Joint linkage and linkage disequilibrium mapping in natural populations

A new strategy for studying the genome structure and organization of natura l populations is proposed on the basis of a combined analysis of linkage an d linkage disequilibrium using known polymorphic markers. This strategy exp loits a random sample drawn from a panmictic natural population and the ope n-pollinated progeny of the sample. It is established on the principle of g ene transmission from the parental to progeny generation during which the l inkage between different markers is broken down due to meiotic recombinatio n. The strategy has power to simultaneously capture the information about t he linkage of the markers las measured by recombination fraction) and the d egree of their linkage disequilibrium created at a historic time. Simulatio n studies indicate that the statistical method implemented by the Fisher-sc oring algorithm can provide accurate and precise estimates for the allele f requencies, recombination fractions, and linkage disequilibria between diff erent markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and posi tional cloning of the genes underlying both simple and complex traits.