TY - JOUR
T1 - Extensive long-range and nonsyntenic linkage disequilibrium in livestock populations
T2 - Deconstruction of a conundrum
AU - Lipkin, E.
AU - Straus, K.
AU - Tal Stein, R.
AU - Bagnato, A.
AU - Schiavini, F.
AU - Fontanesi, L.
AU - Russo, V.
AU - Medugorac, I.
AU - Foerster, M.
AU - Sölkner, J.
AU - Dolezal, M.
AU - Medrano, J. F.
AU - Friedmann, A.
AU - Soller, M.
PY - 2009/2
Y1 - 2009/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=62449120574&partnerID=8YFLogxK
U2 - 10.1534/genetics.108.097402
DO - 10.1534/genetics.108.097402
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C2 - 19087960
AN - SCOPUS:62449120574
SN - 0016-6731
VL - 181
SP - 691
EP - 699
JO - Genetics
JF - Genetics
IS - 2
ER -