Originally published as Genetics Published Articles Ahead of Print on March 31, 2005.

Genetics, Vol. 170, 613-630, June 2005, Copyright © 2005
doi:10.1534/genetics.105.041780

Origins of Host-Specific Populations of the Blast Pathogen Magnaporthe oryzae in Crop Domestication With Subsequent Expansion of Pandemic Clones on Rice and Weeds of Rice

Brett C. Couch*,1, Isabelle Fudal{dagger}, Marc-Henri Lebrun{dagger}, Didier Tharreau{ddagger}, Barbara Valent§, Pham van Kim**, Jean-Loup Nottéghem{ddagger} and Linda M. Kohn*,2

* Department of Botany, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
{dagger} Centre National de la Recherche Scientifique, Bayer Cropscience, Lyon 69263, France
{ddagger} Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR BGPI, Montpellier 34398, France
§ Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
** Department of Plant Pathology, Can Tho University, Can Tho, Vietnam

2 Corresponding author: Department of Botany, University of Toronto, 3359 Mississauga Rd. N, Mississauga, Ontario L5L 1C6, Canada.
E-mail: kohn{at}utm.utoronto.ca

Rice, as a widely and intensively cultivated crop, should be a target for parasite host shifts and a source for shifts to co-occurring weeds. Magnaporthe oryzae, of the M. grisea species complex, is the most important fungal pathogen of rice, with a high degree of host specificity. On the basis of 10 loci from six of its seven linkage groups, 37 multilocus haplotypes among 497 isolates of M. oryzae from rice and other grasses were identified. Phylogenetic relationships among isolates from rice (Oryza sativa), millet (Setaria spp.), cutgrass (Leersia hexandra), and torpedo grass (Panicum repens) were predominantly tree like, consistent with a lack of recombination, but from other hosts were reticulate, consistent with recombination. The single origin of rice-infecting M. oryzae followed a host shift from a Setaria millet and was closely followed by additional shifts to weeds of rice, cutgrass, and torpedo grass. Two independent estimators of divergence time indicate that these host shifts predate the Green Revolution and could be associated with rice domestication. The rice-infecting lineage is characterized by high copy number of the transposable element MGR586 (Pot3) and, except in two haplotypes, by a loss of AVR-Co39. Both mating types have been retained in ancestral, well-distributed rice-infecting haplotypes 10 (mainly temperate) and 14 (mainly tropical), but only one mating type was recovered from several derived, geographically restricted haplotypes. There is evidence of a common origin of both ACE1 virulence genotypes in haplotype 14. Host-haplotype association is evidenced by low pathogenicity on hosts associated with other haplotypes.




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