Cross Validation of Qtl from Linkage Analysis and Linkage Disequilibrium Analysis

Although feed conversion efficiency is one of the key drivers of profitability in beef production, conventional methods of selecting for feed efficiency in beef cattle rely on a costly and time consuming collection of feed intake measurements. If genetic markers were available for this trait, they could greatly reduce the cost of selecting for more efficient cattle. Identification of markers or genes to be used in marker assisted selection can be achieved in several ways. This paper will compare results from two approaches, a linkage approach and a linkage disequilibrium approach. Five chromosomes with both microsatellites and dense SNP markers were analysed using each method. The linkage approach resulted in a QTL 95% confidence region of a total of 214Mb over the 5 chromosomes. The linkage disequilibrium approach resulted in a combined QTL 95% confidence region of 67Mb over the 5 chromosomes. When the QTL 95% confidence was derived from only regions cross validated in the two analyses a total of 27Mb of 95% confidence interval was achieved. The results indicate that a combined approach reduces the size of the QTL region.