Index Table of contents 738 Analysis of Population Genetic Diversity and Differentiation in Hemileia vastatrix by Molecular Markers D. BATISTA 1* , L. GUERRA-GUIMARÃES 1 , P. TALHINHAS 1 , A. LOUREIRO 1 , D.N. SILVA 1,2 , L. GONZALEZ 1 , A.P. PEREIRA 1 , A. VIEIRA 1,2 , H.G. AZINHEIRA 1 , C. STRUCK 3 , M.C. SILVA 1 , O.S. PAULO 2 , V. VÁRZEA 1 1 Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/ Instituto de Investigação Científica Tropical (IICT), Oeiras, Portugal. E-mail: *dccastro@fc.ul.pt 2 Computational Biology and Population Genomics Group (CoBIG 2 ), Centro de Biologia Ambiental (CBA), Faculdade de Ciências da Universidade de Lisboa (FCUL), Lisboa, Portugal 3 Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany SUMMARY The present study intends to assess H. vastatrix population genetic diversity and differentiation, migration/dispersal patterns and gene flow among populations using a comprehensive and across-time coverage of isolates from different geographical origins, as well as to get some insights on the pathogen evolution. Here we report the initial stage of this study with the analysis of a first set of 31 H. vastatrix isolates from 12 coffee-growing countries using AFLPs and gene sequences. Several loci, including the universally used rDNA-ITS region, β-tubulin 1, TEF1 and candidate genes, were tested for marker informative value. Some level of variability could be detected in ITS and β-tubulin 1 loci providing some insights on the discrimination among H. vastatrix populations and a first step to better understand the underlying population structure. On the other hand, among a set of AFLP selective primers tested for sample screening, two AFLP primer combinations generated distinctive fragment patterns among different isolates. Based on both datasets, population structure and diversity parameters will be discussed, as well as inferences on the spatial distribution of the genetic variability. These first results open the way to unravel the molecular differentiation and the dynamics of H. vastarix populations. INTRODUCTION Coffee leaf rust (CLR) caused by the biotrophic fungus Hemileia vastatrix Berk. & Br. has long gained a world-class status, reaching almost all coffee growing countries with severe economical damages. Breeding for rust resistance has proven successful over the years to control the disease, but the highly adaptable nature of the fungus shaped by the dynamic system of host-pathogen co-evolution has shown to be a critical limitation for achieving durable CLR resistance (Várzea and Marques, 2005). As a consequence, gradual breakdowns of resistance have been observed in many of the improved varieties in several countries (Várzea and Marques, 2005; Prakash et al., 2005). In fact, the emergence of new evolving pathotypes under a strong selective pressure and the potential for these new races to become epidemically spread on a continental scale is a serious and constant threat. Thus, a better understanding of the genetic variation of H. vastatrix populations across large geographic areas and periods of time, and their phylogenetic relationships is a priority. High molecular diversity among rust isolates has been documented using RAPD markers (Gouveia et al.,