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Genetic dissection of phenotypic diversity in farm animals

Nature Reviews Genetics volume 2, pages 130–138 (2001)Cite this article

Key Points

  • Farm animals provide unique resources for studying genotype–phenotype relationships of a variety of traits due to the rich genetic diversity within and between breeds.

  • Farm animals were domesticated from their wild ancestors 5,000–15,000 years ago. In several cases, independent domestication from two or more subspecies took place.

  • Genome research in farm animals focuses primarily on non-pathological phenotypes. Thus, the search for mutations modifying phenotypes predominates over the search for mutations with clear pathological consequences.

  • Genetic studies of phenotypic traits, including multifactorial traits, are facilitated by the extensive pedigrees and the long tradition of collecting phenotype information in animal breeding programmes. Furthermore, resource populations for gene mapping can be generated by intercrossing different populations of farm animals.

  • All the basic resources for genome research are in place for the major farm animals, such as large collections of genetic markers (primarily microsatellites), large-insert libraries and radiation hybrid panels. However, the number of ESTs, as well as the number of cloned genes, are low compared with human and mouse.

  • Comparative gene mapping has been a key activity in farm animal genomics to allow access to the more developed genetic maps in other vertebrates. Comparative gene mapping has shown that the organization of the human genome is closer to that of farm animals (including chicken) than to the mouse.

  • The chromosomal localization of trait loci is determined by genome scans. Positional candidate cloning is the main strategy for the molecular identification of trait loci.

  • Linkage disequilibrium mapping seems to be a promising strategy for high-resolution mapping of trait loci as linkage disequilibrium occurs more frequently in farm animal populations than in human populations.

  • Several genes causing monogenic disorders and muscle development have already been identified. Diagnostic DNA tests for these are currently used in practical animal breeding.

  • Genome research in farm animals will lead to important practical applications in the farm animal industry but will also give new basic knowledge of the genetic basis for a variety of phenotypic traits of agricultural, biological and medical significance.

Abstract

Farm animal populations harbour rich collections of mutations with phenotypic effects that have been purposefully enriched by breeding. Most of these mutations do not have pathological phenotypic consequences, in contrast to the collections of deleterious mutations in model organisms or those causing inherited disorders in humans. Farm animals are of particular interest for identifying genes that control growth, energy metabolism, development, appetite, reproduction and behaviour, as well as other traits that have been manipulated by breeding. Genome research in farm animals will add to our basic understanding of the genetic control of these traits and the results will be applied in breeding programmes to reduce the incidence of disease and to improve product quality and production efficiency.

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Figure 1: Phenotypic diversity of domestic animals.
Figure 2: Conserved genome organization among vertebrates.
Figure 3: Half-sib families and breeding value.
Figure 4: The use of intercrosses between divergent populations.
Figure 5: Double-muscling in cattle.

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Acknowledgements

Sincere thanks are due to Erik Bongcam-Rudloff for expert assistance in preparing the illustrations. Work in the author's laboratory is primarily supported by the Swedish Research Council for Forestry and Agriculture.

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Authors and Affiliations

  1. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, Uppsala, S-751 24, Sweden

    Leif Andersson

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  1. Leif Andersson
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DATABASE LINKS

Mc1r

KIT

dominant white coat colour in pigs

dominant white spotting in mice

piebald trait in humans

malignant hyperthermia in pigs

malignant hyperthermia in humans

myostatin

bovine leukocyte adhesion deficiency

severe combined immunodeficiency in Arabian horses

narcolepsy in dogs

oedema disease in pigs

FURTHER INFORMATION

Roslin Institute

US Livestock Genome Mapping Projects

Human SNP Consortium

pig radiation hybrid maps

human transcript map

US Meat Animal Research Center

Online Mendelian Inheritance In Animals

dbEST summary by organism

Glossary

PURIFYING SELECTION

Selection against a deleterious allele.

CHROMOSOME PAINTING

Fluorescent in situ hybridization (FISH) to chromosomes using a probe that represents a whole chromosome or a part of a chromosome.

BREEDING VALUE

The genetic merit of an individual estimated using the phenotypic deviation of its offspring from the population mean.

GENETIC DRIFT

The random fluctuation in allele frequencies as genes are transmitted from one generation to the next.

POPULATION STRATIFICATION

The population is divided into sub-populations. In farm animals, it is very common that some breeding animals are used more frequently in some herds than in others. This generates allele frequency differences between sub-populations and linkage disequilibrium in the population.

ZOO-FISH

Fluorescent in situ hybridization (FISH) of a chromosome-specific probe from one species to chromosomes from another species.

ADVANCED INTERCROSS LINES (AIL).

Subsequent generations (F3, F4 and so on) of an intercross pedigree, maintained to allow high-resolution mapping of trait loci.

RESOURCE POPULATION

A population generated for particular research purposes, such as an intercross between two divergent breeds of farm animal or a population containing particularly interesting phenotypic data.

INTROGRESSION

Transfer of genetic material from one population to another by repeated backcrossing.

GERM PLASM

The physical basis of heredity, and therefore the genetic material used for breeding.

MARKER-ASSISTED SELECTION

The use of genetic markers to predict the inheritance of alleles at a closely linked trait locus.

INTERSEXES

Individuals that have a mixture of male and female characters.

FIMBRIATED

Fimbria are protein molecules (often called adhesins or colonizing factors) that allow the bacteria to adhere to receptors on host cells, such as enterocytes in the intestine.

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Andersson, L. Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet 2, 130–138 (2001). https://doi.org/10.1038/35052563

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