Molecular Breeding 6: 441–449, 2000. © 2000 Kluwer Academic Publishers. Printed in the Netherlands. 441 Mapping candidate genes in Eucalyptus with emphasis on lignification genes Jean-Marc Gion 1,∗ , Philippe Rech 1,2 , Jacqueline Grima-Pettenati 2 , Daniel Verhaegen 1 & Christophe Plomion 3 1 CIRAD-Forêt, Programme Arbres et Plantations, BP 5035, 34032Montpellier, France ( ∗ author for correspon- dence; e-mail gion@cirad.fr); 2 UMR CNRS/Universit´ e Paul Sabatier no. 5546, Pôle de Biotechnologie V´ eg´ etale, BP 17, Auzeville, 31326 Castanet Tolosan, France; 3 Laboratoire de G´ en´ etique et Am´ elioration des Arbres Forestiers, INRA, BP 45, 33610 Cestas, France Received 9 August 1999; accepted in revised form 29 February 2000 Key words: candidate gene, Eucalyptus, lignins, mapping, single-strand conformation polymorphism Abstract We used the single-strand conformation polymorphism (SSCP) technique to map eight genes on Eucalyptus uro- phylla and Eucalyptus grandis linkage maps. These included four genes involved in the common phenylpropanoid pathway (caffeic acid 3-0-methyltransferase, caffeoyl CoA 3-O-methyltransferase, 4-coumarate CoA ligase and phenylalanine ammonia-lyase), two genes involved in the ‘lignin specific’ pathway (cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase), and two symbiosis regulated genes (EgHypar and EgTubA1). A novel source of variation which affects the SSCP pattern, i.e. the presence or absence of electrophoresis buffer upon loading the samples into the polyacrylamide gel, was found. The placement of these genes on the Eucalyptus maps was carried out using an interspecific hybrid mapping population. This will further facilitate the identification or exclusion of ‘positional’ candidate genes for characterizing quantitative trait loci (QTL) for wood quality and vegetative propagation related traits. Abbreviations: PAL, phenylalanine ammonia-lyase; 4CL, 4-coumarate CoA ligase; COMT, caffeic acid 3-O- methyltransferase; CCoAOMT, caffeic CoA 3-O-methyltransferase; CCR, Cinnamoyl CoA reductase; CAD, cinnamyl alcohol dehydrogenase; SSCP, single-strand conformation polymorphism; RFLP, restriction fragment length polymorphism, RAPD, random-amplified polymorphism DNA; AFLP, amplified fragment length polymor- phism; SSR, simple sequence repeat; CAPS, cleaved amplified polymorphic sequence; STS, sequence tagged site; TGGE, thermal gradient gel electrophoresis; CG, candidate gene; QTL, quantitative trait loci; S, syringyl units; G, guaiacyl units. Introduction Genetic linkage maps of Eucalyptus species have been constructed with different types of anonymous mark- ers including RAPDs [16, 38], AFLPs [26], RFLPs [6] and SSRs [5]. The existence of these maps has enabled the localization of QTL (quantitative trait loci) for wood quality, growth, and vegetative propagation related traits [17, 18, 39, 7, 27]. While QTL mapping permits the decomposition of complex traits into their Mendelian components, it does not allow the actual genes underlying trait variation to be identified since the confidence interval of a QTL is often 10–20 cM [25]. Such an interval corresponds to ca. 4.5–9 Mb in Eucalyptus [15], i.e. hundreds of genes. Among the possible strategies used to characterize a QTL, the candidate gene (CG) ap- proach is certainly the most simple one. ‘Functional CG’, i.e. sequenced genes that putatively affect trait expression, can be proposed based on an a priori belief from the understanding of biochemical or develop- mental pathways affecting the trait of interest. The