Quantitative interactions: the disease outcome of Botrytis cinerea across the plant kingdom

Abstract

Botrytis cinerea is a fungal pathogen that causes necrotic disease on more than a thousand known hosts widely spread across the plant kingdom. How B. cinerea interacts with such extensive host diversity remains largely unknown. To address this question, we generated an infectivity matrix of 98 strains of B. cinerea on 90 genotypes representing eight host plants. This experimental infectivity matrix revealed that the disease outcome is largely explained by variations in either the host resistance or pathogen virulence. However, the specific interactions between host and pathogen account for 16% of the disease outcome. Furthermore, the disease outcomes cluster among genotypes of a species but are independent of the relatedness between hosts. When analyzing the host specificity and virulence of B. cinerea, generalist strains are predominant. In this fungal necrotroph, specialization may happen by a loss in virulence on most hosts rather than an increase of virulence on a specific host. To uncover the genetic architecture of Botrytis host specificity and virulence, a genome-wide association study (GWAS) was performed and revealed up to 1492 genes of interest. The genetic architecture of these traits is widespread across the B. cinerea genome. The complexity of the disease outcome might be explained by hundreds of functionally diverse genes putatively involved in adjusting the infection to diverse hosts.

Keywords: Botrytis cinerea; fungus; generalist pathogen; host specificity; plant domestication; plant–pathogen interactions; polygenic virulence.

Figure 1

Disease symptoms caused by B. cinerea observed on plants from the core Eudicots. The list of plant species with disease symptoms was compiled from Elad et al. (2016). The tree represents major orders from the basal Eudicots (in green), Asterids (in orange), and Rosids (in pink). The size of the circle at the end of the branches is proportional to the species diversity of the order. The species diversity was extracted from the Missouri Botanical garden angiosperm phylogeny (http://www.mobot.org/MOBOT/Research/APweb/ [last accessed June 2021]). For each order, the number of species with known disease symptom is indicated.

Figure 2

Experimental design. We tested the virulence of 98 B. cinerea strains on seven eudicot crop species and the plant model A. thaliana using randomized complete block design detached leaf assays with sixfold replication.

Figure 3

Population structure and genetic distances in the Botrytis strain collection. Color represents the host on which the strains were collected. Dashed lines represent strains collected outside of California.

Figure 4

Lesion areas at 72 hours post inoculation on seven crop species shows small and inconsistent effect of domestication on the B. cinerea interaction. Half-violins and boxplots (median and interquartile range) represent the mean lesion area distribution of high (black, n = 588) and low (gray, n = 588) improvement genotypes for all 98 Botrytis strains. Lactuca refers to L. sativa for high and L. serriola for low improvement genotypes. Solanum refers to S. lycopersicum for high and S. pimpenellifolium for low improvement genotypes. As reference, virulence on A. thaliana wild-type (Col-0, n = 98) and jasmonic acid signaling mutant (coi1, n = 98) are presented. The nonscaled tree represents the phylogenetic relationship between eudicot species. A lesion example on an A. thaliana leaf is provided.

Figure 5

Host variation predominates the outcomes of plant-Botrytis interactions across species while Botrytis variation predominates within plant species. (A) Multi-host linear model estimating the contribution of plant species, plant genotypes, improvement status, Botrytis strains and their interaction on the percentage of variance in lesion area. (B) Species-specific linear mixed models that estimate the percentage of variance in lesion area. In gray are the experimental parameters classed as random factors. Two-tailed t-test: *P < 0.05, **P < 0.01, ***P < 0.005.

Figure 6

Variation of plant susceptibility in the Botrytis pathosystem is species specific and does not track plant evolution. Heatmap of standardized (z-scored) least-squares means of lesion area (n = 6) for Botrytis strains (x-axis) interacting with 90 plant genotypes (y-axis). The strains were isolated largely in California (light blue in the origin bar) and on grape (light purple in the host bar). For A. thaliana, five single gene knockout mutants and the corresponding wild-type Col-0 are presented. For the seven crop species, six genotypes with low (gray) and high (black) improvement are presented. The seven crop species were chosen to represent a wide spectrum of phylogenetic distances across Rosids (Brassicales and Fabales) and Asterids (Asterales and Solanales). Branches in the dendrogram that are supported with 95% certainty after bootstrapping are indicated in blue. No branches in the Botrytis strain dendrogram were significant.

Figure 7

Strains with low virulence have high host specificity. (A) Estimates of virulence (average lesion area) and host specificity (coefficient of variation) across eight eudicots for the Botrytis strains are shown. The strains are colored according to the plant host from which they were collected. A quadratic relationship was the optimal description of the relationships between specificity and virulence and is shown with a gray confidence interval (R²=0.44, P = 6.36 × 10⁻¹³). (B) Mean lesion area and standard error (n = 12, except A. thaliana n = 6) across the eight eudicot species is provided for two strains at the extremes of the host specificity/virulence distribution.

Figure 8

Botrytis virulence and host specificity genetic architecture. GWAS significance of 271,749 SNPs estimated as posterior inclusion probability (PIP) of Bayesian sparse linear mixed model for host specificity (in red) and virulence (in green). The dashed lines represent a probability of false-positive P < 0.01 based on the tail of the PIP distribution of 20 random permutation tests.