Understanding the genetic basis of adaptation remains a central objective and a significant challenge for evolutionary genetics at the dawn of the 21st century. Over the last decade, intensive efforts have been made in characterizing intraspecific levels and patterns of molecular diversity in genes, and it is these studies that have provided us with the greatest insights into the nature of the evolutionary forces that shape gene structure. The study of nucleotide variation at specific genes, including those that underlie physiological and developmental phenotypes, has given us unprecedented glimpses into the nature of plant genetic variation and the histories of plant populations.

At the organismal level, phenotypic variation has been amply documented by over a century of evolutionary and ecological research, and some of this variation has also been shown to be adaptive in nature. The development of effective

Kenneth M. Olsen and Michael D. Purugganan1.

Department of Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695, U.S.A. Correct citation: Olsen, K.M., and Purugganan, M.D. 2004. Plant population genomics, linkage disequilibrium mapping, and the genetics of adaptation. In Plant Adaptation: Molecular Genetics and Ecology. Proceedings of an International Workshop held December 11-13, 2002, in Vancouver, British Columbia, Canada. Edited by Q.C.B. Cronk, J. Whitton, R.H. Ree, and I.E.P. Taylor. NRC Research Press, Ottawa, Ontario. pp. 45-52.

Corresponding author e-mail address: [email protected]

approaches for the isolation and functional characterization of genes underlying this phenotypic variation remains a major objective of plant genome research (Tanksley 1993; Remington et al. 2001; Paterson 2002). Much of this variation is quantitative in nature, and identifying the genes or quantitative trait loci (QTLs) underlying phenotypic variation lies at the heart of not only evolutionary genetics, but also studies of functional genomics and plant breeding (Tanksley 1993; Mauricio 2001; Remington et al. 2001; Paterson 2002). In this paper, we describe an emerging approach for identifying the genetic basis of phenotypic variation, linkage disequilibrium (LD) mapping, and the relationship of this approach to the more commonly used approach of QTL linkage mapping.

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