Maize, at all levels of resolution, is one of the most diverse crop species. Large insertions and deletions are common between maize inbreds, and include tandem repeat clusters, abundant retroelement and transposons. At the gene level, single nucleotide polymorphisms are common, especially in introns and untranslated regions of genes. Depending on choice of experimental population and region in the genome, linkage disequilibrium between polymorphic sites could decay very rapidly, or persist for hundreds of Kb. Appropriately chosen germplasm collections may be used for genetic association mapping (also called linkage disequilibrium mapping), either with candidate genes, or by scanning the whole genome with thousands of markers at high density. This approach, in favorite circumstances, could provide high resolution. The power of association mapping is variable, and has not been thoroughly investigated. Rapid advances in genome sequencing and high density genotyping are making this approach to relating genotype with phenotype increasingly attractive.
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Rafalski, A., Ananiev, E. (2009). Genetic Diversity, Linkage Disequilibrium and Association Mapping. In: Bennetzen, J.L., Hake, S. (eds) Handbook of Maize. Springer, New York, NY. https://doi.org/10.1007/978-0-387-77863-1_10
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