Bridging genomics and genetic diversity: linkage disequilibrium structure and association mapping in maize and other cereals

Linkage disequilibrium (LD) and association mapping s receiving considerable attention in the plant genetics community for its potential to use existing genetic resources collections to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. Based on investigations in maize (Zea mays L.) either published or recently conducted in our group, we discuss three elements of particular importance for conducting association mapping or interpreting the results: (i) the analysis of population structure into subgroups, (ii) its use to control for spurious associations and consequences in the specific case of differential selection among subgroups, and (iii) the analysis of the local structure of LD into haplotypes and its consequences on the resolution and the application of LD mapping. Consequences and perspecutives for plant breeding are briefly discussed.