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Open Access Highly Accessed Research article

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

Hendrik-Jan Megens1*, Richard PMA Crooijmans1, John WM Bastiaansen1, Hindrik HD Kerstens1, Albart Coster1, Ruud Jalving2, Addie Vereijken3, Pradeepa Silva4, William M Muir5, Hans H Cheng6, Olivier Hanotte78 and Martien AM Groenen1

Author Affiliations

1 Animal Breeding & Genomics Centre, Wageningen University, Wageningen, The Netherlands

2 Department of Animals, Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands

3 Hendrix Genetics, Boxmeer, The Netherlands

4 Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Sri Lanka

5 Department of Animal Sciences, Purdue University, West Lafayette, IN, USA

6 United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, USA

7 University of Nottingham, Population and Evolutionary Genetics Dept. Nottingham, UK

8 International Livestock Research Institute (ILRI), Nairobi, Kenya, Africa

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BMC Genetics 2009, 10:86  doi:10.1186/1471-2156-10-86

Published: 20 December 2009



The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs).


At a similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing were all lower for the micro- as compared to the macrochromosomes. These differences were consistent across populations. Heterozygosity, genetic differentiation, and derived allele frequencies were also higher for the microchromosomes. Differences in LD, haplotype variation, and haplotype sharing between populations were largely in line with known demographic history of the commercial chicken. Despite very low levels of LD, as measured by r2 for most populations, some haploblock structure was observed, particularly in the macrochromosomes, but the haploblock sizes were typically less than 10 kb.


Differences in LD between micro- and macrochromosomes were almost completely explained by differences in recombination rate. Differences in haplotype diversity and haplotype sharing between micro- and macrochromosomes were explained by differences in recombination rate and genotype variation. Haploblock structure was consistent with demography of the chicken populations, and differences in recombination rates between micro- and macrochromosomes. The limited haploblock structure and LD suggests that future whole-genome marker assays will need 100+K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes in chicken, and, since most birds have microchromosomes, in other avian species as well.