Application of a three-haplotype LDLA model to the French Holstein population

Abstract Text: A new linkage analysis-linkage disequilibrium model was constructed with the aims of correction for long-range linkage disequilibrium and improve separation of closely linked QTLs. H1 hypothesis tested 3 QTLs vs. 2 for H0. Its performance, demonstrated earlier on a simulated dataset, was investigated here in a real-life situation. A French Holstein-Friesian bull population (n = 3940) with phenotypic records on milk protein content and genotypic records from 50,000 SNPs was used for the analysis. With this LDLA model, QTL localization improved significantly and we were able to distinguish 2 closely linked QTLs located on chromosome 20, namely the GHR gene and the PRLR gene, located only 6.9 Mb upstream from the GHR. Similar results were obtained after the analysis of 3 other chromosomes from the bovine genome. In addition, the width of the peaks also decreased considerably, resulting in narrower QTL predictions.

Keywords: LDLA, QTL mapping, Haplotype analysis