A first-generation metric linkage disequilibrium map of bovine chromosome 6

Abstract

We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.

Figure 1.—

Location of SNPs, steps, and LD blocks on integrated map of BTA6. The SNP locations are shown at the bottom in blue. The LD blocks are shown in alternating red and blue at five different levels of stringencies. The steps are shown in black.

Figure 2.—

Distribution of SNP spacing: the distance in base pairs (kilobases) from one SNP marker to the next SNP marker on BTA6.

Figure 3.—

Distribution of D′-values observed between SNP pairs over physical distance (megabases) for BTA6. The shaded line corresponds to the fitted Malecot model that shows the average rate of decline of LD over the chromosome.

Figure 4.—

The LDU map and the MARC linkage map plotted against megabase location on the bLDB integrated map of BTA6.

Figure 5.—

Frequency distribution of the block size (with zero LDU within block) for BTA6.

Figure 6.—

Comparison of recombination rate (centimorgans per megabase) estimated from the MARC genetic map and LDUs per megabase estimated from the LDU map in regular intervals of 5 Mb on BTA6.