J. K. M. Brown

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

From Blight to Powdery Mildew Pathogenic effects of microbes on plants have widespread consequences. Witness, for example, the cultural upheavals driven by potato blight in the 1800s. A variety of microbial pathogens continue to afflict crop plants today, driving both loss of yield and incurring the increased costs of control mechanisms. Now, four reports analyze microbial genomes in order to understand better how plant pathogens function (see the Perspective by Dodds). Raffaele et al. (p. 1540) describe how the genome of the potato blight pathogen accommodates transfer to different hosts. Spanu et al. (p. 1543) analyze what it takes to be an obligate biotroph in barley powdery mildew, and Baxter et al. (p. 1549) ask a similar question for a natural pathogen of Arabidopsis. Schirawski et al. (p. 1546) compared genomes of maize pathogens to identify virulence determinants. Better knowledge of what in a genome makes a pathogen efficient and deadly is likely to be useful for improving agricultural crop management and breeding. A group of papers analyzes pathogen genomes to find the roots of virulence, opportunism, and life-style determinants. Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.

Yield penalties of disease resistance in crops.

Recently, there have been rapid developments in understanding the costs of disease and pest resistance in model plants and their ecological relevance in wild plants. In crop plants, however, much (although not all) of our current understanding of costs of resistance must be inferred from research on model species. To determine the true costs of resistance in crops and the likely benefit of resistance genes in new cultivars, however, other aspects of the plants phenotype must be studied alongside resistance.

Multiple avirulence paralogues in cereal powdery mildew fungi may contribute to parasite fitness and defeat of plant resistance

Powdery mildews, obligate biotrophic fungal parasites on a wide range of important crops, can be controlled by plant resistance (R) genes, but these are rapidly overcome by parasite mutants evading recognition. It is unknown how this rapid evolution occurs without apparent loss of parasite fitness. R proteins recognize avirulence (AVR) molecules from parasites in a gene-for-gene manner and trigger defense responses. We identify AVRa10 and AVRk1 of barley powdery mildew fungus, Blumeria graminis f sp hordei (Bgh), and show that they induce both cell death and inaccessibility when transiently expressed in Mla10 and Mlk1 barley (Hordeum vulgare) varieties, respectively. In contrast with other reported fungal AVR genes, AVRa10 and AVRk1 encode proteins that lack secretion signal peptides and enhance infection success on susceptible host plant cells. AVRa10 and AVRk1 belong to a large family with >30 paralogues in the genome of Bgh, and homologous sequences are present in other formae speciales of the fungus infecting other grasses. Our findings imply that the mildew fungus has a repertoire of AVR genes, which may function as effectors and contribute to parasite virulence. Multiple copies of related but distinct AVR effector paralogues might enable populations of Bgh to rapidly overcome host R genes while maintaining virulence.

A Gene-for-Gene Relationship Between Wheat and Mycosphaerella graminicola, the Septoria Tritici Blotch Pathogen

ABSTRACT Specific resistances to isolates of the ascomycete fungus Mycosphaerella graminicola, which causes Septoria tritici blotch of wheat, have been detected in many cultivars. Cvs. Flame and Hereward, which have specific resistance to the isolate IPO323, were crossed with the susceptible cv. Longbow. The results of tests on F1 and F2 progeny indicated that a single semidominant gene controls resistance to IPO323 in each of the resistant cultivars. This was confirmed in F3 families of Flame x Longbow, which were either homozygous resistant, homozygous susceptible, or segregating in tests with IPO323 but were uniformly susceptible to another isolate, IPO94269. None of 100 F2 progeny of Flame x Hereward were susceptible to IPO323, indicating that the resistance genes in these two cultivars are the same, closely linked, or allelic. The resistance gene in cv. Flame was mapped to the short arm of chromosome 3A using microsatellite markers and was named Stb6. Fifty-nine progeny of a cross between IPO323 and IPO94269 were used in complementary genetic analysis of the pathogen to test a gene-for-gene relationship between Stb6 and the avirulence gene in IPO323. Avirulence to cvs. Flame, Hereward, Shafir, Bezostaya 1, and Vivant and the breeding line NSL92-5719 cosegregated, and the ratio of virulent to avirulent was close to 1:1, suggesting that these wheat lines may all recognize the same avirulence gene and may all have Stb6. Together, these data provide the first demonstration that isolate-specific resistance of wheat to Septoria tritici blotch follows a gene-for-gene relationship.

Comparative analysis of genetic diversity in pea assessed by RFLP- and PCR-based methods.

DNA-based molecular-marker techniques have been proven powerful in genetic diversity estimations. Among them, RFLP was the first and is still the most commonly used in the estimation of genetic diversity of eukaryotic species. The recently developed PCR-based multiple-loci marker techniques, which include RAPD, AFLP, Microsatellite-AFLP and inter-SSR PCR, are playing increasingly important roles in this type of research. Despite the wide application of these techniques, no direct comparison of these methods in the estimation of genetic diversity has been carried out. Here we report a direct comparison of DNA-based RFLP with various PCR-based techniques regarding their informativeness and applicability for genetic diversity analysis. Among ten pea genotypes studied, all the PCR-based methods were much more informative than cDNA-RFLP. Genetic diversity trees were derived from each marker technique, and compared using Mantels test. By this criterion, all trees derived from the various molecular marker techniques, except for the tree derived from inter-SSR PCR, were significantly correlated, suggesting that these PCR-based techniques could replace RFLP in the estimation of genetic diversity. On the basis of this result, AFLP analysis was applied to assess the genetic diversity of a sample of accessions representing the various species and subspecies within the genus Pisum.

Chromosomal location of a gene for resistance to septoria tritici blotch (Mycosphaerella graminicola)in the hexaploid wheat ’Synthetic 6x’

Abstract Septoria tritici blotch, caused by the fungus Mycosphaerella graminicola,is currently the major foliar disease of wheat world-wide, and new sources of resistance and knowledge about the genetics of resistance are needed to improve breeding for resistance to this disease. Sears’s ’Synthetic 6x’ hexaploid wheat, derived from a hybrid of Triticum dicoccoides and Triticum tauschii, was resistant to 12 of 13 isolates of M. graminicola tested. Chromosome 7D of ’Synthetic 6x’ was identified as carrying resistance to all 12 isolates in tests of seedlings of inter-varietal chromosome substitution lines of ’Synthetic 6x’ into ’Chinese Spring’ and to two isolates in tests of adult plants. A septoria tritici blotch resistance gene, named Stb5, was identified using the M. graminicola isolate IPO94269 and mapped on the short arm of chromosome 7D, near the centromere, in a population of single homozygous chromosome-recombinant lines for the 7D chromosome.

Stability of genetic polymorphism in host–parasite interactions

Allelic diversity is common at host loci involved in parasite recognition, such as the major histocompatibility complex in vertebrates or gene-for-gene relationships in plants, and in corresponding loci encoding antigenic molecules in parasites. Diverse factors have been proposed in models to account for genetic polymorphism in host–parasite recognition. Here, a simple but general theory of host–parasite coevolution is developed. Coevolution implies the existence of indirect frequency-dependent selection (FDS), because natural selection on the host depends on the frequency of a parasite gene, and vice versa. It is shown that polymorphism can be maintained in both organisms only if there is negative, direct FDS, such that the strength of natural selection for the host resistance allele, the parasite virulence allele or both declines with increasing frequency of that allele itself. This condition may be fulfilled if the parasite has more than one generation in the same host individual, a feature which is common to most diseases. It is argued that the general theory encompasses almost all factors previously proposed to account for polymorphism at corresponding host and parasite loci, including those controlling gene-for-gene interactions.

QTL analysis of flowering time inArabidopsis thaliana

Quantitative trait loci (QTL) analyses based on restriction fragment length polymorphism maps have been used to resolve the genetic control of flowering time in a cross between twoArabidopsis thaliana ecotypes H51 and Landsbergerecta, differing widely in flowering time. Five quantitative trait loci affecting flowering time were identified in this cross (RLN1-5), four of which are located in regions containing mutations or loci previously identified as conferring a late-flowering phenotype. One of these loci is coincident with theFRI locus identified as the major determinant for late flowering and vernalization responsiveness in theArabidopsis ecotype Stockholm.RLN5, which maps to the lower half of chromosome five (between markers mi69 and m233), only affected flowering time significantly under short day conditions following a vernalization period. The late-flowering phenotype of H51 compared to Landsbergerecta was due to alleles conferring late flowering at only two of the five loci. At the three other loci, H51 possessed alleles conferring early flowering in comparison to those of Landsbergerecta. Combinations of alleles conferring early and late flowering from both parents accounted for the transgressive segregation of flowering time observed within the F2 population. Three QTL,RLN1,RLN2 andRLN3 displayed significant genotype-by-environment interactions for flowering time. A significant interaction between alleles atRLN3 andRLN4 was detected.

Genetic and forma specialis diversity in Blumeria graminis of cereals and its implications for host-pathogen co-evolution.

SUMMARY The grass powdery mildew fungus, Blumeria graminis is classified into eight formae speciales (ff.spp.) based on strict host specialization. However, evidence suggests that host ranges extend to more than one genus and are particularly diverse among samples from the Middle East, the proposed centre of origin and diversification of crop plants. This study investigated whether geographical origin, host species or both determine the genetic variation in B. graminis that is found in cereals, sampled from Europe, Asia and North America, and whether there is any evidence for co-evolution between pathogen and host. Phylogenetic analysis of nucleotide sequence variation within the ribosomal DNA Internal Transcribed Spacer (ITS) regions and the beta-tubulin (tub2) gene gives rise to two dendrograms with different topologies. In both trees, isolates of B. graminis from cultivated cereals are grouped according to their principal host genus. This grouping was supported by amplified fragment length polymorphism (AFLP) analysis and cross-infectivity tests. However, there was no evidence of co-evolution. There was far greater divergence between ff.spp. in tub2 sequences than ITS regions and a faster rate of mutation of tub2, especially in the third base position of exons. It is proposed that variation in the rDNA-ITS regions is constrained either by their functional role in the processing of rDNA precursor molecules or by concerted evolution, hence limiting their use in phylogenetic studies. AFLP data suggests an overall lack of correlation between geographical and genetic distances. This may be related to the long distance dispersal exhibited by B. graminis.

Mycosphaerella graminicola: from genomics to disease control.

UNLABELLED This Mycosphaerella graminicola pathogen profile covers recent advances in the knowledge of this ascomycete fungus and of the disease it causes, septoria tritici blotch of wheat. Research on this pathogen has accelerated since publication of a previous pathogen profile in this journal in 2002. Septoria tritici blotch continues to have high economic importance and widespread global impact on wheat production. TAXONOMY Mycosphaerella graminicola (Fuckel) J. Schröt. In Cohn (anamorph: Septoria tritici Roberge in Desmaz.). Kingdom Fungi, Phylum Ascomycota, Class Loculoascomycetes (filamentous ascomycetes), Order Dothideales, Genus Mycosphaerella, Species graminicola. HOST RANGE Bread and durum wheat (Triticum aestivum L. and T. turgidum ssp. durum L.). Disease symptoms: Initially leaves develop a chlorotic flecking, which is followed by the development of necrotic lesions which contain brown-black pycnidia. Necrosis causes a reduction in photosynthetic capacity and therefore affects grain yield. Disease control: The disease is primarily controlled by a combination of resistant cultivars and fungicides. Rapid advances in disease control, especially in resistance breeding, are opening up new opportunities for the management of the disease. USEFUL WEBSITES http://genome.jgi-psf.org/Mycgr3/Mycgr3.home.html.