An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

Rx-mediated extreme resistance against potato virus X in potato does not involve a necrotic hypersensitive response at the site of initial infection and thereby differs from the more usual type of disease resistance in plants. However, the Rx protein is structurally similar to products of disease resistance genes conferring the hypersensitive response. We show in both Nicotiana spp and potato that Rx has the potential to initiate a cell death response but that extreme resistance is separate and epistatic to necrosis. These data indicate that cell death and pathogen arrest are separate disease resistance responses in plants.

Rx -mediated extreme resistance against potato virus X in potato does not involve a necrotic hypersensitive response at the site of initial infection and thereby differs from the more usual type of disease resistance in plants. However, the Rx protein is structurally similar to products of disease resistance genes conferring the hypersensitive response. We show in both Nicotiana spp and potato that Rx has the potential to initiate a cell death response but that extreme resistance is separate and epistatic to necrosis. These data indicate that cell death and pathogen arrest are separate disease resistance responses in plants. INTRODUCTIONRx-mediated resistance against potato virus X (PVX), like that controlled by many disease resistance ( R ) genes, can be described in terms of an elicitor-receptor model. According to this model, there are separate stages in the process involving pathogen recognition and the plant's response (Staskawicz et al., 1995). In Rx -mediated resistance, the recognition stage involves an interaction between Rx (Bendahmane et al., 1997), which is thought to encode the receptor, and the PVX coat protein (CP), which is the elicitor (Bendahmane et al., 1995). The response stage consists of mechanisms able to suppress accumulation of viruses, including those that are taxonomically unrelated to PVX (Köhm et al., 1993; Bendahmane et al., 1995).Although the Rx -mediated mechanism is consistent with the elicitor-receptor model, the Rx response is distinct from that of other well-characterized R genes. The most striking feature of Rx -mediated resistance is the rapid arrest of PVX accumulation in the initially infected cell (Köhm et al., 1993). Unlike other disease resistance responses, this extreme resistance is not associated with a hypersensitive response (HR) at the site of inoculation. In addition, Rx -mediated resistance is active in protoplasts via mechanisms that either suppress virus replication or promote degradation of the viral RNA (Adams et al., 1986; Köhm et al., 1993; Bendahmane et al., 1995). In contrast, the HR type of resistance is not expressed in isolated protoplasts (Otsuki et al., 1972;Adams et al., 1985; Baulcombe et al., 1994). It is thought that expression of the HR type of viral resistance mechanisms requires cell-to-cell contact and is a tissue-related phenomenon (Adams et al., 1986).With the exception of the Rx response, it is not clear whether an HR is an essential component of disease resistance mechanisms in plants. One view is that cell death removes the substrate for growth of biotrophic pathogens. Alternatively, the dying cells may be able to release signals that are themselves antibiotics or disinfectants (Lamb and Dixon, 1997). This latter view is supported by earlier studies on tobacco N gene-mediated resistance to tobacco mosaic virus (TMV). TMV particles could be found in cells surrounding the necrotic HR lesion, even when lesion expansion had stopped (Da Graça and Martin, 1976). Several candidates have been identified for the putative cell death-associated ...

Deployment of fast-evolving disease-resistance genes is one of the most successful strategies used by plants to fend off pathogens. In gene-for-gene relationships, most cloned disease-resistance genes encode intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) recognizing pathogen-secreted isolate-specific avirulence (Avr) effectors delivered to the host cytoplasm. This process often triggers a localized hypersensitive response, which halts further disease development . Here we report the map-based cloning of the wheat Stb6 gene and demonstrate that it encodes a conserved wall-associated receptor kinase (WAK)-like protein, which detects the presence of a matching apoplastic effector and confers pathogen resistance without a hypersensitive response . This report demonstrates gene-for-gene disease resistance controlled by this class of proteins in plants. Moreover, Stb6 is, to our knowledge, the first cloned gene specifying resistance to Zymoseptoria tritici, an important foliar fungal pathogen affecting wheat and causing economically damaging septoria tritici blotch (STB) disease.

Summary Rx2 confers resistance against potato virus X (PVX). To clone Rx2, we developed a system based on Agrobacterium‐mediated transient expression of candidate R genes in transgenic tobacco leaves expressing the PVX coat protein elicitor of Rx2‐mediated resistance. Using this system, a potato gene eliciting HR specifically in the presence of the elicitor was identified. Based on genetical and functional analysis, it is concluded that the cloned gene is Rx2. The transient expression system is potentially adaptable to cloning of any other resistance gene. The Rx2 locus is on chromosome V of potato and the encoded protein is highly similar to the products of Rx1 and Rxh1 encoded on potato chromosome XII. Rxh1 has been shown elsewhere to encode a potato cyst nematode resistance gene Gpa2. All three proteins are in the leucine zipper‐nucleotide binding site‐leucine rich repeat class of resistance gene products. Rx1 and Rx2 are functionally identical and are almost identical in the C terminal region consistent with a role of the leucine rich repeats in recognition of the PVX coat protein. In the N terminal, half there are some regions where the Rx1 and Rx2 proteins are more similar to each other than to the Rxh1 protein. However, in other regions these proteins are more similar to Rxh1 than to each other. Based on this mosaic pattern of sequence similarity, we conclude that sequence exchange occurs repeatedly between genetically unlinked disease resistance genes through a process of gene conversion.

Race-specific resistance genes protect the global wheat crop from stem rust disease caused by f. sp. () but are often overcome owing to evolution of new virulent races of the pathogen. To understand virulence evolution in , we identified the protein ligand (AvrSr50) recognized by the Sr50 resistance protein. A spontaneous mutant of virulent to contained a 2.5 mega-base pair loss-of-heterozygosity event. A haustorial secreted protein from this region triggers-dependent defense responses in planta and interacts directly with the Sr50 protein. Virulence alleles of have arisen through DNA insertion and sequence divergence, and our data provide molecular evidence that in addition to sexual recombination, somatic exchange can play a role in the emergence of new virulence traits in.

SummaryThe isolation of the nematode-resistance gene Gpa2 in potato is described, and it is demonstrated that highly homologous resistance genes of a single resistance-gene cluster can confer resistance to distinct pathogen species. Molecular analysis of the Gpa2 locus resulted in the identi®cation of an R-gene cluster of four highly homologous genes in a region of approximately 115 kb. At least two of these genes are active: one corresponds to the previously isolated Rx1 gene that confers resistance to potato virus X, while the other corresponds to the Gpa2 gene that confers resistance to the potato cyst nematode Globodera pallida. The proteins encoded by the Gpa2 and the Rx1 genes share an overall homology of over 88% (amino-acid identity) and belong to the leucine-zipper, nucleotide-binding site, leucine-rich repeat (LZ-NBS-LRR)-containing class of plant resistance genes. From the sequence conservation between Gpa2 and Rx1 it is clear that there is a direct evolutionary relationship between the two proteins. Sequence diversity is concentrated in the LRR region and in the C-terminus. The putative effector domains are more conserved suggesting that, at least in this case, nematode and virus resistance cascades could share common components. These ®ndings underline the potential of protein breeding for engineering new resistance speci®cities against plant pathogens in vitro.