Lack of specialization of P. oryzae populations to
their hosts.
Cross-infection compatibility was tested for 33 rice plants and their
paired P. oryzae isolates from YYT (1,089 possible combinations;
Supplementary information SI3, Fig. SI3.1). Qualitative results showed a
lack of phenotypic specificity for the vast majority of P. oryzaeisolates to their native rice accession or to plants belonging to the
same landrace as their native plant. Indeed, among the 1,082
combinations yielding analysable results (data were missing for 7
combinations), 1,025 interactions (94.7%) were fully compatible, only 3
(0.3%) were incompatible, and 54 (5%) were scored as undetermined. YYT
indica landraces were previously shown to include numerous R genes: not
less than 16 known R genes were detected in two fully sequenced genomes
of the accessions Acuce and Xiaogu (Liao et al. 2016), and they probably
also include more unknown R genes. Our result suggest that all major
resistance genes present in this set of indica landraces
genotypes are overcome by P. oryzae .
Analysis of quantitative interactions in the matrix, measured as the
average diseased leaf area, revealed a lack of adaptation of P.
oryzae to their native host or landrace. ANOVA of the average diseased
leaf area, which can be interpreted as the performance of a givenP. oryzae isolate on a given accession, showed that the effect of
the isolate*accession combination (F = 1.8, P <
10-16, df = 1088) remains highly significant after
removing the significant effect of the experimental replicate (F =
2092.6, P < 10-16, df = 1). We used this
ANOVA model to estimate the adjusted performance of each isolate on each
accession. Heatmaps of the adjusted performance (Fig. 4) showed
differential quantitative responses on the different rice accessions for
all P. oryzae isolates, with only one isolate being very weakly
aggressive (green color on Fig. 4) on all rice accessions (CH1877) and
no isolate being highly aggressive (red color on Fig. 4) on all rice
accessions. Except for four isolates (CH1897, CH1900, CH1901, CH1905),
the adjusted performance of each P. oryzae isolate was not
significantly better on its native rice accessions than on all other
accessions (Fig. 4A, Fig. SI3.3). Also, the average performance of allP. oryzae isolates originating from plants of a given landrace
was not significantly better on all plants from this landrace than on
plants of other landraces (Fig. 5). Local adaptation of P. oryzaeto different rice accessions should also imply that different genes are
involved in the interaction with different rice accessions. To test this
hypothesis, we performed GWAs analyses on the fungal side, using the 33
adjusted performances on the different YYT accessions as phenotypic
traits to analyse (Supplementary Information SI4). Among the 27 markers
statistically correlated with at least one phenotypic trait, the
majority (22/27) was involved in the interaction with at least two
accessions.
Hierarchical clustering by columns and lines (Fig. 4B) showed a lack of
structure in the matrix, neither according to rice landraces, or to
genetic lineages of P. oryzae isolates themselves. We further
analysed nestedness and modularity within the matrix following Moury et
al. (2021). The WINE estimate of nestedness was 0.55 and was significant
(P=0 and 0.01 after 100 random with null models R1 and R2,
respectively). According to Moury et al., this shows that the variance
of the quantitative trait value is better explained by a statistical
model that does not include a rice accession*P. oryzae isolate
interaction term, in other words, that there is no specificity between
accessions (or groups of accessions) and P. oryzae isolates (or
groups of isolates). The modularity estimated with the spinglass
algorithm was low (0.06), albeit significant (P=0 after 100 random
simulations with null models R1 and R2).
Altogether, these results strongly suggest that P. oryzaepopulation in YYT did not adapt specifically to their native rice
accessions or to any indica landrace.