Salads Under Siege, E10: Connecting the dots



Ever since the establishment of civilisation, humanity has been at the mercy of available food supplies. With the advent of early subsistence agriculture and crop domestication, therefore, came the emergence of diseases that caused crop losses and incited famines (Figure 1). Interestingly and despite intense breeding efforts, contemporary agriculture still faces significant biotic threats that affect our food security. Indeed, diseases are caused by pathogens that represent nearly every branch on the tree of life, each of which is subject to intense study.

Figure 1. THE FAMINE MEMORIAL by William Murphy (Source). The Irish potato famine, which raged in the 1840, was caused by Phytophthora infestans (plant destroyer) causing the death and migration of millions of Irish people. 

The Science addressing Pathogen virulence 

Ever since organisms were identified as the cause of disease, there has been much interest in their biology. In particular and with the advent of molecular biology and genomics, the mechanisms of pathogen virulence became the main focus. Consequently, many plant pathogens, collectively affecting our food security have been identified, sequenced and characterised to varying extents. Perhaps the most important observations emanating from the community are that: (i) Microbes produce sets of molecules (Microbe or Pathogen Associated Molecular Patterns or M/PAMPs) that act as danger signals in plants and induce plant immune responses (Pattern-Triggered Immunity or PTI), (ii) pathogens secrete proteins (effectors) that can counter PTI and induce susceptibility (Effector-Triggered Susceptibility, ETS).

Salads under Siege; diseased crops

Similarly, advanced genetics, functional genomics and biochemical work have revealed factors and their activities that lead to enhanced crop immunity. These include the identification of the receptors required for M/PAMP recognition (Pattern Recognition Receptors, PRRs), their regulators, the signalling factors these receptors activate as well as the downstream processes that are associated with PTI. Importantly, plant genetics and genomics also has allowed the identification of another class of plant receptors (R-proteins) that can recognise pathogen effector activities and induce a powerful immune response (Effector-Triggered Immunity or ETI). These collective efforts have not only led to a better understanding of plant-microbe interactions but also have led to conceptual models that describe plant-microbe warfare from an evolutionary perspective (Figure 2, From Jones and Dangl, 2006).

Figure 2. The Zig-zag-zig model. A conceptual framework explaining the co-evolutionary battles between pathogens and their hosts. Source

Battling plant pathogens in the Post-Genomics age  

(Re-)sequencing of pathogenic microbes is a fairly straightforward exercise, provided that the resources for sequencing, quality control and data analyses are present. It is therefore not surprising that genome sequences along with gene expression data for both crop and pathogen species are readily available. Arguably, however, their generation and subsequent productive use have required conceptual models that could help interpret extensive data sets, or more importantly, guide experimental design and subsequent data analyses. Forays into large datasets with predictive tools have helped identify large suites of candidate effectors (on the basis of a signature that predicts on protein secretion), Avr factors (effectors that trigger ETI) and candidate receptor proteins in plants (both PRR as well as Resistance protein-coding genes) that conform to and validate existing conceptual models. The main question of course is; how can we use this information to battle pathogens in the field? The answers (or the ideas that we think will be the answer) are not that complicated, but yet the answer quite extensive.  I will, therefore, explain some of the advances in more detail in the coming posts.  


Economically important diseases on crops are complex associations whose outcomes are determined by host-and pathogen-encoded molecules. It is clear that a molecular battle takes place in the host cells, where immunity and susceptibility to pathogens are specified. Therefore, defining the basis of pathogenicity or immunity will lead to a multitude of distinct answers. It is equally interesting, however, to think of the pathogen cell as another battleground, where plant-derived defensive molecules engage pathogen-encoded pieces of machinery or processes to stop an infection. How do pathogens cope with such signals? Are such signals co-opted and used to regulate This is another area of research that has received limited attention in recent years but is ripe for exploration.

To read more about our salads and their adversaries, please find links to other episodes below:

What sets a pathogen apart from its innocent relatives?

Episode 1

Episode 2

Episode 3

Episode 4

Episode 5

Episode 6

Episode 7

Episode 8

Episode 9

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