This is a brief glossary that I use in my Forest Genetics classes. Most of the definitions are fairly general and would apply to most organisms and applications, but a few are forest-genetics specific. The glossary is very much a work-in-progress. I have borrowed definitions from a number of sources, and when I get done polishing it up, I will write a short acknowledgment.

Feel free to link to it, or if you would like a copy on disk, send me a formatted disk (Mac only, I'm an elitist.)

If you have comments or suggestions, send me an e-mail:

A... B... C... D... E... F... G... H... I... J... K... L... M... N... O... P... Q... R... S... T... U... V... WXYZ

Additive genes -

A form of allelic interaction in which there is no dominance. The heterozygote is intermediate in phenotype between homozygotes for the alternative alleles. For multiple-gene traits, approximately equal contributions made by many loci.

Allele -

One of several alternative forms of a gene occupying the same locus on a particular chromosome.

Analysis of variance -

A statistical analysis by which F values (variance ratios) are composed in such a manner as to determine the probability that differences among populations or treatments are too large to be due to chance.

Backcross -

Crossing a hybrid back to one of the original parents, called the recurrent parent. In agronomy, the recurrent parent is usually a single genotype, often a named variety. In forestry, the recurrent parent is usually a different genotype from the same species or population. (This is done to prevent inbreeding depression.) Example: collecting pollen from a pitch pine x loblolly pine F1 hybrid and pollinating a pure loblolly pine. The seed produced would be called first backcross and the loblolly pine the recurrent parent.

Backward selection -

Selection of parent trees based on results from a progeny test. (See Forward selection.)

Best linear prediction (BLP) -

A statistical method which utilities matrix algebra to predict breeding values for any trait or selection index; in BLP fixed effects are assumed to be known. BLP is especially suited for analyses of messy or unbalanced data. (See unbalanced)

Best linear unbiased prediction (BLUP) -

A statistical method which predicts breeding values for any trait or selection index; unlike BLP, in BLUP the fixed effects are estimated. Like BLP, BLUP is well suited for analyses of messy or unbalanced data. (See unbalanced)

Biodiversity -

(biological diversity) The variety and variability (both in numbers and frequency) of the organisms and the genetic variability within each species. The term can be used to describe a particular site, a general habitat type, a small or large geographic region, or (less correctly), the genetic diversity of a particular species or population. (See gene pool, breeding population, heterozygosity, and germplasm conservation.)

Block -

In a field study arranged in a randomized complete-block design, a block is a unit of land upon which at least one plot of all of the entries (families, clones provenances) are planted. (In this case a replication and a block are the same.)

Breeding orchard -

(breeding seed orchard, breeding arboretum) A planting of selected trees, usually clonally propagated, designed to ease breeding work.

Breeding population -

A group of individuals selected from a wild population for use in a breeding program. Usually phenotypically selected for desirable traits. In species with large natural ranges, there are usually several to many, more-or-less separate breeding populations, each designed to provide progeny suited to a particular geographic region (See seed zone and breeding zone.)

Breeding value -

The genetic value of an individual determined by the mean value of its progeny. May be on the basis of individual traits or a selection index.

Breeding zone -

An area within which a single population of improved trees can be planted without fear of mis-adaptation. (See seed zone.)

Candidate tree -

A tree that has been tentatively selected for inclusion in a breeding program, but has not yet been measured or compared with surrounding trees. (See plus tree and elite tree.)

Character (trait) -

A distinctive but not necessarily invariable feature exhibited by all individuals of a group and capable of being described or measured; e.g. color, size, performance. A character of a given individual will have a certain phenotype as determined by the individual's genotype and environment.

Chromosome number -

The number of chromosomes found in a typical individual of a particular species. Typically the sex cells of a species have one-half the number of chromosomes found in the vegetative portion and are said to be haploid. (See polyploid.)

Cline -

An environmental gradient (temperature, rainfall, soil ph . . .) and a corresponding phenotypic gradient in a population of plants or animals. Where these have been evaluated by provenance tests, clines are often found to have a genetic basis.

Clonal test -

A field planting of several to many vegetatively propagated plants. Such tests furnish estimates of the relative performance of different genotypes, but do not necessarily provide information on breeding behavior.

Clone -

1. To propagate a plant asexually usually by grafting, rooting cuttings, tissue culture, or apomictic seed. Except for an extremely low level of mutation, all plants from a clone are genetically identical. (This is the usage most common in agronomy, horticulture and forestry.) (See ortet and ramet.)
   
   
2. To regenerate a whole plant from a single cell.(This usage is common in tissue culture research.)
   
   
3. To identify and isolate a gene controlling a specific trait from an organism. (This usage is common in molecular biology.)
   
   
4. A group of plants produced from cuttings, stump or root sprouts, tissue culture, or some other method that produces offspring genetically identical to the original plant. Most commonly used in forestry to establish grafted seed orchards, but becoming more common for commercial plantations.

Combining ability -

The ability of an individual, when crossed, to produce progeny with strong expression of a particular trait.

Combining ability, general -

Good general combining ability (GCA) is the ability of an individual to produce progeny with high genetic quality, when crossed to many other individuals in the population.

Combining ability, specific -

Good specific combining ability (SCA) is when the progeny from a particular full-sib cross perform better than what would be predicted from the general combining ability of either parent.

Conelet -

An immature cone (strobilus) in the conifers.

Control pollination -

To purposely pollinate the female flowers of a tree with pollen from a known source, usually one specific tree. Usually the flowers are Protected from undesirable pollen by covering them with a pollen-tight cloth or paper bag before they are receptive and adding known-source pollen at receptivity. Full-sib families are produced.

Cross -

(1) To collect pollen from one tree and pollinate a second tree.
(2) The progeny of a control pollination.

Cross-pollination -

Pollination by genetically different plants

Crossing groups -

Any group of individuals which comprises a unique set of parents. A diallel CG is one in which controlled crosses are made between each pair of parents in the group but crosses with parents outside the group are excluded. A factorial CG is one in which a limited number of parents are used as male testers in controlled crosses with an unlimited number of female parents. An open-pollinated CG is one in which all parents in a breeding population are included in a progeny test or series of tests and which may be used for reforestation with genetically improved material.

Diallel, complete or full-

A mating design and subsequent progeny test resulting from the crossing of 'n' parents in all possible 'n2' combinations including selfs and reciprocals. (Because of severe inbreeding depression in the selfs, these are often skipped and the test still called a "full" diallel.)

Diallel, incomplete or partial

A partial sampling - any individual family or type of family may be omitted. In either the complete or incomplete diallel, identities of both seed and pollen parents are maintained for each family.( See Pedigree)

Dominance -

In classical Mendelian genetics, the masking of the action of one allele by another. If an individual with red flowers is crossed with an individual with white flowers and all progeny have red flowers, then the allele for red pigment is fully dominant over the allele for white flowers.

Dominance, partial -

The incomplete masking of the action of one allele by another. If an individual with red flowers is crossed with an individual with white flowers and all progeny have pink flowers, then the allele for red pigment is partially dominant over the allele for white flowers.

Dysgenic -

An action or process that is detrimental to the genetic qualities of a population. Usually applied to human actions, such as high grading or land clearing, which would reduce the local gene pool.

Ecotype -

A sub-population of a species that occurs in a particular well-defined environment, usually showing better adaptation to that environment than the species as a whole. (See cline.)

Elite tree -

A tree that has been shown by progeny testing to produce superior offspring (See plus tree and candidate tree.)

Endemic -

A plant or animal species or subspecies native to a small region.

ex situ management -

The management of planted stands of trees to protect them and insure survival, growth and identity; the conservation or preservation of trees as seed, pollen, tissue culture, or excised plant parts. (See germplasm conservation, ex situ.)

Exotic -

Broad definition: A non-native population introduced into a new area. Narrow definition: a species introduced from another country.

F1 -

The first (filial) generation of a cross. Usually the progeny from an F1 cross will be phenotypically fairly uniform.

F2 -

The second (filial) generation of a cross, produced by intercrossing individuals from the F1 generation. The progeny of an F2 cross will be more variable phenotypically than the F1.

Family - A group of closely related genotypes. (See sib)

Family selection -

The selection of progeny families on their mean performance. In addition, the best individuals are usually selected in the best families.

Fertilization -

Union of the nucleus and other cellular constituents of a male gamete (sperm) with those of an egg to form a zygote. In some species, fertilization may occur months after pollination.

Fitness -

In classical genetics, the ability of an individual or population to both survive and reproduce in a particular environment.

Fitness, adaptive -

The ability of a population to survive, reproduce, and adapt genetically to a changing environment for at least a modest number (usually fewer than 50) generations. (See gene pool and heterozygosity.)

Fitness, evolutionary -

The ability of a population (usually a whole species or ecotype) to survive, reproduce, and adapt genetically to a changing environment for many (usually more than 50) generations. (See gene pool and heterozygosity.)

Flower -

Angiosperm reproductive structure bearing pistils, stamens, or both, and usually also sepals and petals. So-called flowers of conifers are the male and female strobili before and during pollination.

Forest genetics -

The study of heredity in forest trees.

Forest tree improvement -

The application of genetic principles to the improvement and management of forest trees.

Forward selection -

Choosing the best individuals out of a progeny test for use in seed orchards and/or subsequent generations of breeding. (See Backward selection.)

Gain -

(See genetic gain.)

Gene bank -

A collection of germplasm (seeds, pollen, whole plants, extracted DNA) collected and maintained so as to sample as much as possible of the genetic variability in a population. (See germplasm conservation.)

Gene flow -

The movement of specific alleles among different populations of a species or among related species.

Gene pool -

The sum total of all the genetic variation in the breeding population of a species and closely related species capable of crossing with the species.

Gene pool, primary -

The sum total of all the genetic variation in the breeding population of a species and closely related species that commonly interbreed with, or can be routinely crossed with, the species.

Gene pool, secondary -

The sum total of all the genetic variation in the breeding populations of related species that can be crossed with the species using mentor pollen, embryo rescue or other unusual measures.

Gene pool, tertiary -

The sum total of all the genetic variation in other organisms that cannot be crossed with the species. (With the development of genetic engineering, it is theoretically possible to transfer genes isolated from any organism (plant, animals, virus, or bacterium) into a plant. This makes the line between the secondary and tertiary gene pools somewhat fuzzy.)

Gene -

The basic unit of inheritance.

Genetic diversity -

General concept: the amount of genotypic variability in a population. (See gene pool.) Quantitative definition: the number of different alleles per loci and the proportion of loci with more than one allele in a species or population.

Genetic drift -

Changes in gene frequency in small populations due to random chance. Usually a loss of rare alleles.

Genetic gain -

The change achieved by artificial selection in a specific trait. Gain is usually expressed as the change per generation or the change per year. Gain is influenced by selection intensity, parental variation, and heritability.

Genetics -

Genetics is the basic science dealing with causes of resemblances and differences among organisms related by descent. It takes into account the effects of genes and the environment.

Genotype -

The specific set of genes possessed by an individual, both expressed and recessive.

Genotype-environment interaction -

Changes in rank or levels of performance among individuals when tested in different environments. (See progeny tests and clonal tests.)

Geographic variation -

The phenotypic differences among native trees growing in different portions of a species' range. If the differences are largely genetic rather than environmental, the variation is usually specified as racial, ecotypic, or clinal.

Germplasm conservation -

Maintenance of the genetic variability of a population. (The term is used in preference to oegermplasm preservation” to reflect the ever-changing nature of living populations.)

Germplasm conservation, ex situ -

Maintaining the genetic variability of a population in a different environment or geographic location than where it evolved, i.e., plantations of exotic species, breeding orchards, cold storage of seed or pollen. (See gene bank.)

Germplasm conservation, in situ -

Maintaining the genetic variability of a population in approximately the same geographic and ecological conditions under which it evolved. (This should always be the first choice.)

Heritability -

General concept: The degree to which progeny resemble their parents. Quantitative definition: A ratio of genetic relative to environmental factors that influence the expression of a trait.

Heritability, broad sense -

The proportion of the total phenotypic variability for which genetic differences are responsible.

Heritability, narrow sense -

The proportion of the total phenotypic variability that is due to additive genetic variability.

Heterozygous -

Having two different alleles at a locus. When used to refer to the whole genotype, indicates that the individual has different alleles at most loci. When used to refer to a species as having low or high heterozygosity relative to other species, indicates that the species has a relatively high number of variable loci.

Homozygous -

Having two identical alleles at a locus, at most loci, or in the entire species. (See heterozygous.)

Hybrid -

Progeny from a cross among dissimilar genotypes. In forestry, the term is usually used for crosses between species.

Ideotype -

The ideal type or perfect specimen. A description or illustration of what the final goal of genetic improvement for a species would look like. The ideotype is developed without regard to heritabilities for the individual traits involved. It is not intended to be a practical field guide for selecting "+" trees, but as a starting point for developing a field-selection guide.

Inbreeding depression -

The reduction in vigor often observed in progeny from matings between close relatives. Inbreeding depression is due to the expression of recessive deleterious alleles and is usually severe in open-pollinated outcrossing species (most forest trees) that occur in fairly high population densities.

Inbreeding -

Matings between related individuals. In open pollinated tree species, inbreeding usually leads to mild to poor seed set, low germination, and severe growth reduction.
(See selfing.)

Introgression -

The movement of genes from one population into another through hybridization followed by backcrossing. Usually refers to movement of genes from one species to another or among sub-species that have been geographically isolated then brought back together by changes in the species ranges or planting of exotic populations. (See gene flow.)

Land race -

A population of trees of a non-native species that has undergone one or more generations of natural selection in a new environment, i.e., Norway spruce in New York State.

Locus -

The position of a gene on a chromosome.

Mutation -

A sudden change in the genotype, usually caused by a small change in the DNA sequences in the chromosomes. It may also be caused by changes in chromosome number or breakage of individual chromosomes.

Neighborhood -

The largest population in which mating occurs at random. Generally, a small population within which individuals can be expected to be closely related. Neighborhoods may be created by barriers to pollen and seed movement, or other isolating factors.

Open pollinated-

Pollination occurring due to wind or insects. (See sib.)

Ortet-

The original plant from which a clone is started through rooted cuttings, grafting, or tissue culture, or other means of vegetative propagation. The original plus tree used to start a grafted clone for inclusion in a seed orchard is the ortet. (See ramet and clone.)

Outcrossing-

Matings (controlled or natural) among unrelated individuals. May also refer to a species that has specific barriers to selfing, or exhibits such inbreeding depression that inbred individuals never reach maturity. (See selfing.)

Pedigree - Record of ancestry.

Pedigree, full-

All parents, grandparents . . . of a particular genotype are known all the way back to some natural population.

Pedigree, partial-

Some, but not all, ancestors of a particular genotype are known, usually the female parents. Partial pedigrees are most common where open-pollinated or polycross seed is used for progeny tests.

Pedigree breeding-

A breeding system where all the ancestors of any individual in the population are known back to the original "+" trees selected in wild stands. The system depends on control pollination for all matings.

Phenotype-

The visible characteristics of a tree. The phenotype is determined by the genotype interacting with the environment in which it is grown.

Plot-

In a field study, a group of trees, all from the same entry (family, clone, provenance . . .) planted together (usually). (See block and randomized-block design.)

Plot, contiguous-

In a field study, a group of trees, all from the same entry (family, clone, provenance . . .) planted together. A five-tree row-plot is probably the most common design for forest genetics experiments. (See block and randomized-block design.)

Plot, non-contiguous-

In a field study, a group of trees, all from the same entry (family, clone, provenance . . .) planted in the same block, but not planted together. The non-contiguous interlocked-plot design is a recent innovation that allows tests to be thinned systematically and still maintaining uniform spacing. (See block and randomized-block design.)

Plus tree-

A phenotypically superior but untested tree. (See elite tree and candidate tree.)

Pollination -

Deposition of pollen on the receptive part of the female flower.

Polycross test-

A progeny test to assess general combining ability from crosses among selected parents. Identities can be maintained only for the seed parents. A mixture of pollen is artificially applied to each female parent, or the selections naturally and randomly open-pollinate themselves.

Polyploid-

A cell, tissue, individual, population, or whole species having more than twice the basic number oex” of chromosomes of the ancestral species. Polyploidy may lead to increased growth rates (Populus) or severe dwarfing (Pinus). Three sets of chromosomes is called triploid, four sets-tetraploid, six sets-hexaploid, etc. (See chromosome number.)

Population-

A group of individual trees having some characteristics in common, either location, family ancestry, or intended use.

Progeny test-

A test to compare the offspring of different parents. (See backward selection.)

Propagule-

Any type of plant to be used for reproduction. It might be a seedling, a rooted or unrooted cutting, a graft, or a tissue-cultured plantlet.

Provenance test-

A test comparing trees grown from seed or cuttings collected in many parts of a species range. (See seed source.)

Race-

A sub-population, usually fairly large, of a species exhibiting some degree of phenotypic (and presumably genotypic) uniformity among individuals within the population and distinct from the species as a whole.

Ramet-

A vegetatively reproduced copy of a plant. Each ramet will have almost precisely the same genotype as the original parent tree, known as the ortet. (See clone and ortet.)

Randomized complete-block design-

The most common experimental design used in progeny, provenance and clonal field tests. Each entry in the test is replicated once in each block. All the entries are arranged randomly within a block and a new randomization pattern is used for each block. (See replication, block, and plot.)

Reciprocal cross -

The repetition of a cross where the sexual function of the parents is reversed, i.e., female B x male A is the reciprocal of female A x male B.

Recurrent selection-

Selection of individuals or families and intermating them or allowing them to interpollinate to produce the next generation. Usually the process is repeated several times (for long-lived perennials such as trees) or many times (for annuals.) The technique is used to improve the overall performance of the population rather than to select outstanding varieties for immediate use.

Replication-

In a genetics test a replication contains one plot of each entry in the test. (See Randomized block design , block, and plot.)

Resilience-

The ability of a population to persist in a given environment despite disturbance or reduced population size. The resilience of a population is based upon the ability of individuals within the population to survive (fitness) and reproduce (fecundity) in a changed environment and the genetic variability of the population which allows the production of new genotypes.

Rogue-

To remove trees that have an undesirable phenotype, or that have been shown through progeny tests to have a less desirable genotype from a seed orchard, seed production area, or nursery bed.

Rootstock-

A rooted plant, usually a seedling, on which a scion is grafted.

Scion-

A twig, bud, or other vegetative cutting to be grafted onto the root-system of another plant. (See seed orchard, ramet, and clone.)

Screening-

Selecting for a particular trait, often used when referring to the application of a specific treatment such as white pine blister rust spores or a herbicide, and then looking for resistant individuals. Usually implies checking large number of individuals at one time.

Seed orchard-

A plantation established for the production of tree seed.

Seed orchard, clonal-

A seed orchard established from vegetatively propagated trees, usually grafts. Usually clonal seed orchards are established with single-tree plots with different ramets of each clone located as far apart as possible to reduce self pollination.

Seed orchard, seedling-

A seed orchard established from seedlings (as opposed to grafts). Usually seedling seed orchards are established with multiple-tree plots so that selection can take place first among families and then among the individuals within each family plot, reducing each plot to a single tree.

Seed production area-

A stand or plantation not originally planted to produce seed, but rogued of inferior trees and treated in such a manner as to produce large quantities of seed. Usually the stand or plantation is from a known origin or selected seedlot.

Seed source-

The location where a seedlot was collected. If different seedlots of an exotic species are collected and tested, the test is called a seed-source test to distinguish it from a provenance test.

Seed transfer guide-

A set of rules for collecting seed and planting seedlings so that genotypes are not moved to microclimates or soils within which they will be mis-adapted. Usually seed transfer guides describe the maximum movement from the point of collection in miles east and west, north and south as well as feet in elevation. (See seed zones.)

Seed zone-

An area within which seed can be collected from any natural stand and planted in any new site without fear of mis-adaptation.

Seedlot-

A designation of a group of seeds with some factor in common, i.e., year of collection, stand or seed orchard, individual "+" trees, point of origin in a provenance test, a half- or full-sib family.

Selection differential-

The difference between a selected tree, family, or clone and the average of the population from which it is taken.

Selection-

Choosing individual trees or populations with desirable characters to obtain genetic improvement.

Selection, clonal-

Choosing the best clones from a clonal test.

Selection, index-

Choosing parents on the basis of a weighted score which combines economic value and heritability of several desirable traits.

Selection, mass-

(phenotypic selection) Choosing trees on the basis of their phenotypes (appearance) alone.

Selection, recurrent-

Choosing individuals out of families, making crosses, then progeny testing. The process is usually repeated several to many times. Most tree improvement programs are based on recurrent selection.

Selection, tandem-

Selecting for two or more traits sequentially rather than simultaneously. The technique is useful when one trait can be evaluated early and a second trait only after a number of years, or when one trait is much more expensive to measure.

Self pollination-

The natural or artificial pollination of a female flower with pollen from the same genotype. (See inbreeding, outcrossing, and homozygosity.)

Sib-

(sibling) A term meaning brother or sister. Half sibs have one parent in common. Full sibs have both parents in common.

Sublining-

Dividing a breeding population into several to many smaller populations. All controlled crosses for forward selection are made within a subline, leading to inbreeding within sublines. Production seed orchards are planted with clones or seedlings from several to many sublines to minimize inbreeding in the production orchard.

Tissue culture-

A technique for cultivation cells, tissues, or organs of plants in a sterile, synthetic medium; includes the tissues excised from a plant and the culture of pollen or seeds.

Unbalanced-

In experimental design, refers to an experiment or set of data in which all treatments or treatment combinations are not equally represented. The most common cause of unbalanced experiments is unequal mortality among entries in a test. (See randomized-block design and replication.) Also used to describe any plant breeder specializing in an organism with nearly as long a life cycle as his or her own.

Variability-

Differing from the average value. Absence of uniformity, usually referring to lack of genetic uniformity in a population. (See heterozygosity and resilience.)

Variance-

A statistical measure of variability.

Variety-

A distinctive seedling population or clone, usually one that possesses enough desirable characteristics to be commonly cultivated. In agriculture and horticulture all the plants within a variety would usually be quite uniform genetically. In forestry the term is more loosely used and the variability within a seedling variety is usually much greater.

Vegetative propagation-

Propagation of a plant by asexual means, as in budding, dividing, grafting, rooting, and air layering. (See clone)

Viability-

A populations ability to live, grow and develop. It is affected by physical habitat factors (climate, geology, topography, and aquatic features) and by biotic habitat factors (plant and animal populations and communities).

Wind pollination-

Pollination by wind-borne pollen.