The Lowdown on Linkage Disequilibrium

Flowering time varies among Arabidopsis accessions. Some of the genes that contribute to this polygenic trait have been localized using quantitative trait loci (QTL) mapping, eventually leading to the identification of genetic variants that contribute to observed differences in flowering time (El-Assal et al., 2001). Despite this and other similar successes with the positional cloning of QTL, the path from a mapped QTL to a gene underlying trait variation is fraught with obstacles. One obstacle is the lack of fixed genetic differences between parental lines used to create the mapping population. This “diversity hurdle” can be overcome by repeating QTL analyses in many mapping populations (or by mapping variance components in a number of families), but this approach is not feasible for most taxa and phenotypes. Linkage disequilibrium (LD) mapping steps into this void. Unlike traditional linkage mapping, which maps genes using gametic phase disequilibrium created in a singleor multiple-generation cross, LD mapping can rely on segregating variation in natural populations. As a result, LD mapping samples contain many more informative meioses (i.e., all those that have occurred in the history of the sample) than a traditional mapping population. Although not without its own problems (Lander and Schork, 1994), LD mapping holds great promise for finemapping genes and variants that contribute to a trait of interest, such as flowering time. Here, we briefly review LD (What is it? How is it measured? What biological and evolutionary factors shape its distribution?), summarize recent studies of LD in plant systems, and relate genomic patterns of LD to mapping genes that underlie variation in complex phenotypic traits.