The AbacusBio genetics glossary

Let's not let jargon get in the way of a great relationship! Here is a glossary of the quantitative genetics lingo used on this site

Accuracy         

A measure of the relationship between true breeding values and estimated breeding values (EBVs). Estimated breeding values have a degree of accuracy that is due to amount (number of performance records), type of information (e.g. who data is recorded on – the animal itself and/or relatives), trait heritability, and other possible information from correlated traits. 

Accuracy can range from 0 to 1.

Related term: reliability. In dairy evaluations, EBV reliability is frequently reported; reliability is simply the square of accuracy therefore is a smaller number.

Best Linear Unbiased Prediction (BLUP)          

A methodology used to calculate estimated breeding values (EBVs). BLUP uses sophisticated statistical models to estimate genetic effects (EBVs) and environmental effects from individual animal performance (phenotypes) and pedigree data.

BLUP requires good pedigree information and a hefty piece of software such as ASReml.  

Breeding objective      

Practical: “A general goal for a breeding program – a notion of what constitutes the best animal” .  A measurable description of the benefits of genetic improvement of a list of traits (goal traits) which have a direct impact on profitability.

Mathematical:  A weighted combination of traits used to construct an economic selection index ; “The sum of the product of the additive genetic value for each trait and the trait’s net economic value” (Van Vleck et al. 1987)

Other terms often used: aggregate breeding value, total genetic merit, overall genetic value

Breeding program

The combination of a breeding objective, a selection index, mating decisions and inbreeding management.

Economic value (EV)     

In a breeding objective, the change in profit ($) due to an independent, one-unit increase in performance in a trait.  The value is expressed in $ per unit change whilst all other traits remain constant.            

Economic weight (EW)               

In a selection index, the economics-based weighting applied to a trait EBV.  The EWs are calculated from trait economic values, industry weighting factors, and numbers of genetic expressions. The EW are the final weights applied to each trait in the index.

Estimated Breeding Value (EBV)   

An estimate of the value of an individual animal as a parent for a specific trait, relative to the population mean. EBVs refer to gene effects that are transmitted to offspring, so they describe the individuals’ ability to generate progeny with more or less production potential.

EBVs are trait-specific and are in trait units (e.g., litres, kg). Because they are estimates, EBVs have a degree of accuracy or reliability.

EBVs are calculated in genetic evaluation programs from performance records and pedigree information. Most advanced genetic evaluation systems use Best Linear Unbiased Prediction (BLUP) to calculate EBVs based on animals’ own and/or relatives’ performance records. 

More formal or academic term: additive genetic value

Genetic correlation (rG)            

A measure of the strength (consistency, reliability) of the relationship between breeding values for one trait and breeding values for another trait. Usually due to common genes influencing both traits. For example, how much one trait changes as you select for another trait.

Genetic evaluation         

Calculation of estimated breeding values (EBVs).

A “genetic evaluation system” is a system of procedures to estimate breeding values. This includes measurement of data, statistical procedures, and computation techniques for predicting breeding values and related values (such as accuracy).

Similar term: Genetic prediction

Genetic variation              

Variability of breeding values for a trait within a population (under selection).

Genetic trend        

Change in the mean breeding value in a population over time. Usually a historical trend calculated from changes in estimated breeding values.

Genetic gain

In essence, genetic gains are genetic trends that are heading in the correct direction. However, these are often predicted for the future by analysing past trends and current breeding objectives.

Heritability (h2)  

A measure of the strength of the relationship between individuals’ genetic value (breeding value) and performance (phenotypic value) for a trait in a population

Inbreeding

When closely related animals are bred together. An inbreeding coefficient is calculated by analysing pedigree information. High levels of inbreeding can result in poorer animal performance (inbreeding depression).  AbacusBio also offers a mating allocation service, Ani-Mate, to minimise inbreeding.

Multiple-trait selection              

Exactly what it sounds like: selection for more than one trait in a breeding program.

Nucleus breeding scheme      

A cooperative breeding program in which elite animals are concentrated in a nucleus herd and superior genetics is then distributed among cooperating herds through semen, embryos or live animals

Pedigree information       

Information on the genotype or performance of ancestors and/or collateral relatives of an individual

Performance record/ Phenotype               

An observation or measurement of performance for a trait on an individual.

Progeny test           

A test used to help predict an individual’s breeding values involving multiple matings of that individual and evaluation of its offspring

Repeatability 

For a trait for which individuals commonly have more than one performance record (e.g. milk yield, reproduction), a measure of the strength of the relationship between repeated records in a population.

Selection     

The process that determines which individuals become parents, how many offspring they produce, and how long they remain in the breeding population

Selection criterion / criteria  

A piece of information (e.g., performance on a trait, EBV, multi-trait index value, DNA genotype) that forms the basis for selection decisions.

Selection index     

Selection indexes are used in multiple-trait selection to rank individuals according to their genetic values for several different traits. An index is a way of combining several traits into one overall number. In a breeding program, selection indexes are based on the program’s breeding objectives.

An economic selection index is a sum of EBVs for each trait, each weighted by the trait’s economic weight.

For each individual, an index value is calculated by entering their EBVs for each trait into the selection index equation. This index value represents an estimate of the animals’ overall genetic merit across all the traits. Individuals can then be ranked and selected according to their index value.

E.g. the New Zealand dairy Breeding Worth (BW) index is a weighted combination of EBVs for milk production (fat, protein, volume), fertility, live weight, survival, and somatic cell. Bulls and cows are ranked based on their BW index value.

Trait

Any observable or measurable characteristic of an individual.

Variance component analysis

The method by which heritabilty and genetic correlations are estimated.