Originally published as Genetics Published Articles Ahead of Print on December 15, 2008.

Genetics, Vol. 181, 691-699, February 2009, Copyright © 2009
doi:10.1534/genetics.108.097402

Extensive Long-Range and Nonsyntenic Linkage Disequilibrium in Livestock Populations: Deconstruction of a Conundrum

E. Lipkin^*,1, K. Straus^*, R. Tal Stein^*, A. Bagnato, F. Schiavini, L. Fontanesi, V. Russo, I. Medugorac, M. Foerster, J. Sölkner^**, M. Dolezal^**,, J. F. Medrano, A. Friedmann^* and M. Soller^*

^* Department of Genetics, Hebrew University of Jerusalem, 91904 Jerusalem, Israel, Department of Veterinary Sciences and Technologies for Food Safety, Università degli Studi di Milano, 20133 Milano, Italy, Dipartimento di Protezione e Valorizzazione Agroalimentare, Sezione di Allevamenti Zootecnici, Università di Bologna, 42100 Reggio Emilia, Italy, Institute for Animal Breeding, Faculty of Veterinary Medicine, The Ludwig-Maximilians-University Munich, 80539 Munich, Germany, ^** Department of Sustainable Agricultural Systems, University of Natural Resources and Applied Life Sciences, 1180 Vienna, Austria, Institute of Population Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria and Department of Animal Science, University of California, Davis, California 95616

¹ Corresponding author: Department of Genetics, Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
E-mail: lipkin{at}vms.huji.ac.il

Great interest was aroused by reports, based on microsatellite markers, of high levels of statistically significant long-range and nonsyntenic linkage disequilibrium (LD) in livestock. Simulation studies showed that this could result from population family structure. In contrast, recent SNP-based studies of livestock populations report much lower levels of LD. In this study we show, on the basis of microsatellite data from four cattle populations, that high levels of long-range LD are indeed obtained when using the multi-allelic D' measure of LD. Long-range and nonsyntenic LD are exceedingly low, however, when evaluated by the standardized chi-square measure of LD, which stands in relation to the predictive ability of LD. Furthermore, specially constructed study populations provided no evidence for appreciable LD resulting from family structure at the grandparent level. We propose that the high statistical significance and family structure effects observed in the earlier studies are due to the use of large sample sizes, which accord high statistical significance to even slight deviations from asymptotic expectations under the null hypothesis. Nevertheless, even after taking sample size into account, our results indicate that microsatellites testify to the presence of usable LD at considerably wider separation distances than SNPs, suggesting that use of SNP haplotypes may considerably increase the usefulness of a given fixed SNP array.

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