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

Additional files

Additional file 1:

An overview of the SNP selection. Two regions were sampled per chromosome, each region was ~1 cM in size. SNPs were selected with a spacing of ~2 kb. Coordinates of the regions are based on chicken genome build WASHU2.

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Additional file 2:

Minor allele frequency (MAF) spectrum for the eight populations and Ceylon Jungle Fowl.

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Additional file 3:

Ancestral allele frequency spectrum for the eight populations.

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Additional file 4:

Estimates of past effective popution size. Estimates from microchromosomes were comparable to estimates from macrochromosomes.

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Additional file 5:

Haploblock structure in the eight selected regions for eight populations derived from the Gabriel method [10]. Top and middle sections show two regions for GGA 1 and GGA 2 (macrochromosomes). Bottom section shows the four regions derived from the two microchromosomes (GGA26 and GGA27). 1 = white egg layer; 2 = brown egg layer; 3 = dam broiler E5 (closed line); 4 = sire broiler line; 5 = dam broiler A3 (open line); 6 = Frisian Fowl; 7 = Owl Bearded; 8 = Red Jungle Fowl.

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Additional file 6:

Proportion of macro- and microchromosomes capture in haploblocks of different size. Block definitions were according to the 4 Gamete Rule [20].

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Additional file 7:

estimated number of major haplotypes (haplotypes occurring with a frequency > 5% in the populations studied). The second column for each of the populations shows the percentage of haplotype diversity explained by the major haplotypes.

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