Segregation
the separation of alternative forms of a genetic locus. Every individual possesses a pair of alleles (assuming diploidy, the cause is more complicated for polyploidy) for any particular trait. Each parent passes a randomly selected copy (allele) of only one of these to its offspring. The offspring then receives its own pair of alleles for that trait (one form each parent). The relationship (dominant, recessive, co-dominant, etc.) between these two alleles results in the visible or measurable phenotype.
Aromas
The perception(s) that people have upon smelling odorant compounds. For example, many people will describe isoamyl acetate, an odorant, as smelling like 'banana'.
Avirulent
Not virulent or having lost virulence; no longer pathogenic.
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Berry Flesh Cell Wall Material Binding Capacity
the ability of the plant cell wall to bind specific compounds. In grape, this generally refers to tannins (see Tannins below). It is suggested that the grape's ability to bind tannins may influence the ability to extract tannins during fermentation and ultimately affect overall wine flavor.
Biotic
Associated or derived from living organisms. The biotic factors in an environment include the organisms themselves as well as predation, competition for food resources, and symbiotic relationships.
Bacterial and fungal infections are examples of biotic stress.
Black Rot
A name used for various diseases of cultivated plants caused by fungi or bacteria, producing dark brown discoloration and decay in the leaves of fruit and vegetables. Black rot in grape vines is caused by the fungus Guignardia bidwellii. This fungus affects the aboveground part of the vine and favors warm, humid weather.
Breeding Population
A designated, defined group within which interbreeding can take place. For the purposes of this project, the lineages (parents) of the group are known and have been selected because they possess certain traits of interest.
Budbreak
Initiation of growth from a bud.
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Cultivar
A variety of a plant that has been created or selected intentionally and maintained through cultivation.
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DNA Extraction
The process of isolating DNA from a cell, biological sample or organism. Extraction involves breaking open a cell (lysis), removing the cellular proteins and RNA, and precipitating the DNA (forcing it out of solution).
DNA Sequencing
The process of determining the order of nucleotides (which are: adenine, guanine, cytosine, and thymine) of any particular DNA strand. Modern technology has resulted in the advent of fast, cost-effective methods for determining sequence. These methods rely on the detection of fluorescent molecules and complex computer systems to collect raw data or trace files (the initial information that results from sequencing), analyze the information (assessing quality through comparison to reference markers, record the actual sequence nucleotides and compare it to other sequences) and ultimately store the huge amount of data that results from large sequencing projects.
Downy Mildew
Any of several types of oomycete microbes that are obligate parasites of plants. Downy mildews exclusively belong to Peronosporaceae. Yield loss associated with downy mildew is most likely related to soft rots that occur after plant canopies collapse and sunburn occurs on fruit.
Dried on the Vine
The process of letting grapes dry directly on the vine to result in raisins. The more traditional method involves harvesting and drying the fruit on trays. Different methods produce subtle taste differences and preferences among raisin eaters.
Dynamic Simulation
The use of a computer program to model the time varying behavior of a system.
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Economic Modeling
A theoretical and/or mathematical construct that represents economic processes by a set of variables and a set of logical and/or quantitative relationships between them. The economic model is a simplified framework designed to illustrate a complex processes, often but not always using mathematical techniques.
Etiology
Cause or origin.
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Foliar Phylloxera
Grape phylloxera, Daktulosphaira vitifoliae, is a tiny insect that forms galls on the leaves and roots of grapevines. In the US, damage is now most prevalent on leaves of French-American hybrid grapevines. High populations of foliar phylloxera can result in premature defoliation, reduced shoot growth, and reduced yield and quality of the crop.
Fruit Quality
Characteristics that impact taste, smell, color, consumer preference, harvesting and post-harvest handling, storage and shipping. Fruit quality can be referred to in positive (e.g. high sugar, deep color, early ripening) or negative (e.g. too soft for mechanical handling, rots quickly) terms.
Full-Sibling Progeny
Offspring that share the same two parents.
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GC-TOF-MS
Gas chromatograph time of flight mass spectrometer. A combination of analysis methods that allows for the examination of organic compounds both quantitatively and qualitatively. The gas chromatograph separates the compounds and a time of flight mass spec determines an ion's mass-to-charge ratio via a time measurement (lighter and heavier ions will have different measurements).
Gene
The fundamental physical and functional unit of heredity. It consists of a sequence of DNA that occupies a specific location on a chromosome and may determine a particular characteristic in an organism.
Genetic Background
All the genes (and sometimes the specific alleles) present in a particular individual organism.
Genetic Map (also known as a "Linkage map")
A map that shows the position of known genes, or markers, relative to each other in terms of recombination frequency, rather than a specific physical distance along each chromosome. Genes that are nearer to each other are more likely to be inherited together (and not separated during meiosis) and are therefore said to be genetically linked. The closer two genes (or markers) are, the lower the recombination events between them will be, and thus the smaller the physical distance between them. A genetic map is not a physical map, however when sequence information is available, a physical location for genetic markers may be established.
Genome
The genetic material of an organism, specifically, the genes contained within one haploid set of chromosomes.
Genome-Wide Selection (GWS)
Selecting new breeding material/cultivars based on DNA sequence rather than field data. DNA variations responsible for either positive or negative traits must first be identified and a screening mechanism (e.g. markers) must be available.
Genomics
A discipline of that aims to sequence, assemble, and analyze the function and structure of genomes
Genotype
The specific allele composition of a gene, set of genes, cell or organism.
Genotyping by Sequence (GBS)
A new system associated with new Illumina sequencing formats that allow for the acquisition of DNA sequence information faster and at a lower cost than experienced in the past.
Germplasm
A collection of genetic resources for an organism. For grape, this would include seeds, cuttings, maintained nurseries and even stored DNA samples.
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High-Performance Liquid Chromatography (HPLC)
Sometimes also referred to as high-pressure liquid chromatography. A technique used to separate a mixture of compounds.
High Resolution
See Molecular marker map.
Hybrid
A genetic hybrid carries two different alleles of the same gene. Hybrid can refer to differences at a single gene or offspring resulting from the mating of two genetically distinct individuals (which may carry different alleles across many different genes). Hybrids between different subspecies of the same species are known as intra-specific hybrids. Hybrids between different species within the same genus are known as interspecific hybrids.
Hybrid Population
The offspring from the mating of two genetically distinct individuals. Hybrid populations exhibit a continuum of variation, spanning the gap between parental types. The term may be used in reference to a single gene, a single trait or to a whole organism.
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Isolates
A population of organisms that has little genetic mixing with other organisms within the same species.
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Linkage Map
See Genetic Map.
Locus (plural: loci)
The specific location of a gene or DNA sequence on a chromosome. A variant of the similar DNA sequence at a given locus is called an allele.
Low Temperatures
Can refer either to the temperature at which green tissue experiences frost injury (28-30°F), or the temperature that can injure dormant buds or other permanent structures (trunk, cordons, canes) of the vine during the winter. These latter temperatures are highly dependent on variety, growing conditions, climatic factors and more. See also Low temperature tolerance.
Low Molecular Weight Phenolic Species
A sub-class of phenolics found in grapes and wines that include compounds responsible for bitterness and color. This group of phenolics does not include the tannins, and are not strongly astringent.
Low Temperature Tolerance
The ability of a dormant grapevine to tolerate cold temperatures, may also be referred to as cold hardiness. Grapevine cold hardiness is a highly dynamic condition, influenced by environmental and growing conditions, and varying over time and among grapevine varieties and tissues.
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Macerated
The softening or breaking into pieces using a liquid. Maceration occurs when you chew or can also occur in an experimental format by breaking down fruit tissue in a liquid (e.g. blending or homogenizing).
Marker Application
The process of utilizing established or identified markers for selection.
Marker Assays
A method by which an identified marker can be utilized/applied. It could be a visual identification (e.g. measurement of plant height), biochemical (e.g. chemical assay to measure tannins) or molecular (e.g. DNA sequencing).
Marker Assisted Selection (MAS)
A process whereby a marker (morphological, biochemical or molecular) is used for selection of a trait of interest (e.g. disease resistance, fruit quality, low temperature tolerance).
Marker Discovery
The process of identifying a morphological, biochemical or molecular marker. This can be done in many ways, such as DNA sequencing, biochemical assay or field measurements.
Molecular Marker
An identifiable difference, or variation, in DNA sequence. To be useful, markers must be easily identifiable (by some kind of assay) and polymorphic (have a certain level of diversity).
Molecular Marker Map
A collection of molecular markers oriented relative to one another. Molecular markers can also be associated with a physical location in a genome (physical map). A map may cover a single gene, a chromosome or an entire genome. The denser (more markers/smaller gaps between markers) the map, the higher the resolution, the more useful it can be for identifying specific genes, or DNA sequences, associated with specific traits. A less dense map will identify a larger genomic area associated with a specific trait.
Muscat Flavor
The Muscat variety of grapes of the species Vitis vinifera is widely grown for wine, raisins and table grapes. Their color ranges from white to near black and almost always has a pronounced sweet floral aroma. Muscat grapes are grown around the world and it is perhaps the oldest domesticated grape variety.
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Off-Aroma Volatiles
Volatile compounds that result in aromas undesired by most consumers when present at high enough concentrations to be smelled.
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Phenolics
A class of chemical compounds produced by grapes, and other plants, which include tannins (responsible for 'astringency') and anthocyanins (responsible for red wine color). Some phenolics have also been implicated as the cause of health benefits gained from fruit or wine consumption.
Phenome
The physical and biochemical traits of an organism.
Phenomics
The field of science focused on measuring phenomes, particularly as they are modified by genetic mutation and environmental effects.
Phenotype
The detectable outward manifestation of a specific genotype. Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two.
Phenotypic Analysis
Determination and assessment a phenotype of interest (color, small, taste etc).
Phomopsis
Also called grape canker or Dead-arm. A disease of grapes caused by a deep-seated wood rot of the arms or trunk of the grapevine. As the disease progresses over several years, one or more arms may die, hence the name "deadarm". Eventually the whole vine will die. Dead-arm has been identified as really being two diseases, caused by two different fungi, Eutypa lata and Phomopsis viticola (syn. Cryptosporella viticola).
Pierce's Disease
Caused by Xylella fastidiosa, a xylem-limited bacterium that clogs the vascular tissue of susceptible grape cultivars. This vascular constriction inhibits the movement of water through the grapevine and often results in visible symptoms during periods of heat or drought stress.
Pipeline
A sequential path of steps. In research, 'pipelines' are often defined for multi-step experimental procedures e.g. A VitisGen pipeline may look as follows: tissue samples will be taken from grape lines of interest, DNA will be isolated from this tissue, markers will be mapped with each tissue sample, marker results will be conveyed to grape breeders, and grape breeders will select relevant individuals to be parents of new crosses or from resulting previous crosses.
Powdery Mildew
A disease caused by many different species of fungi in the order Erysiphales. Infected plants display the distinctive symptoms of white powdery spots on the leaves and stems, with the lower leaves most affected. Powdery mildew grows well in environments with high humidity and moderate temperatures and can result in significantly reduced crop yields. In an agricultural setting, the pathogen can be controlled using chemical methods, genetic resistance, and careful farming methods.
Precocious
Early, premature, having developed certain abilities or proclivities at an earlier age or stage than usual.
Precocious Flowering
Having flowers that blossom before the leaves emerge.
Primary Bud Hardiness
Refers to the cold-tolerance of a primary grape bud. Buds are the small part of the vine that rest between the vine's stem and the leaf stem. Grapevine buds contain a primary, secondary and tertiary bud. The primary bud is most well-developed and is typically less cold-hardy than secondary or tertiary buds. Freeze injury in response to low temperatures typically affects the primary bud first.
Progeny
Offspring, descendants.
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Qualitative Trait
Traits that are easily classified into distinct phenotypic categories. These discrete phenotypes are under the genetic control of only one (monogenic) or a very few genes with little or no environmental modification to obscure the gene effects. Classic examples include such things as eye color in animals or skin color in grapes.
Quantitative Trait
Also called polygenic traits. A quantitative trait shows continued phenotypic variation, due to the trait being the sum of several small effects caused by the gene. Classic examples include weight and stature.
Quantitative Trait Loci (QTL)
A stretch of DNA containing, or linked to, the genes that underlie a quantitative trait. QTLs link quantitative genetic traits (which are largely phenotype-based) to the molecular basis of the trait.
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Race-Specificity
With regard to resistance to plant pathogens (viruses, bacteria, etc). The gene/genes/part of a gene that allow for resistance to a specific pathogen.
Resistance
The ability of an organism to defend itself against a disease.
Rootknot Nematode
Plant-parasitic nematodes from the genus Meloidogyne. They exist in soil in areas with hot climates or short winters. Root-knot nematode larvae infect plant roots, causing the development of root-knot galls that drain the plant's photosynthate and nutrients. Infection of young plants may be lethal, while infection of mature plants causes decreased yield.
Rootstock
A root or part of a root used as a stock for plant propagation.
Screen - an experimental technique used to identify individuals who possess a characteristic, or phenotype, of interest.
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Secondary Metabolites
Also known as Natural Products. Organic compounds that are not directly involved in the normal growth, development or reproduction. Secondary metabolites are often restricted to a narrow set of species and may play an important role in plant defense. Humans use secondary metabolites as medicines and flavorings.
Selection
The increase, or decrease, of the prevalence of a specific trait. If the trait of interest has a genetic basis, selection will increase, or decrease, the occurrence of the genes involved in the population of interest. In Vitisgen, we are selecting for low temperature tolerance, fruit quality and resistance to powdery mildew.
Segregation
Separation. In genetics, segregation refers to the separation of paired alleles or homologous chromosomes.
Segregating population – a set of offspring form the same parents that demonstrate separation or variation in phenotype, genotype or both.
Simple Sequence Repeat (SSR)
A small segment of DNA, usually 2 to 5 base pairs in length that repeats itself a number of times.
Socioeconomics - the interrelation between economics and social behavior. In the case of VitisGen, the impact of social preferences – e.g., color, flavor, specific grapes (Cabernet Sauvignon) - on the development of new grape cultivars.
Single-Nucleotide Polymorphism (SNP)
A single base-pair change in the DNA sequence.
SNP Calling
The identification of single nucleotide polymorphisms that are a result of sequence level variation rather than errors produced by the underlying sequencing technology.
Sugars
Chemical compounds in grapes, and other fruits, that are responsible for a sweet taste, and can also can be fermented by yeasts into ethanol. The major sugars in grapes and wines are fructose and glucose.
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Tannins
Chemical compounds in grapes and wines responsible for the perception of "astringency", or the feeling of stickiness and drying in the mouth. Tannins are a sub-class of phenolics.
Teinturier flesh
A French term meaning to dye or stain. It is a wine term applied to grapes whose flesh and juice is red in color due to anthocyanin pigments accumulating within the pulp of the grape berry itself.
Trait
A genetically determined characteristic or condition.
Trait Marker association
A statistical tool for detecting DNA variants responsible for genetic traits. In practice, it is common to specify an analysis model of the average genetic effects of the genotypes. If the selected model is close to the actual underlying trait model, Trait Marker Selection may provide higher mapping resolution than methods based solely on closely related meiosis events.
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UV/Vis Spectrophotometry (spec)
An analytical instrument used to measure the concentration of compounds in grapes, or other samples, based on the absorbance of light. Spectrophotometry can be used to measure sugars, acids, YAN, phenolics, and other compounds in grapes or wines.
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Virulent
The ability of an infective agent (e.g. bacteria) to overcome an organism's defensive mechanisms. It can also refer to resulting disease severity or the specific traits of a pathogen that make the host ill.
Vitis cinerea (V. cinerea)
An American native variety of grape. It has leaves that are cordiform-emarinate, with blunt teeth, grey-ashy-violet buds, and small black berries that are mildly unpleasant to eat. It grows in Oklahoma and Texas and also known by the name "winter grape" or "possum grape."
Vitis vinifera (V. vinifera)
A species of grape native to the Mediterranean region, central Europe, and southwestern Asia. The leaves are alternate, palmately lobed, and the berries can be green, red, or purple. Cultivars of V. vinifera form the basis of the majority of wines produced around the world.
Volatiles
Chemical compounds that exist, at least partially, as a gas. "Odorants" are a sub-class of volatiles that have an aroma and can potentially affect how a wine smells.
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Yeast Assimilable Nitrogen (YAN)
A critical nutrient for fermentation. YAN is used by yeast to make proteins, cell walls, and other biomolecules necessary for growth. YAN is present in grapes, but may need to be supplemented by winemakers prior to fermentation if its concentration is too low.
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Funding for VitisGen "Accelerating grape cultivar improvement via phenotyping centers and next generation markers" is provided by a Specialty Crop Research Initiative Competitive Grant, Award No. 2011-51181-30635, of the USDA National Institute of Food and Agriculture. This site is hosted at Cornell University. Copyright © 2015.