Extensive genome-wide linkage disequilibrium in cattle

A genome-wide linkage disequilibrium (LD) map was generated using microsate llite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled From the dutch black-and-white dairy cattle population. LD was measured bet ween all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounce d for closely linked marker pairs, extended over several tens of centimorga n. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies o f the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long ra nge disequilibrium between syntenic loci using low-density marker maps indi cates that LD mapping has the potential to be very effective in livestock p opulations. The frequent occurrence of gametic associations between nonsynt enic loci, however, encourages the combined use of linkage and linkage dise quilibrium methods to avoid false positive results when mapping genes in li vestock.