Glossary

this glossary provides descriptions of commonly used names and definitions within the gem database platform note that some users may find they commonly use these words differently than described here, with these definitions provided to facilitate understanding of their usage within the database word or phrase definition breeding value (bv) or index a breeding value (bv) is an estimate of genetic merit, and is typically derived by an external analysis involving pedigree and trait data from one or more trials within any given analysis, breeding values are often reported for multiple traits, and can be used in conjunction with economic weightings to estimate an overall index value within gem the breeding value and index table can also be used to store alternate forms of performance information such as standardised means bv or index statistic a statistic that gives an indication of the quality/reliability of the bv or index comment a note about an observation of a trait on a specific tree at a specific date control (ctl) a genetic entity being tested in a trial with a known performance for the purpose of being a reference or a baseline comparison with the other genetic entities genetic entities in trials are made up of entities under test (eut) plus controls (ctl) derived statistic a statistic that is calculated outside of gem but is stored and retrieved using gem derived trait a trait that is calculated by gem using data either from observed traits or from other derived traits the derivation of a derived trait is specified by the client company and set up by gemnetics data administrators the value of a derived trait is automatically calculated whenever new data is entered entity under test (eut) a genetic entity being tested in a trial genetic entities in a trial are defined either as entity under test (eut) or as a control (ctl) establishment date the date on which a trial is planted or begins estimation description a user defined description of the specific data or methodology used to calculate a particular genetic parameter experimental role a classification of genetic entities in a trial into either entities under test (eut) or controls (ctl), or any other predefined role favourites a subset of trials, traits, and/or ages that are saved for use in extract screens field code a code assigned to each trial entry within a trial that is used to identify it in field documents field codes are assumed to be specific to each trial, so that trial entries can have different field codes in different trials (but are often given the same code within a trial series) users most often specify field codes at planting, but sometimes they are assigned when data is imported full sib family a set of progeny that have the same mother and the same father full sib family register a list of all the full sib families in gem this list will at a minimum contain full sib families that are represented in trials and/or in pedigrees of genotypes represented in trials genetic entity a group of trees which represent a particular genetic background genetic entities fall into one of three genetic entity types depending on their genetic status (see genetic entity type) genetic entity list the list of genetic entities or individual trees in trials shown in the choose genetic entity screen and used by a data extract genetic entity name the name of a genetic entity genetic entity type a classification of genetic entities which represents their genetic make up a genetic entity belongs to one and only one genetic entity type, that is, a genetic entity is either a selection, a full sib family, or a seedlot genetic entity owner a company or organisation that controls the naming of seedlots and selections (full sib family names are made up of the selection names of the parents) the association of a genetic entity with an owner within gem does not necessarily imply legal ownership genetic parameter a statistic that applies to a particular trait or set of traits observed in a specific trial or set of trials within a particular time frame genetic parameters characterise the genetics of a specific observation of a trait in a trial or a specific performance index they are calculated outside of gem but stored in gem for easy retrieval genotype code a unique name or label for each genotype within a database genotype codes can be used to represent the pedigree in analyses of extracted data (for example, using the trial+pedigree extract) and to track unique genotypes represented in trials that have not yet been given a name the genotype code for a selection or ortet is the selection name with any embedded spaces stripped out (to allow the code to be input for other software easily) half sib family a set of progeny with one known parent in common examples of a half sib family are an open pollinated seedlot, and a polycross (that is, a known mother pollinated with a mixture of fathers) indexed trait an indexed trait is where multiple measurements of a tree are done at the same time, and intended to be averaged, summed or processed using some other function in order to obtain one number which then becomes the observation individual progeny in trials trees in trials which are unique genotypes that have not been added to the selection register mating design the crosses that are tested in a trial or set of trials name in trial the name for a genetic entity used in a specific trial a name in trial is either the genetic entity name or an other name ortet the original plant from which a clone is started through rooted cuttings, grafting, or tissue culture, or other means of vegetative propagation other name an alternate name for a genetic entity if desired a preferred other name can be specified to be the default name to be displayed owner a company or organisation that controls the names of genetic entities that are seedlots and selections the association of a genetic entity with an owner within gem does not necessarily imply any legal ownership of the genetic entity plant code an optional, customer assigned identifier for individual trees within trials plant codes are assigned to individual trees according to rules which combine attributes of the tree to form composite descriptors these attributes can be any of genetic entity, section, trial entry or trial, as well as any of the udfs (user defined fields) (e g replicate, set, experimental block, column, row, tree, etc) plant id an optional customer assigned identifier for individual trees within trials plant id is generated by a customer and imported along with meta data and/or observational data plant id must be unique within a trial if it is to be used to uniquely reference the spatial location of each tree on a map plant location a composite descriptor for unambiguously referring to individual trees within trials, which is usually referenced on a trial map one of two plant location conventions is chosen for each trial to uniquely identify all individual trees typically, this choice will be determined by how the trees have been recorded on a map of the trial the two choices are a) trial id + plant id b) trial id + section + tree position if the trial uses the section and tree position convention, plant id can be assigned to trees without association with any spatial map position tree position the position of a tree within a section it is expressed as an integer which is normally a relative position within a systematic numbering convention often this convention will specify an order for traversing rows and columns within the section from a standard start point, but any systematic pattern may be used see also plant id above propagation method the method of propagation of a genetic entity in a trial propagation methods are user defined section a specifically delineated and contiguous plot of land on which trees in a trial are planted a trial may have only one section, but is typically made up of multiple sections seedlot a group of trees of mixed parentage, that is, with two or more mothers and two or more fathers seedlot register a list of all the seedlots in gem selection a name assigned to a specific genotype when it is brought into a breeding program a selection can be tested as a replicated clone, or as a half sib family selection register a list of all the selections in gem summary statistics simple statistics calculated by gem for genetic entities, trial entries, or trees in a trial these include mean, number of observations, standardized mean, standard deviation, minimum, maximum, and rank tested as a category which specifies the way that a genetic entity is tested in a specific trial selections can be tested as either a replicated genotype (c) or as half sib progeny (h) full sib family progeny are always tested as a full sib (f), and seedlot are always tested as a genetic mixture (s) trait a characteristic of a plant or tree that is observed and recorded trait age the trial age at the time of assessment of a trait trait group a group of traits displayed together in gem the name of the group is assigned by the gemnetics data administrators trial a group of trees that are planted in the same time frame for the same purpose, usually in a systematic experimental design trial id the name given by the user for a specific trial trial age the time in either months or years after the date that a trial was planted trial entries a list of genetic entities being tested in a particular trial which distinguishes the way in which they are propagated (propagation method) or tested (tested as) for example, the same genetic entity tested with two different propagation methods in the same trial would be assigned two different trial entry names also, a selection might be tested as a replicated clone or as a half sib family in the same trial in both cases there would be one genetic entity designated but two trial entries trial materials genetic entities that are tested in a trial trial series a group of trials that have a similar purpose, experimental design, and trial entries trials in the same trial series are usually planted at about the same time and usually analysed together user defined field (udf) a column of data that is associated with trees in a trial which store the value of experimental design parameters or other information about the individual trees in the trial udf values may be assigned by users at both the section level and the individual tree level variety (type) a classification assigned to selections it is defined by each client and is optional