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Navigating complexity to breed disease-resistant crops

Key Points

  • Resistance breeding is an important strategy for reducing crop losses caused by disease.

  • The innate immune system allows plants to recognize their pathogens, often providing strong levels of resistance. Such qualitative resistance is, however, often rapidly overcome as pathogens evolve to evade recognition.

  • In addition to innate immunity, plants also have diverse defences that are more subtle in their effects and are only beginning to be understood. Quantitative resistance is considered to be more durable than qualitative resistance.

  • Breeding for long-lasting resistance is critical in many plant–pathogen systems and typically involves combining multiple and diverse resistance genes.

  • Sustainable approaches to disease management involve breeding for genotypes with diverse resistance loci but can also entail the use of diversity among plants at different spatial and temporal scales.

  • New breeding methods can increase crop improvement. However, which resistance genes are used, their performance over time (durability) and their influences on other traits (trade-offs) must be considered and assessed as part of the breeding process.


Plant diseases are responsible for substantial crop losses each year and pose a threat to global food security and agricultural sustainability. Improving crop resistance to pathogens through breeding is an environmentally sound method for managing disease and minimizing these losses. However, it is challenging to breed varieties with resistance that is effective, stable and broad-spectrum. Recent advances in genetic and genomic technologies have contributed to a better understanding of the complexity of host–pathogen interactions and have identified some of the genes and mechanisms that underlie resistance. This new knowledge is benefiting crop improvement through better-informed breeding strategies that utilize diverse forms of resistance at different scales, from the genome of a single plant to the plant varieties deployed across a region.

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Figure 1: A comparison of quantitative and qualitative resistance.
Figure 2: Resistance mechanisms at the tissue and cellular levels.
Figure 3: Challenges for designing sustainable disease resistance at different scales.


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The authors acknowledge support from the United States National Science Foundation grant IOS-1127076.

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Correspondence to Rebecca Nelson.

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Traditional plant varieties that have been developed through informal (farmer-based) breeding.


Living material, such as seeds or tissues, from which new plants can be grown that is maintained for the purpose of preservation, breeding and other uses.


A property that enables resistance to remain effective when deployed over a large area under substantial disease pressure over a long time.


Resistance genes of large effect that are inherited in a Mendelian fashion and typically, but not always, encode nucleotide-binding leucine-rich repeat proteins.

Genetic architecture

The number, locations and effects of genomic variants that give rise to phenotypic variation.


Ecological subsystems defined by a specific disease. A plant pathosystem includes one or more host plant species along with the pathogen(s) that cause(s) the disease.

Effector protein

A protein that is secreted into host cells by a pathogen to suppress defence responses and alter other host biological processes.

Nucleotide-binding domain leucine-rich repeat containing (NLR) genes

A family of plant genes involved in pathogen recognition. Many resistance genes of large effect are NLR genes.

Biotrophic pathogens

Pathogens that obtain nutrients from living plant tissue.

Necrotrophic pathogens

Pathogens that obtain nutrients from dead plant tissue.

Quantitative resistance locus

(QRL). A genetic region that has been statistically associated with quantitatively inherited resistance to a disease and that is presumed to contain alleles or genes that affect resistance.


Variants within a pathogen species that elicit differential responses from resistance genes.

Genetic linkage

The co-inheritance of loci that are close together on a given chromosome.


A phenomenon in which one gene influences multiple traits.

Monogenic resistance

Resistance that relies on a single resistance gene.


Agricultural systems involving a single crop. The concept is used in contrast to systems that involve crop diversity in time and/or space, such as intercropping and rotation systems.

Elite lines

Crop genotypes that have been selected for high performance in a breeding programme, often re-used as parents for further breeding cycles.


Cultivated varieties (genetic strains) of a domesticated crop plant.

Transgressive segregation

A phenomenon in which the progeny derived from a cross have more extreme phenotypes than either parent.


Mixtures of plant cultivars that are genetically very similar but differ in their resistance genes that are grown together in a single plot.


Alleles of a gene or locus present in the homeologous chromosomes of a polyploid species.


Agricultural systems involving multiple crops in a single plot.

Cultivar mixtures

A mixture of multiple plant cultivars of the same species that are not necessarily closely related and are grown together in a single plot.

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Nelson, R., Wiesner-Hanks, T., Wisser, R. et al. Navigating complexity to breed disease-resistant crops. Nat Rev Genet 19, 21–33 (2018).

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