R-Avr Genes Interactions and Plant Defense System
Authors: Ruchi V. Trivedi and Bhupendra Singh Panwar

The resistance of the host plant is controlled by single R (resistance) gene (usually dominant) .The corresponding gene in the pathogen is called an Avr (avirulence) gene (also usually dominant). It is important to note that the actions of the R genes and the Avr genes can only be detected by test inoculations of pathogens on plants (i.e. using infection assays for resistance or susceptibility).

Plant resistance proteins (R proteins) recognize corresponding pathogen avirulence (Avr) proteins either indirectly through detection of changes in their host protein targets or through direct R-Avr protein interactions. Although indirect recognition imposes selection against Avr effector function, pathogen effector molecules recognized through direct interaction may overcome resistance through sequence diversification rather than loss of function.

There are four classes of R predicted protein .

⋆ NBS/LRR class (Nulceotide binding site /leucine rich repeat)

⋆ LRR/TM class (Leucine rich repeat/ transmembrane receptor)

⋆ Kinase class

⋆ LRR/TM/Kinase class.

Based on the predicted protein structures the cloned resistance genes can be grouped in to five classes.

• Hm1 (This gene is distinct from the interactions which involve in R genes that may couple the recognition of specific pathogen races to expression of defence related genes.)

• Pto (Pseudomonas tomato resistance)

• RPM1(Resistance to Pseudomonas syringae ssp. maculicola 1)

• Cf9 (Resistance to Cladosporium fulvum-9)

• Xa 21 (Xanthomonas campestris resistance 21)

Mechanism of R-Avr interaction

Direct recognition ( ‘Gene-for-Gene’ hypothesis ).

The ‘Gene-for-Gene’ hypothesis proposed by Flor (1971) suggests that for each avirulence gene product synthesized by the pathogen, the resistant host carries a complementary, single, dominant R gene whose product recognizes the Avr product. During infection, an interaction between these two components induces a defence response.

1) Flax resistance genes - flax rust avirulence genes (Peter N. Dodds et al., 2006)

The flax rust fungus Avr L567 genes, whose products are recognised by the L5, L6, and L7 R proteins of flax, are highly diverse, with twelve sequence variants identified from six rust strains. Out of twelve seven show necrotic response within corresponding R gene. Yeast Two- Hybrid assay indicates that recognition is based on direct R- Avr protein interaction.

2) Pseudomonas tomato resistance (Pto)– AvrPto. (Mucyn, T. S. et al., 2006)

Pto is a tomato serinethreonine protein kinase. Pto is polymorphic and hence satisfies the genetic criteria for the definition of a disease resistance protein. Pto activity requires the NB-LRR protein Prf, and the proteins form a molecular complex. Prf is monomorphic, at least in the tomato species analyzed to date. Pto is the direct target of two unrelated P. syringae effectors, AvrPto and AvrPtoB, each of which contributes to pathogen virulence in Pto mutants. It is thus likely that Prf guards Pto. The Pto kinase is apparently not required for PTI, though there may be redundancy in its function because it is a member of a gene family.

3) Tomato Cf-2 – Cladosporium fulvum Avr2 (Rooney et al., 2005)

The transmembrane RLP Cf-2 guards the extracellular cysteine protease Rcr3. Cf-2 recognizes the C. fulvum extracellular effector Avr2, which encodes a cysteine protease inhibitor. Avr2 binds and inhibits the tomato Rcr3 cysteine protease. Mutations in Rcr3 result in the specific loss of Cf-2-dependent recognition of Avr2. Hence, Cf-2 seems to monitor the state of Rcr3, and activates defense if Rcr3 is inhibited by Avr2.

Indirect interaction (Guard hypothesis)

The R proteins interact, or guard, a protein known as the ‘guardee’ which is the target of the Avr protein. When it detects interference with the guardee protein, it activates resistance.

1. Arabidopsis RPM1(Resistance to Pseudomonas syringae ssp. maculicola 1) AvrRpm1 (Jonathan D. G et al.,2006)

Arabidopsis RPM1 is a peripheral plasma membrane NB-LRR protein. It is activated by either the AvrRpm1 or the AvrB effector proteins. AvrRpm1 enhances the virulence of some P. syringae strains on Arabidopsis as does AvrB on soybeans. AvrRpm1 and AvrB are modified by eukaryote-specific acylation once delivered into the cell by the type III secretion system (red syringe) and are thus targeted to the plasma membrane. The biochemical functions of AvrRpm1 and AvrB are unknown, although they target RIN4(RPM1 interacting 4), which becomes phosphorylated (1P), and activate RPM1. In the absence of RPM1, AvrRpm1 and AvrB presumably act on RIN4 and other targets to contribute to virulence.

How to Use the Gene-for-Gene Concept in Disease Management

  1. Use diverse resistance genes in crops to minimize damage through stabilizing the pathogen population.
  2. Develop cultivars with multigenic resistance that may last longer than a single gene resistance through pyramiding resistance genes.
  3. Obtain resistance through transgenic plants with natural resistance genes
  4. Modify or design resistance genes to avoid being “broken-down” by pathogen.
  5. Chemical control with resistance gene products.
  6. Use durable resistance controlled by genes that are not involved in gene-for-gene recognition


There are two approaches through which R genes control diseases.

1) Classical method- This involves conventional breeding approach.

Perez et al., (2007) introgressed three bacterial blight resistance genes, Xa4, Xa7 and Xa21, in to a temperature-sensitive genetic male sterile (TGMS1) line through three way crosses

2) Transgenic method- This involves non-conventional method or Transgenic approach.

Tang et al., (2001) used particle bombardment to co-transform mature seed-derived rice callus (Oryza sativa L., ssp. japonica, cv.) with plasmids containing the linked marker genes gusA and hpt, and the ap1 gene encoding an amphipathic protein previously shown to delay the hypersensitive response induced in non-host plants by the pathogen Pseudomonas syringae pv. syringae (Pss). A bacterial blight inoculation test was carried out on ten lines. In each case, plants carrying the ap1 gene showed enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo) race 6 at various levels.


  1. R-Avr interaction is necessary to induce resistance against specific pathogen. These interactions may be direct or indirect.
  2. The isolation and preliminary characterization of R genes provide opportunities for producing plant varieties with disease resistance.
  3. There is considerable conservation of defence signaling mechanisms between plant species because several different classes of R genes also confer resistance when expressed in heterologous plant species.
  4. There may be a rapid convergence of the initially activated Avr-R gene dependent signaling events into one or a few common pathways that coordinate the overall defense response.
  5. R-Avr gene-mediated resistance is a cell-autonomous trait in which the hallmark of successful pathogen containment is rapid pathogen perception leading to the coordinate induction of a diverse array of defense mechanisms both within the initially attacked cell as well as in the surrounding cells.
  6. Genomics can also be used to identify the genes expressed by the pathogen over a time course of infection.
Future thrust

  1. There is need to elucidate the biochemical functions of pathogen avirulence proteins and plant R proteins.
  2. Focus on better understanding of what controls the defense signal transduction pathways in the host leading to the expression of resistance.
  3. Concomitant biochemical and cell biological effort will also be necessary to unravel the molecular complexities to understand the mechanisms involved in plant disease resistance.
  4. Genomics and proteomic studies related plant defense system should be under taken.
There is need to understand the population biology of pathogen effectors, and their co-evolving host NB-LRR genes.


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Plant Cell 16: 2809–2821

About Author / Additional Info:
I did Ph. D. with specialization in Plant Molecular biology and Biotechnology and 3 years of research experience in Agriculture biotechnology.