TRENDS in Ecology & Evolution Vol.17 No.12 December 2002 http://tree.trends.com 0169-5347/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII: S0169-5347(02)02624-1 577 Review Peter H. van Tienderen* Institute for Biodiversity and Ecosystem Dynamics, PO Box 94062, 1090 GB, University of Amsterdam, Amsterdam, the Netherlands. *e-mail: tienderen@science.uva.nl Anita A. de Haan Netherlands Institute of Ecology, NIOO-CTO, PO Box 40, 6666 ZG Heteren, the Netherlands. C. Gerard van der Linden Ben Vosman Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands. Biodiversity within species concerns the amount, distribution and adaptive value of variation within and among populations in their natural environment [1]. Many biodiversity studies within species to date have focused on random molecular markers, such as microsatellites [2,3]. The breeding structure of populations, population bottlenecks and the biogeographical history of a species are expected to affect all markers in similar ways. By contrast, variation in functional regions (expressed or regulatory sequences) might reflect the past influences of selection, which can be different for each gene, superimposed on the pattern of variation as a result of history, migration and drift. The characteristics that enable a species or ecotype to occupy a certain geographical range or niche might depend on a limited set of genes, so that variation in such traits might not be detected by their correlation with random markers. Reed and Frankham [4] concluded that variation in molecular markers was not indicative of the adaptive evolutionary potential or differentiation of populations with respect to quantitative traits, and suggested that measuring quantitative genetic variation should be done directly. By contrast, Merilä and Crnokrak found a significant correlation between diversity in quantitative traits and molecular markers [5] but, at the same time, diversity in quantitative traits was consistently higher, indicative of a role for local adaptation and natural selection. Thus, studies of genetic diversity could benefit from targeting genes that exhibit ecologically relevant variation, rather than targeting random markers. Clearly, this is not a trivial exercise. One needs to assess which traits matter, identify the genes that potentially affect such traits, and develop markers within, or flanking the genes. For crop plants, the traits of interest are defined by the targets of the breeders. However, worldwide, 780 000 and 480 000 accessions of wheat and barley have been collected, respectively [6]. Genetic profiling of the accessions is essential, as to determine which have the most potential for use in breeding programmes. Furthermore, it is too expensive to maintain all accessions indefinitely ex situ in gene banks. Here, we review the potential of a gene-targeting approach for biodiversity studies within species. Marker systems for functional genes are now being developed, and existing sequence information is being used to develop markers that tag variation within the gene or in a flanking region. Although gene targeting appears to be technically feasible, more work is needed to increase our knowledge of candidate genes. Finally, we compare the merits of gene targeting with alternative approaches using random markers, gene expression profiling, and direct measurements of functional variation. SSAPs and SNPs for diversity assessment In the European Union biotechnology programme ‘molecular tools for screening biodiversity’ [7], different approaches are being evaluated for the development of markers within and flanking genes in plants and animals. The markers do not necessarily carry the mutations that cause the phenotypic effect. They are putative tags for functional variation at a nearby position within the targeted genes. Two types of strategy are being developed: (1) the use of conserved sequence motifs as anchors for sequence-specific amplification polymorphisms (SSAP: see Glossary) [8]; and (2) the selection of genes involved in key processes and sequencing of several genotypes to detect single nucleotide polymorphisms (SNPs). Most studies of genetic variation within species to date are based on random markers. However, how well this correlates w ith quantitative variation is contentious. Yet, functional, or ‘ecotypic’ variation in quantitative traits determines the ecological niche of a species,its future evolutionary potential, and, for livestock, crops and their wild relatives, their usefulness as a genetic resource for breeding. But nowadays we can also assess genetic diversity using markers directly targeted at specific genes or gene families. Such gene-targeted, multilocus profiles of markers can contribute to ex-situ management of genetic resources, ecological studies of diversity, and conservation of endangered species. Published online: 26 September 2002 Biodiversity assessment using markers for ecologically important traits Peter H. van Tienderen, Anita A. de Haan, C. Gerard van der Linden and Ben Vosman determined by use of different host plants in Drosophila mojavensis and Drosophila arizonae. J. Chem. Ecol. 23, 2803–2824 57 Etges, W.J. and Ahrens, M.A. (2001) Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. V. Deep geographic variation in epicuticular hydrocarbons among isolated populations. Am. Nat. 158, 585–598 58 McClintock, W.J. and Uetz, G.W. 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