Applying the New LD Measures That Correct the Bias Due to Structure and Relatedness to Maize Panels

Linkage disequilibrium mapping of sequence polymorphisms underlying the phenotypic variability of quantitative agronomical traits has become a widely used method in plant genetics. For this approach, the extent of linkage disequilibrium (LD), which is the non-independence of alleles at difference loci, is of great interest since it reflects the precision of mapped association and gives an idea about the marker density required. To limit the rate of spurious associations, several methods are used to deal with panel structure and relatedness but the usual LD measures do not account for these bias. Recently, new LD measures were proposed to correct the LD from the structure and/or relatedness of the individuals genotyped. These new LD measures were applied to estimate the LD extent within maize panels, genotyped with about 68,000 SNPs and the results were compared with those obtained from the usual LD measure (r²). These results showed that the LD estimates obtained with the new measures are in accordance with the association mapping results and are more relevant than those of the usual LD measure (r²) within structured panels.