THE CHOICE OF MOLECULAR MARKER METHODS FOR POPULATION GENETIC-STUDIESOF PLANT-PATHOGENS

DNA markers have been used in many studies of fungal plant pathogens, and in particular in investigations of mating systems, gene flow, the establishment of epidemics and adaptation to host crops. Many aspects of population structure can be analysed by means of contingency tables , using chi(2) tests. Some extensions of such tests, with particular a pplications to plant pathology, are described. One test is applicable to situations where there is more than one le iel of subdivision of po pulations, while another is appropriate when there are two types of di vision, for instance by geographical area and by host crop. Furthermor e, the chi(2) test offers a convenient way of combining information fr om several independent markers. Tests for the differentiation of subpo pulations are based on certain underlying assumptions, and it is argue d that the primary consideration in choosing a marker system should be whether or not it fits the appropriate genetic criteria. Other consid erations, such as time, cost and difficulty, should be evaluated if tw o or more methods are capable of generating markers which fit the gene tic assumptions adequately. Although a large number of markers should be examined in order to estimate the extent of population subdivision, it might only be necessary to use a few markers to test whether such subdivision exists. Likewise, only a few markers may be needed to dist inguish clones of a pathogen in a partially sexual population. However , in all of these tests, these markers should be well characterized ge netically. It is shown that an existing genetic fingerprinting system for the barley powdery mildew fungus, Erysiphe graminis f. sp. hordei, is suitable for identifying clones but not for describing the differe ntiation of subpopulations. It may be possible to use markers based on random amplified polymorphic DNA (RAPD) or on amplified fragment leng th polymorphism (AFLP) in quantitative research in population genetics of E. graminis f. sp. hordei.