Glossary of Genetic Terms

This glossary provides concise definitions of key terms used throughout the book. Terms are listed alphabetically.

A

Accuracy (r): Correlation between estimated breeding value (EBV) and true breeding value (TBV). Range: 0 to 1. Higher accuracy means more reliable prediction.

Additive genetic effect: The sum of the average effects of alleles at all loci affecting a trait. Determines breeding value and is transmitted to offspring.

Additive genetic variance (σ²_A): Variance in breeding values within a population. Determines heritability and response to selection.

AI (Artificial Insemination): Technique for breeding animals by collecting and depositing semen artificially rather than through natural mating.

Allele: One of two or more alternative forms of a gene at a specific locus.

Allele frequency: Proportion of a specific allele in a population. Example: If 70% of alleles at a locus are “A”, the allele frequency of A is 0.70.

B

BLUP (Best Linear Unbiased Prediction): Statistical method for estimating breeding values that uses all available information (own records, relatives, genomic data) optimally.

Breeding goal (H): The aggregate genetic merit we want to improve, typically a weighted combination of multiple traits based on their economic importance.

Breeding value (BV): The sum of the average effects of an animal’s alleles. Represents the genetic merit of an animal as a parent. Often estimated as EBV.

C

Contemporary group: A group of animals raised in the same environment and time period (e.g., same herd-year-season). Used to account for environmental effects in genetic evaluation.

Correlated response: Change in one trait (Y) as a result of selection on another trait (X), due to genetic correlation between the traits.

Crossbreeding: Mating animals from different breeds or lines to exploit heterosis and breed complementarity.

D

Dominance effect: Within-locus interaction between alleles, where the heterozygote deviates from the midparent value. Does not breed true.

E

EBV (Estimated Breeding Value): Statistical prediction of an animal’s true breeding value (TBV) based on available information (phenotypes, pedigree, genomics).

Environmental effect (E): All non-genetic factors affecting phenotype, including management, nutrition, health, measurement error, etc.

EPD (Expected Progeny Difference): Term used in beef cattle breeding for EBV. Predicts the expected difference in offspring performance compared to offspring of an average parent.

Epistasis: Interaction between genes at different loci. Complex and generally not reliably transmitted to offspring.

F

F₁ (First filial generation): The first generation offspring from a cross between two different breeds or inbred lines.

G

GBLUP (Genomic BLUP): Extension of BLUP that uses genomic relationship matrix (G) instead of pedigree-based relationship matrix (A).

GEBV (Genomic Estimated Breeding Value): Breeding value estimated using genomic information (SNP genotypes) in addition to pedigree and phenotypes.

Generation interval (L): Average age of parents when their offspring are born. Shorter L allows faster genetic progress.

Genetic correlation (r_A): Correlation between additive genetic effects for two traits. Ranges from -1 to +1. Caused by pleiotropy or linkage.

Genetic variance (σ²_G): Total variance due to genetic effects. Can be partitioned into additive, dominance, and epistatic components.

Genome: The complete set of DNA in an organism, including all genes.

Genomic relationship matrix (G): Matrix of relationships among animals calculated from SNP genotypes. Captures realized (actual) relationships.

Genomic selection: Using genome-wide DNA markers (SNPs) to predict breeding values, enabling selection of young animals without waiting for phenotypes or progeny.

Genotype: The genetic makeup of an individual at one or more loci.

Genotype-by-environment interaction (G×E): Different genotypes respond differently to environmental changes. Can complicate breeding across diverse environments.

GWAS (Genome-Wide Association Study): Statistical analysis to identify SNPs or genomic regions associated with traits.

H

Heritability (h²): Proportion of phenotypic variance due to additive genetic effects. h² = σ²_A / σ²_P. Range: 0 to 1.

Heterosis (hybrid vigor): Superior performance of crossbred offspring compared to the average of the purebred parents. Most pronounced for fitness traits.

Heterozygote: An individual with two different alleles at a locus (e.g., Aa).

Homozygote: An individual with two identical alleles at a locus (e.g., AA or aa).

I

Imputation: Predicting missing or ungenotyped SNPs using information from a reference panel of animals genotyped at higher density.

Inbreeding: Mating of related individuals. Increases homozygosity and can lead to inbreeding depression.

Inbreeding coefficient (F): Probability that two alleles at a locus are identical by descent. Range: 0 to 1.

Inbreeding depression: Reduction in performance (especially for fitness traits) in inbred animals due to increased expression of deleterious recessive alleles.

Index (Selection Index): Linear combination of information sources (phenotypes or EBVs) used to rank animals for selection. Maximizes correlation with the breeding goal.

L

Linkage: Physical proximity of genes on the same chromosome. Linked genes are inherited together more often than expected by chance.

Linkage disequilibrium (LD): Non-random association between alleles at different loci. Basis for genomic selection (SNPs in LD with causal mutations).

Locus (plural: loci): A specific position on a chromosome where a gene or DNA marker is located.

M

MAF (Minor Allele Frequency): Frequency of the less common allele at a locus in a population.

Marker: A DNA sequence (e.g., SNP) with a known physical location on a chromosome, used to track inheritance.

Mendelian sampling: Random sampling of parental alleles passed to offspring. Causes offspring to deviate from midparent average.

Mixed model: Statistical model with both fixed effects (e.g., contemporary groups) and random effects (e.g., breeding values).

N

Nucleus herd/flock: Elite population at the top of a breeding pyramid where selection is most intense and genetic improvement originates.

O

OCS (Optimum Contribution Selection): Method that simultaneously optimizes selection and mating decisions to maximize genetic gain while constraining inbreeding.

P

Pedigree: Record of an animal’s ancestors (parents, grandparents, etc.).

Permanent environmental effect (PE): Non-genetic environmental effect that persists across all records on an animal (e.g., udder damage in dairy cows).

Phenotype: Observable characteristic of an individual (e.g., body weight, milk yield). Determined by genotype and environment.

Phenotypic variance (σ²_P): Total variance in a trait observed in a population.

Pleiotropy: A single gene affects multiple traits. Major cause of genetic correlations.

Polygenic trait: Trait controlled by many genes, each with small effect. Most economically important traits are polygenic.

Q

QTL (Quantitative Trait Locus): A region of DNA associated with variation in a quantitative trait. May contain one or more genes affecting the trait.

QTN (Quantitative Trait Nucleotide): A specific causal mutation (nucleotide change) affecting a quantitative trait.

Quantitative trait: Trait with continuous distribution in a population, controlled by many genes and influenced by environment (e.g., growth rate, milk yield).

R

Reliability (r²): Squared correlation between EBV and TBV. Measure of confidence in EBV. Same as accuracy squared.

Repeatability (r): Correlation between repeated records on the same animal. r = (σ²_A + σ²_PE) / σ²_P. Upper limit of heritability.

Response to selection (R): Genetic change per generation (or per year) resulting from selection. Predicted by breeder’s equation.

S

Selection differential (S): Difference between the mean of selected parents and the population mean. Expressed in phenotypic units.

Selection index: See Index.

Selection intensity (i): Standardized selection differential (S / σ_P). Function of the proportion of animals selected.

Simply inherited trait: Trait controlled by one or few genes with major effects (e.g., coat color). Follows Mendelian ratios.

SNP (Single Nucleotide Polymorphism): A single base pair difference in DNA sequence between individuals. Most common type of genetic marker.

SNP chip (array): Platform for genotyping thousands to millions of SNPs simultaneously.

ssGBLUP (Single-Step Genomic BLUP): Combines pedigree and genomic information in one analysis using H matrix. Industry standard for genomic evaluation.

T

TBV (True Breeding Value): The actual (unknown) breeding value of an animal. Goal of genetic evaluation is to estimate TBV.

Terminal cross: Crossbreeding system where all offspring are marketed (none retained for breeding). Maximizes heterosis in market animals.

Trait: Any measurable or observable characteristic (e.g., body weight, litter size, milk yield, coat color).

V

Variance component: A component of phenotypic variance (e.g., σ²_A, σ²_E, σ²_PE). Estimated from data and used to calculate heritability and other parameters.

W

WGS (Whole Genome Sequencing): Determining the complete DNA sequence of an organism’s genome. Provides ultimate resolution but is expensive.

Notes

Greek letters used frequently:
- σ² (sigma squared) = variance
- σ (sigma) = standard deviation
- μ (mu) = population mean
- h² = heritability
- r = correlation or repeatability (context-dependent)
Subscripts indicate the specific variance:
- σ²_P = phenotypic variance
- σ²_A = additive genetic variance
- σ²_E = environmental variance
- σ²_PE = permanent environmental variance

# Glossary of Genetic Terms {#sec-glossary .unnumbered} This glossary provides concise definitions of key terms used throughout the book. Terms are listed alphabetically. --- ## A **Accuracy (r)**: Correlation between estimated breeding value (EBV) and true breeding value (TBV). Range: 0 to 1. Higher accuracy means more reliable prediction. **Additive genetic effect**: The sum of the average effects of alleles at all loci affecting a trait. Determines breeding value and is transmitted to offspring. **Additive genetic variance (σ²_A)**: Variance in breeding values within a population. Determines heritability and response to selection. **AI (Artificial Insemination)**: Technique for breeding animals by collecting and depositing semen artificially rather than through natural mating. **Allele**: One of two or more alternative forms of a gene at a specific locus. **Allele frequency**: Proportion of a specific allele in a population. Example: If 70% of alleles at a locus are "A", the allele frequency of A is 0.70. --- ## B **BLUP (Best Linear Unbiased Prediction)**: Statistical method for estimating breeding values that uses all available information (own records, relatives, genomic data) optimally. **Breeding goal (H)**: The aggregate genetic merit we want to improve, typically a weighted combination of multiple traits based on their economic importance. **Breeding value (BV)**: The sum of the average effects of an animal's alleles. Represents the genetic merit of an animal as a parent. Often estimated as EBV. --- ## C **Contemporary group**: A group of animals raised in the same environment and time period (e.g., same herd-year-season). Used to account for environmental effects in genetic evaluation. **Correlated response**: Change in one trait (Y) as a result of selection on another trait (X), due to genetic correlation between the traits. **Crossbreeding**: Mating animals from different breeds or lines to exploit heterosis and breed complementarity. --- ## D **Dominance effect**: Within-locus interaction between alleles, where the heterozygote deviates from the midparent value. Does not breed true. --- ## E **EBV (Estimated Breeding Value)**: Statistical prediction of an animal's true breeding value (TBV) based on available information (phenotypes, pedigree, genomics). **Environmental effect (E)**: All non-genetic factors affecting phenotype, including management, nutrition, health, measurement error, etc. **EPD (Expected Progeny Difference)**: Term used in beef cattle breeding for EBV. Predicts the expected difference in offspring performance compared to offspring of an average parent. **Epistasis**: Interaction between genes at different loci. Complex and generally not reliably transmitted to offspring. --- ## F **F₁ (First filial generation)**: The first generation offspring from a cross between two different breeds or inbred lines. --- ## G **GBLUP (Genomic BLUP)**: Extension of BLUP that uses genomic relationship matrix (G) instead of pedigree-based relationship matrix (A). **GEBV (Genomic Estimated Breeding Value)**: Breeding value estimated using genomic information (SNP genotypes) in addition to pedigree and phenotypes. **Generation interval (L)**: Average age of parents when their offspring are born. Shorter L allows faster genetic progress. **Genetic correlation (r_A)**: Correlation between additive genetic effects for two traits. Ranges from -1 to +1. Caused by pleiotropy or linkage. **Genetic variance (σ²_G)**: Total variance due to genetic effects. Can be partitioned into additive, dominance, and epistatic components. **Genome**: The complete set of DNA in an organism, including all genes. **Genomic relationship matrix (G)**: Matrix of relationships among animals calculated from SNP genotypes. Captures realized (actual) relationships. **Genomic selection**: Using genome-wide DNA markers (SNPs) to predict breeding values, enabling selection of young animals without waiting for phenotypes or progeny. **Genotype**: The genetic makeup of an individual at one or more loci. **Genotype-by-environment interaction (G×E)**: Different genotypes respond differently to environmental changes. Can complicate breeding across diverse environments. **GWAS (Genome-Wide Association Study)**: Statistical analysis to identify SNPs or genomic regions associated with traits. --- ## H **Heritability (h²)**: Proportion of phenotypic variance due to additive genetic effects. h² = σ²_A / σ²_P. Range: 0 to 1. **Heterosis (hybrid vigor)**: Superior performance of crossbred offspring compared to the average of the purebred parents. Most pronounced for fitness traits. **Heterozygote**: An individual with two different alleles at a locus (e.g., Aa). **Homozygote**: An individual with two identical alleles at a locus (e.g., AA or aa). --- ## I **Imputation**: Predicting missing or ungenotyped SNPs using information from a reference panel of animals genotyped at higher density. **Inbreeding**: Mating of related individuals. Increases homozygosity and can lead to inbreeding depression. **Inbreeding coefficient (F)**: Probability that two alleles at a locus are identical by descent. Range: 0 to 1. **Inbreeding depression**: Reduction in performance (especially for fitness traits) in inbred animals due to increased expression of deleterious recessive alleles. **Index (Selection Index)**: Linear combination of information sources (phenotypes or EBVs) used to rank animals for selection. Maximizes correlation with the breeding goal. --- ## L **Linkage**: Physical proximity of genes on the same chromosome. Linked genes are inherited together more often than expected by chance. **Linkage disequilibrium (LD)**: Non-random association between alleles at different loci. Basis for genomic selection (SNPs in LD with causal mutations). **Locus (plural: loci)**: A specific position on a chromosome where a gene or DNA marker is located. --- ## M **MAF (Minor Allele Frequency)**: Frequency of the less common allele at a locus in a population. **Marker**: A DNA sequence (e.g., SNP) with a known physical location on a chromosome, used to track inheritance. **Mendelian sampling**: Random sampling of parental alleles passed to offspring. Causes offspring to deviate from midparent average. **Mixed model**: Statistical model with both fixed effects (e.g., contemporary groups) and random effects (e.g., breeding values). --- ## N **Nucleus herd/flock**: Elite population at the top of a breeding pyramid where selection is most intense and genetic improvement originates. --- ## O **OCS (Optimum Contribution Selection)**: Method that simultaneously optimizes selection and mating decisions to maximize genetic gain while constraining inbreeding. --- ## P **Pedigree**: Record of an animal's ancestors (parents, grandparents, etc.). **Permanent environmental effect (PE)**: Non-genetic environmental effect that persists across all records on an animal (e.g., udder damage in dairy cows). **Phenotype**: Observable characteristic of an individual (e.g., body weight, milk yield). Determined by genotype and environment. **Phenotypic variance (σ²_P)**: Total variance in a trait observed in a population. **Pleiotropy**: A single gene affects multiple traits. Major cause of genetic correlations. **Polygenic trait**: Trait controlled by many genes, each with small effect. Most economically important traits are polygenic. --- ## Q **QTL (Quantitative Trait Locus)**: A region of DNA associated with variation in a quantitative trait. May contain one or more genes affecting the trait. **QTN (Quantitative Trait Nucleotide)**: A specific causal mutation (nucleotide change) affecting a quantitative trait. **Quantitative trait**: Trait with continuous distribution in a population, controlled by many genes and influenced by environment (e.g., growth rate, milk yield). --- ## R **Reliability (r²)**: Squared correlation between EBV and TBV. Measure of confidence in EBV. Same as accuracy squared. **Repeatability (r)**: Correlation between repeated records on the same animal. r = (σ²_A + σ²_PE) / σ²_P. Upper limit of heritability. **Response to selection (R)**: Genetic change per generation (or per year) resulting from selection. Predicted by breeder's equation. --- ## S **Selection differential (S)**: Difference between the mean of selected parents and the population mean. Expressed in phenotypic units. **Selection index**: See **Index**. **Selection intensity (i)**: Standardized selection differential (S / σ_P). Function of the proportion of animals selected. **Simply inherited trait**: Trait controlled by one or few genes with major effects (e.g., coat color). Follows Mendelian ratios. **SNP (Single Nucleotide Polymorphism)**: A single base pair difference in DNA sequence between individuals. Most common type of genetic marker. **SNP chip (array)**: Platform for genotyping thousands to millions of SNPs simultaneously. **ssGBLUP (Single-Step Genomic BLUP)**: Combines pedigree and genomic information in one analysis using H matrix. Industry standard for genomic evaluation. --- ## T **TBV (True Breeding Value)**: The actual (unknown) breeding value of an animal. Goal of genetic evaluation is to estimate TBV. **Terminal cross**: Crossbreeding system where all offspring are marketed (none retained for breeding). Maximizes heterosis in market animals. **Trait**: Any measurable or observable characteristic (e.g., body weight, litter size, milk yield, coat color). --- ## V **Variance component**: A component of phenotypic variance (e.g., σ²_A, σ²_E, σ²_PE). Estimated from data and used to calculate heritability and other parameters. --- ## W **WGS (Whole Genome Sequencing)**: Determining the complete DNA sequence of an organism's genome. Provides ultimate resolution but is expensive. --- ## Notes - Greek letters used frequently: - **σ²** (sigma squared) = variance - **σ** (sigma) = standard deviation - **μ** (mu) = population mean - **h²** = heritability - **r** = correlation or repeatability (context-dependent) - Subscripts indicate the specific variance: - **σ²_P** = phenotypic variance - **σ²_A** = additive genetic variance - **σ²_E** = environmental variance - **σ²_PE** = permanent environmental variance --- ## Further Reading For more detailed definitions and mathematical derivations, see: - Falconer and Mackay (1996): *Introduction to Quantitative Genetics* - Lynch and Walsh (1998): *Genetics and Analysis of Quantitative Traits* - Mrode (2014): *Linear Models for the Prediction of Animal Breeding Values*