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Mapping genes for complex traits in domestic animals and their use in breeding programmes

Key Points

  • Genome-wide association (GWA) studies are being used in livestock, as in humans, to map genes affecting complex traits.

  • SNP panels for use in these GWA studies have recently become commercially available in cattle, dogs, sheep, chickens, pigs and horses.

  • GWA studies have successfully identified mutations causing single-gene traits, such as white spotting in dogs.

  • Associations for complex traits have been reported, but in most cases verification in independent studies has not yet occurred.

  • The SNP panels can be used in the selection of livestock even before they have been used to identify specific mutations causing variation in the economically important traits. This process is called genomic selection. It uses all the SNPs to estimate the genetic value of animals at a young age. By reducing the generation interval, the rate of genetic improvement can be doubled.

  • Genomic selection is already being implemented by dairy industries around the world, and other livestock industries are expected to follow in the near future.


Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for complex traits. However, the genetic merit of animals can still be estimated by genomic selection, which uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously. This approach is expected to double the rate of genetic improvement per year in many livestock systems.

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Figure 1: Key events in the history of cattle.
Figure 2: Linkage disequilibrium (LD) in cattle breeds.
Figure 3: Calculation of number of animals in a reference population and accuracy of breeding values.


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The authors would like to thank H. Campbell and H. Burrow for cattle pictures used in this Review.

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Corresponding author

Correspondence to Michael E. Goddard.

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APIL's Genomic Comparison of Young Bulls


Quantitative trait

A measurable trait that depends on the cumulative action of many genes and the environment, and that can vary among individuals over a given range to produce a continuous distribution of phenotypes.

Estimated breeding value

An estimate of the additive genetic merit for a particular trait that an individual will pass on to its descendents.


The proportion of phenotypic variance caused by additive genetic variation.

Genetic improvement

Deliberate genetic change in a population of domestic animals or plants brought about by human control of their selection and breeding that makes them more suitable for the purpose for which they are kept.

Genomic selection

Selection of animals for breeding based on estimated breeding values calculated from the joint effects of genetic markers covering the whole genome.

Linkage disequilibrium

The absence of linkage equilibrium so that the allele at one locus is correlated with the allele at another locus.

Effective population size

The number of individuals in an idealized population with random mating and no selection that would lead to the same rate of inbreeding as observed in the real population. The effective population size can be much less than the actual population size owing to the unequal genetic contribution of individuals to the next generation.

Linear model

A statistical model that assumes that the observed phenotypic value can be explained by the sum of the effects of independent variables and a random error, which is usually assumed to be normally distributed.

Polygenic breeding value

The additive genetic merit an individual passes on to its descendents owing to the combined contribution of many genes of small effect, but possibly excluding some specified genes.


A population or sample of individuals derived from more than one race or breed and that have not undergone random mating.

LD phase

If linkage disequilibrium (LD) exists between genes A and B, each with two alleles (A or a and B or b), then gametes that carry allele A can carry B or b. Thus, LD can exist in one of two phases: gametes that are more commonly AB and ab, or gametes that are more commonly Ab and aB.

Beavis effect

The tendency for statistically significant effects to be overestimated when many effects are tested for significance.

Minor allele frequency

The frequency of the less frequent allele in a two-allele polymorphism.

Genomic breeding value

An estimate of an animal's genetic merit, including genomic information

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Goddard, M., Hayes, B. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10, 381–391 (2009).

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