Abstract：
: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.
journal_name
Geneticsjournal_title
Geneticsauthors
Lipkin E,Straus K,Stein RT,Bagnato A,Schiavini F,Fontanesi L,Russo V,Medugorac I,Foerster M,Sölkner J,Dolezal M,Medrano JF,Friedmann A,Soller Mdoi
10.1534/genetics.108.097402subject
Has Abstractpub_date
2009-02-01 00:00:00pages
691-9issue
2eissn
0016-6731issn
1943-2631pii
genetics.108.097402journal_volume
181pub_type
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