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Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

Jossi Hillel1*, Martien AM Groenen2, Michèle Tixier-Boichard3, Abraham B Korol4, Lior David1, Valery M Kirzhner4, Terry Burke5, Asili Barre-Dirie6, Richard PMA Crooijmans2, Kari Elo7, Marcus W Feldman8, Paul J Freidlin1, Asko Mäki-Tanila7, Marian Oortwijn2, Pippa Thomson5, Alain Vignal9, Klaus Wimmers10 and Steffen Weigend6

Author Affiliations

1 Department of Genetics, The Hebrew University of Jerusalem, Faculty of Agriculture, Food and Environmental quality sciences, Rehovot 76100, Israel

2 Institute of Animal Sciences, Wageningen Agricultural University, Wageningen, The Netherlands

3 Institut national de la recherche agronomique, Centre de Jouy-en-Josas, France

4 Institute of Evolution, University of Haifa, Israel

5 Department of Animal and Plant Sciences, Sheffield University, S10 2TN, UK

6 Institute for Animal Science, Federal Agricultural Research Centre, Mariensee, 31535 Neustadt, Germany

7 Agricultural Research Centre, Institute of Animal Production, 31600 Jokioinen, Finland

8 Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA

9 Institut national de la recherche agronomique, Centre de Toulouse, France

10 Institute of Animal Breeding Science, Rheinische Friedrich-Wilhelms-Universitat Bonn, Germany

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Genetics Selection Evolution 2003, 35:533-557  doi:10.1186/1297-9686-35-6-533

The electronic version of this article is the complete one and can be found online at:

Received:2 September 2002
Accepted:13 March 2003
Published:15 September 2003

© 2003 INRA, EDP Sciences


In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.

genetic distance; polymorphism; red jungle fowl; DNA markers; domesticated chicken


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