Prospects for whole genome linkage disequilibrium mapping in thoroughbreds

Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D′ coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D′ coefficient for LD mapping of a trait in a thoroughbred population. Microsatellite genotype data and grey coat colour as a trait model in a thoroughbred population were used to assess the extent of LD. We demonstrated that LD mapping was a reasonable approach for initial genome-wide scans in a thoroughbred population. Significant LD was demonstrated at approximately 7 cM, implying that roughly 430 appropriately spaced microsatellites were needed for systematic whole-genome LD mapping in this model. LD mapping methods using D′ in a thoroughbred population were useful for identifying the chromosomal regions for diseases and economic trait loci (ETL). It was suggested that a thoroughbred population represented a population particularly suitable for LD mapping.