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Title: Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken

item MEGENS, HENDRIK-JAN - Wageningen University And Research Center
item CROOIJMANS, RICHARD P.M. - Wageningen University And Research Center
item BASTIAANSEN, JOHN W.M. - Wageningen University And Research Center
item KERSTENS, HINDRIK H.D. - Wageningen University And Research Center
item COSTER, ALBART - Wageningen University And Research Center
item JALVING, RUUD - Utrecht University
item VEREIJKEN, ADDIE - Hendrix Genetics
item SILVA, PRADEEPA - University Of Peradeniya
item MUIR, WILLIAM M - Purdue University
item Cheng, Hans
item HANOTTE, OLIVIER - University Of Nottingham
item GROENEN, MARTIEN A.M. - Wageningen Agricultural University

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2009
Publication Date: 12/20/2009
Citation: Megens, H., Crooijmans, R., Bastiaansen, J., Kerstens, H., Coster, A., Jalving, R., Vereijken, A., Silva, P., Muir, W., Cheng, H.H., Hanotte, O., Groenen, M. 2009. Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken. BioMed Central (BMC) Genetics. Available:

Interpretive Summary: Genetic markers are the basis for modern genetic analyses. A key parameter is linkage disequilibrium (LD), which is the measure of two or more adjacent markers that are co-inherited. If markers are in complete LD, then they are always inherited together. Determining the relationship of all genetic markers in an organism’s genome allows one to develop blocks of markers, which in turn, defines the minimal number of genetic markers one would need for a whole-genome analysis. In this study, the extent of LD was determined for chicken. Specifically, we analyzed two different regions on large (macro) and small (micro) chicken chromosomes with genetic markers that were very tightly spaced. We found that for chickens, one hundred thousand or more genetic markers are needed to fully capture all the genetic variation in domestic chickens. This information is essential for the development of future DNA chips to genotype chickens and, thus, any group that wishes to understand the genetic basis for complex traits and their genetic improvement.

Technical Abstract: Background Chicken, like most birds have a very distinct karyotype consisting of many microchromosomes and a few macrochromosomes. While it is known that recombination frequencies are much higher for the microchromosomes, little is known on differences in linkage disequilibrium (LD) and haplotype diversity between these classes of chromosomes. Using a very high density genotyping approach, LD in chicken was systematically characterized in various chicken populations, and most importantly, across both macro- and microchromosomes. Results At similar physical distance, LD, haplotype homozygosity, haploblock structure, and haplotype sharing are all lower for the microchromosomes compared to the macrochromosomes. These differences are consistent across a wide population sample. Heterozygosity, genetic differentiation, and derived allele frequencies are also higher for the microchromosomes. Chicken shows evidence for declining population size, and differences in LD, haplotype variation, and haplotype sharing between populations are largely in line with known population history. Conclusion Differences in LD were almost completely explained by differences in recombination rate between chromosomes. Haplotype diversity and haplotype sharing in addition are different due to increased genotype variation genotype differentiation on the microchromosomes. Paucity in haploblock structure can be explained by demography of chicken populations, and indicate that future whole-genome marker assays will need in excess of 100K SNPs to exploit haplotype information. Interpretation and transferability of genetic parameters will need to take into account the size of chromosomes. The findings of this study are important for designing and interpreting marker-phenotype and diversity studies, not only in chicken but for all avian species that have microchromosomes.