Use of Observed Genomic Information to Infer Linkage Disequilibrium between Markers and QTLs

Abstract

Conducting genomic selection in admixed populations is challenging and its accuracy in this case largely depends on the persistence of linkage disequilibrium between single nucleotide polymorphisms (SNP) and quantitative trait loci (QTL). Inferring linkage disequilibrium (LD) between SNP markers and QTLs could be important in understanding the change of SNP marker effects across different breeds. Predicting the change in linkage disequilibrium between markers and QTLs across two divergent breeds was explored using information from the genotype data. Two different models (M1, M2) that differ in the definition of the explanatory variables were used to infer the level of LD between SNP markers and QTLs using all markers in the panel or windows of fixed number of markers. Three simulation scenarios were conducted using different number of SNPs and QTLs. In the first scenario, the resulting coefficient of determination (R 2 ) was 0.65 and 0.52 using M1 and M2, respectively. In the second scenario, average R 2 equaled 0.12 using all markers in the panel and 0.25 using 100 marker windows. Across the three simulation scenarios, it was clear that a significant portion of the variation in the change in LD between SNP markers and QTLs could be explained by information already available in the observed SNP marker data.