How can we exploit functional genomics approaches for understanding the nature of plant defences? Barley as a case study

Abstract

The concept 'functional genomics' refers to the methods used for the functional characterisation of genomes. The methods utilised provide new opportunities for studying the nature and role of defence mechanisms in plants. Unlike Arabidopsis, poplar and rice, the full genomic sequence of barley is not available. In this case, the analysis of barley gene expression data plays a pivotal role for obtaining insight into the functional characterisation of individual gene products. Many genes are activated transcriptionally following attack by pathogens and these often contribute to the defence mechanisms which underlie disease resistance. The use of large-scale complementary DNA library constructions and genome-wide transcript profiles of plants exposed to biotic stress provide the data required to drive hypotheses concerning the function of newly identified genes. In this paper, we illustrate how publicly available gene expression data has proved valid for studies of plant defence responses; enabling a costeffective workflow starting from isolated gene transcripts to elucidation of biological function upon biotic stress.

Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley

“…Whereas a number of defence genes were activated in response to Ph -infection, none was found to be a promising candidate for Rphq 2 or Rphq 3. Our results support the notion that components of the general defence response have incremental, rather than deterministic, roles in the outcome of an interaction between a plant and a pathogen [ 39 ]. Many attempts to identify genes for disease resistance have highlighted those involved in signal transduction [ 40 , 41 ] or physiological and cellular functions [ 42 , 43 ] rather than defence per se [ 44 , 45 ].…”

An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley

“…As the threshold we adopted for detection of Ph -responsive genes was stringent (fold change>2, FDR<0.05), it is likely that we would mostly detect highly differentially regulated genes involved in general defense responses. Individual components of the general defense response most often have incremental, rather than determinative, roles in the outcome of an interaction with a pathogen [58] . The observation that none of the eQTL hotspots overlapped with pQTL suggests that genes responsible for natural variation in partial resistance to Ph in this population are not trans- eQTL that control general defense responses.…”

Convergent evidence for a role of WIR1 proteins during the interaction of barley with the powdery mildew fungus Blumeria graminis

“…hordei (Bgh) is one of the wellstudied examples of PTI as well as ETI, with several key loci and genes that mediate either response being known or cloned (Azevedo et al, 2002;Buschges et al, 1997;Shen et al, 2007;Shirasu et al, 1999;Zhou et al, 2001). The knowledge of the barleypowdery mildew interaction ranges from well-defined cytological interaction phenotypes including re-orientation of the cytoskeleton, membrane modifications, cell-wall appositions over a large number of race-specific major powdery mildew resistance (R) genes to the localization of a considerable number of QTL for race-nonspecific resistance to Bgh (Collinge et al, 2008;ThordalChristensen et al, 2000). The best studied major R gene is Mla (for Mildew resistance locus a) encoding a coiled-coil, nucleotidebinding-site, leucine-rich-repeat (CC-NBS-LRR) protein, of which over 30 alleles have been described until present (Wei et al, 2002).…”