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

Abstract

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.

Figure 1.—

One of 160 MPTs for the combined data from all 10 loci. Numerical designations prefixed by an “H” refer to a total of 37 unique multilocus haplotypes from 497 isolates of M. oryzae. The host genus or genera from which each haplotype was isolated is in parentheses. Only base substitutions were included in this analysis. Branch lengths are shown above each branch. Partitioned Bremer support values (Baker and DeSalle 1997; Baker et al. 1998) are given below long branches. Partitioned Bremer support values for branches indicated with letters are A: Bt1 (2), CH7-BAC7 (−0.9) and MPG1 (0.5). B: BAC6 (0.2), CH7-BAC7 (−1.6), CH7-BAC9 (−0.4), CHS (1.4), and MPG1 (0.9). C: BAC6 (0.3), CH7-BAC7 (−0.7), CH7-BAC9 (−0.5), CHS (0.5), and MPG1 (0.9). D: BAC6 (0.3), CH7-BAC7 (0.2), CH7-BAC9 (0.2), CHS (−0.2), and MPG1 (0.1). E: CH7-BAC7 (−0.9), CH7-BAC9 (−0.1), CHS (0.1), EF1 (1), and MPG1 (0.5). F: CH7-BAC7 (−0.4) and MPG1 (2).

Figure 2.—

A pairwise compatibility matrix for all phylogenetically informative sites from 9 of the 10 polymorphic loci generated using RETICULATE (Jakobsen and Easteal 1996). Incompatible sites that support conflicting phylogenies are indicated by solid boxes. Loci are labeled along the x- and y-axes. Thick bars bracketing the informative sites from each locus have been added as visual aids. As an additional visual aid, rows and columns containing blocks of sites from a single locus have been delimited using thick lines. Loci are organized according to chromosomal location and the chromosomal location of each locus is indicated with Roman numerals. For loci on a single chromosome, the minimum distance between loci (in base pairs) was calculated from the genome sequence and is indicated in the chevrons between loci. Exact distances between loci were available only for CH7-BAC7 and CH7-BAC9. The distances between all other loci are minimum estimates due to gaps in the genome sequence. The minimum distance reflects the distances between loci, ignoring gaps in the genome sequence.

Figure 3.—

A splits graph for M. oryzae haplotypes based on combined data from all 10 loci. Numerical designations refer to each of a total of 37 multilocus haplotypes from 497 isolates of M. oryzae. Indels were excluded from the analysis. Nodes containing sampled haplotypes are indicated by boxes. Colors are used to indicate the host of origin for each haplotype: red, O. sativa; yellow, Setaria; blue, L. hexandra; green, P. repens; black, other grass hosts. Bootstrap support values are indicated along one edge of each split; all edges of a given split have the same bootstrap support. For splits represented by bands of parallel edges the bootstrap value is indicated only along one edge. In reticulate parts of the network, splits are represented by bands of parallel edges. For example, the split that partitions the haplotypes into the two sets {1, 2, 3–19, 21–23, 29, 31–35} and {20, 24–28, 30, 36, 37} is represented by the four parallel edges indicated by thick lines.

Figure 4.—

The statistical parsimony network constructed for haplotypes 3–19, 29, and 31–34. Each haplotype or group of haplotypes is represented by a solid circle. The relative frequency of each haplotype is linearly related to the area of each circle. The geographic locations where isolates originated are represented by patterns indicated in the legend. Groups of haplotypes isolated from the same host are indicated with boxes and the host of origin is indicated within each box. Although haplotype 10 is mainly associated with rice (123 isolates), 2 isolates were from barley (Hordeum vulgare) and 1 isolate was from Pennisetum clandestinum. Each branch represents a single mutational step. In cases where haplotypes are connected by branches of more than a single mutational step, unsampled intermediates differing by a single mutational step have been inferred and are indicated by small solid circles. The midpoint root is indicated by an arrow. Haplotypes 13 and 29 are distinguished from haplotype 10 only by indels, not nucleotide polymorphisms; indels were not employed in this analysis.

Figure 5.—

The Bayesian consensus tree for M. oryzae haplotypes inferred from the combined data from all 10 loci. Numerical designations prefixed by an “H” refer to a total of 37 unique multilocus haplotypes from 497 isolates of M. oryzae. The values above the branches are the posterior probabilities associated with the branch supporting a particular clade. Branch lengths are proportional to the posterior probability for each branch. Posterior probabilities are not given for branches terminating in a single haplotype. Haplotypes 13 and 29 are not shown since they are distinguished from haplotype 10 only by indels, not nucleotide polymorphisms; indels were not employed in this analysis. The host of origin for each haplotype is given to the right of the haplotype designation. The presence or absence of AVR1-Co39 and AVR-Pita were assessed using a PCR test: “+” indicates that an amplification product was produced, “−” indicates that no amplification product was produced and that presumably the gene is absent from these strains. For the ACE1 gene, two haplotypes had alleles that confer a virulent phenotype, ACE1-vir1, ACE1-vir2. All other rice-infecting isolates are likely to be ACE1-avr, although some rare virulent isolates with PCR amplicons similar to that of ACE1-avr cannot be detected with current methods.