Marker to Marker LD: Dependence on Separation Distance and Difference in MAF between the Markers in Relation to the History of the Site, as it Affects Number and Frequency of Marker Haplotypes

Marker to marker LD, measured by r², was examined using Illumina Bovine SNP50 v1 chip in the Italian Brown Swiss dairy cattle population, and a custom Illumina 36K microarray SNP chip in a chicken brown-egg layer line. In both populations, maximum LD showed a strong inverse relation to the distance between the markers of the pair (dS); and, independently of this, to the difference between them in minor allele frequency (dMAF). In both cases, LD values occupied the entire range between the maximum LD for the given dS or dMAF, and zero. Maximum LD values for given dMAF were sharply and precisely defined (i.e., there was no “scatter” about the best curve fitted to the points representing maximum LD values against dMAF); while maximum LD values for given dS were “fuzzy”, i.e., points representing LD against dS were dispersed about the best fit curve to these points. It is shown that maximum LD is set deterministically for dMAF, but stochastically for dS. These relationships are further explored in terms of the number and frequency of haplotypes of the two markers as these develop historically, taking into account that the mutations that created the polymorphic sites at the two markers were necessarily separated in time. Acknowledgement. This study funded by EC (FP7/2007-2013), agreement n° 222664, “Quantomics” (this Publication reflects only the authors’ views and the EC is not liable for any use that may be made of the information contained herein). Hy-Line International and Italian Brown Cattle Breeders' Association provided data.