The most efficient method of controlling rhynchosporium is for barley crops to express effective and durable resistance to R. commune, whilst maintaining yield and quality. As such, resistance is an important target for breeders. The resistance genetics work at the James Hutton Institute aims to identify novel sources of resistance, characterise their methods of action, locate them on a genetic map and identify the genes underlying these traits. This will produce a resource that can be used by breeders to improve barley cultivars.

Host defences

Plant defences can take a number of forms, which act at different points of the infection cycle. Broadly, these can be divided into the following.

• Disease escape. In which the plant avoids contact with the pathogen. Such defences may be temporal (timing growth to avoid favourable disease conditions) or morphological, for example, growing above spore dispersal regions.
• Resistance. The plant is able to prevent or inhibit infection following contact with the pathogen.
• Tolerance. Whereby the plant minimises the deleterious effects following successful infection by the pathogen.

In practice a combination of all of these defence mechanisms will determine the field performance of a given cultivar under disease pressure.

Resistance

There are two major forms of resistance that are of interest for resistance breeding. Major gene mediated resistance refers to a specific interaction between a single major (R) gene from the host, and a corresponding avirulence (Avr) gene in the pathogen that encode effector molecules. The specific combination of alleles at the R and Avr locus determine whether the interaction between host and pathogen is compatible or incompatible. Because of the specificity of the interaction, major gene mediated resistance is highly effective at preventing disease. However, because of the simple genetic architecture of the resistance, this type of resistance is relatively simple for the pathogen to overcome. In the case of R. commune, this can occur after only a few seasons of commercial deployment.

Quantitative resistance is also based on interactions between host and pathogen genes, but the specificity is lower and may involve numerous host and pathogen genes. Because of this, quantitative resistance is generally assumed to be more durable than major gene mediated resistance.

Sustainable resistance breeding is likely to require the effective combination of numerous major and quantitative resistances in a single cultivar, thus providing resistance that is both effective and durable.

Identifying new sources of resistances

A number of sources have been used to identify novel resistance to R. commune. These include the wild relatives of barley (Hordeum sponteneum, and H. bulbosum) and locally adapted varieties (landraces). In addition, cultivated barley may also harbour specific resistances that have yet to be widely exploited. In particular significant differences exist between winter and spring barley types, with winter barley showing consistently and higher levels of resistance to rhynchosporium. Mapping work at the James Hutton Institute has suggested that these differences are not a consequence of seasonal growth habit, and as such represent a useful resource for improving spring barley.

Scoring disease resistance

The method used to assess resistance to rhynchosporium can have crucial consequences for the interpretation of results. Field trials, using natural inoculum, are the most relevant to how varieties will perform following commercial deployment, but the combination of resistance mechanisms, coupled with the presence of substantial R. commune genetic variation make specific conclusions about the nature and specificity of resistance difficult.

Controlled environment resistance scoring under glasshouse conditions using single rhynchosporium isolates allow specific resistances to be matched with specific pathogen virulences. A notable feature of R. commune is the long period between infection and symptom development means that a large proportion of the infection cycle is invisible to traditional scoring methods. Recent development of alternative methods, comprising R. commune specific primers for qPCR and GFP transformed R. commune isolates have allowed infection levels and growth patterns to be easily determined during early infection.

Mapping resistance traits

Locating resistances on genetic maps relies on identifying statistical relationships between genotypes and phenotypes. These can broadly be divided into two approaches. Quantitative trait locus (QTL) mapping methods use a population derived from a cross between parents that vary both for resistance traits and a set of genetic markers. Associations between marker genotypes and resistance scores indicate linkage between the marker and loci influencing the resistance trait.

This approach allows the detection and mapping of specific resistances. However, over just several generations, recombination is limited and therefore map resolution can be low. In addition, QTL mapping will only identify genetic variation that is present in the two parents, thus requiring many separate populations to capture a wide range of variation. Association mapping also relies on associations between segregating markers and QTL. However, association mapping uses diverse collections of genotypes, thus capturing a large amount of variation in a single experiment, whilst also exploiting historical recombination for improved map resolution.

Association mapping can be severely affected by population structure (which can create spurious associations between markers and traits) and also relies on QTL being present at sufficiently high frequency in the association panel to be detected.