Genetic analysis of the obligate parasitic barley powdery mildew fungus based on RFLP and virulence loci

Genetics of avirulence genes in Blumeria graminis f.sp. hordei and physical mapping of AVR(a22) and AVR(a12)

Powdery mildew fungi are parasites that cause disease on a wide range of important crops. Plant resistance (R) genes, which induce host defences against powdery mildews, encode proteins that recognise avirulence (AVR) molecules from the parasite in a gene-for-gene manner. To gain insight into how virulence evolves in Blumeria graminis f.sp. hordei, associations between segregating AVR genes were established. As a prerequisite to the isolation of AVR genes, two loci were selected for further analysis. AVR(a22) is located in a tightly linked cluster comprising AVR(a10) and AVR(k1) as well as up to five other AVR genes. The ratio between physical and genetic distance in the cluster ranged between 0.7 and 35 kB/cM. The AVR(a22) locus was delimited by the previously isolated gene AVR(a10) and two cleaved amplified polymorphic sequence (CAPS) markers, 19H12R and 74E9L. By contrast, AVR(a12) was not linked to other AVR genes in two crosses. Bulk segregant analysis of over 100,000 AFLP fragments yielded two markers, ETAMTG-285 and PAAMACT-473, mapping 10 and 2cM from AVR(a12), respectively, thus delimiting AVR(a12) on one side. All markers obtained for AVR(a12) mapped proximal to it, indicating that the gene is located at the end of a chromosome. Three more AVR(a10) paralogues were identified at the locus interspersed among genes for metabolic enzymes and abundant repetitive elements, especially those homologous to the CgT1 class of retrotransposons. The flanking and close markers obtained will facilitate the isolation of AVR(a22) and AVR(a12) and provide useful tools for studies of the evolution of powdery mildew fungi in agriculture and nature.

Analysis of the structure and inheritance of a linear plasmid from the obligate biotrophic fungus Blumeria graminis f. sp. hordei

A linear plasmid is widespread among isolates of the obligate biotrophic fungus Blumeria graminis f.sp. hordei (synonym Erysiphe graminis) (Bgh), the organism that causes the disease powdery mildew on barley. We cloned and sequenced the entire plasmid of 7965 bp. The plasmid contains two identical terminal inverted repeats (TIR) of 610 bp. Two ORFs are present on opposite strands, one encoding a phage-type DNA polymerase and the other a phage-type RNA polymerase. Two large transcripts of approximately 4.2 and 5.6 kb were identified in conidia, germinating conidia and Bgh -infected barley leaves, indicating that the polymerases are transcribed at most stages of the lifecycle. The transcription start sites were localised within the TIR regions, where a putative 11-bp ARS consensus sequence was also identified. To follow the sexual transmission of the plasmid we screened 27 Bgh isolates for mitochondrial polymorphisms. One polymorphism allowed us to carry out a cross between two isolates that differed in both mitochondrial genotype and presence/absence of the Bgh plasmid. The plasmid was transmitted independently of the origin of the mitochondria. No transfer of the plasmid was observed between two Bgh isolates that were co-cultivated for 1.5 years on a common susceptible barley variety. The plasmid appears to be an autonomous replicon with no phenotypic effect on Bgh.

A genetic map of Blumeria graminis based on functional genes, avirulence genes, and molecular markers

A genetic map of the powdery mildew fungus, Blumeria graminis f. sp. hordei, an obligate biotrophic pathogen of barley, is presented. The linkage analysis was conducted on 81 segregating haploid progeny isolates from a cross between 2 isolates differing in seven avirulence genes. A total of 359 loci were mapped, comprising 182 amplified fragment length polymorphism markers, 168 restriction fragment length polymorphism markers including 42 LTR-retrotransposon loci and 99 expressed sequence tags (ESTs), all the seven avirulence genes, and a marker closely linked to the mating type gene. The markers are distributed over 34 linkage groups covering a total of 2114 cM. Five avirulence genes were found to be linked and mapped in clusters of three and two, and two were unlinked. The Avr(a6) gene was found to be closely linked to markers suitable for a map-based cloning approach. A linkage between ESTs allowed us to demonstrate examples of synteny between genes in B. graminis and Neurospora crassa.

Non-Mendelian and skewed segregation of DNA markers in wide crosses of the bean rust fungus, Uromyces appendiculatus

The inheritance of DNA markers was investigated in 27 F2 progeny from a single F1 hybrid derived from a wide cross in Uromyces appendiculatus. This cross was unusual because asexual spores were used to fertilize sexual fruiting structures. Sixty percent of the DNA markers failed to segregate according to simple Mendelian ratios. Segregation bias was evident, in that F2 progeny inherited on average 91% of maternal bands and 52% of paternal bands, which deviates significantly from the expected value for each of 75% for dominant markers. Because of these distortions, linkage mapping was not possible with this population. Evaluation of two F1s from a second wide cross, reciprocals obtained by normal fertilization, also showed non-Mendelian inheritance of one of three co-dominant RFLPs and five of six isozyme markers, indicating that the method of crossing was probably not responsible for the abnormal segregation patterns in the first cross. Either genetic incompatibility, similar to that of an interspecific cross, or selection of particular genotypes could explain the genetic anomalies reported here.

Chance and selection in the evolution of barley mildew

Populations of the barley powdery mildew fungus are genetically very diverse. However, when a new resistance gene is introduced into barley to control mildew, the population of the pathogen may respond by rapid growth of a few virulent clones. These phases of rapid clonal evolution cause radical changes in the frequencies of mildew genotypes.

Genetic diversity among wild and cultivated barley as revealed by RFLP

Genetic variability of cultivated and wild barley, Hordeum vulgare ssp. vulgare and spontaneum, respectively, was assessed by RFLP analysis. The material consisted of 13 European varietes, single-plant offspring lines of eight land races from Ethiopia and Nepal, and five accessions of ssp. spontaneum from Israel, Iran and Turkey. Seventeen out of twenty-one studied cDNA and gDNA probes distributed across all seven barley chromosomes revealed polymorphism when DNA was digested with one of four restriction enzymes. A tree based on genetic distances using frequencies of RFLP banding patterns was estimated and the barley lines clustered into five groups reflecting geographical origin. The geographical groups of land-race lines showed less intragroup variation than the geographical groups of spontaneum lines. The group of European varieties, representing large variation in agronomic traits, showed an intermediate level. The proportion of gene diversity residing among geographical groups (FST) varied from 0.19 to 0.94 (average 0.54) per RFLP pattern, indicating large diversification between geographical groups.

Genetic analysis of DNA fingerprints and virulences in Erysiphe graminis f.sp. hordei

A DNA probe, E9, which has been used extensively in population genetic studies of the barley powdery mildew pathogen, Erysiphe graminis f.sp. hordei, was shown to be homologous to dispersed sequences in the genome of this fungus. In a cross of the isolates CC52 and DH14, fragments with homology to E9 mapped to six clusters of loci. Avirulences matching five resistance genes in barley were controlled by single genes, in accordance with the gene-for-gene hypothesis, while avirulence matching a sixth resistance gene, Mla13, was controlled by two genes. A gene which controls the response to a fungicide, ethirimol, was not linked to any other gene. In all, seven linkage groups, comprising 22 loci, were detected. The results indicate that E9 can be used to identify members of a clone of E.g. f.sp. hordei, but should not be used for quantitative population genetic analysis.

Genome manipulation in recalcitrant species: construction and characterization of a yeast artificial chromosome (YAC) library from Erysiphe graminis f. sp. hordei, an obligate fungal pathogen of barley

Extraction of DNA from organisms where spores are the only source of pure material is a major problem. Methods are described which allow the isolation of high-M(r) DNA, from small quantities of Erysiphe graminis f. sp. hordei (Egh) conidia, suitable for cloning in yeast artificial chromosomes (YACs). A YAC library of 1500 clones was constructed in the vectors, pYAC4 and pYACRC. The average size of YAC inserts is 220 kb and range from 70 to 500 kb, providing ten haploid genome equivalents. Multicopy RFLP markers and an Egh-specific repetitive SINE element were used to characterize the library. The SINE element is effective in fingerprint analysis and contig assembly. Four out of five representative clones containing more than one YAC were mitotically unstable.

SINE-like properties of a highly repetitive element in the genome of the obligate parasitic fungus Erysiphe graminis f.sp. hordei

The genomic organization of repetitive DNA in the obligate parasitic fungus Erysiphe graminis DC ex Mérat f.sp. hordei Em. Marchal was investigated using a cosmid library of the fungal genome. Three repetitive sequences were shown to be dispersed throughout the genome, and in a few cases they were found closely associated with long poly(dA) tracts. The most prevalent sequence is 903 bp long and accounts for at least 5% of the genome. Sequence analysis revealed features resembling mammalian Short INterspersed Elements (SINEs), namely the presence of a poly(dA) tail (33 bp), flanking direct repeats (13 bp), putative "A" and "B" blocks for RNA polymerase III binding; the corresponding transcript would be capable of forming a complex secondary structure.

The inheritance of restriction fragment length polymorphisms in the flax rust Melampsora lini

Random cDNA sequences synthesized from poly A(+) RNA extracted from germinated urediospores of the flax rust fungus, Melampsora lini, were used as probes to detect restriction fragment length polymorphisms (RFLPs) in three races of M. lini originating from cultivated flax, Linum usitatissimum, and one race originating from Australian native flax, L. marginale. Fourteen out of 22 probes tested detected RFLPs in the three races from cultivated flax while 19 of the probes detected polymorphisms between these three races and the race from L. marginale. The segregation of seven RFLPs was determined in a family of 19 F2 progeny derived from a cross between two of the rust races. With six of these the inheritance was consistent, in each case, with the segregation of alleles at a single locus. Inheritance of the seventh was unusual and an explanation involving two loci with null alleles at each was proposed. No linkage was detected between any of the RFLP loci and nine unlinked loci specifying avirulence.

DNA restriction fragment length polymorphisms in the wheat stem rust fungus, Pucinia graminis tritici

A cDNA library was synthesized from poly A(+) RNA extracted from germinated urediospores of the wheat stem rust fungus, Puccnia graminis tritici (race 343-1,2,3,5,6). The library was used as a source of probes to detect RFLPs in genomic DNA from three major races of P. graminis tritici in Australia, as well as two formae speciales of P. graminis. DNA extracted from another Puccnia species infecting wheat, P. recondita tritici (wheat leaf rust), was included in the analysis. Nine different cDNA probes were analysed, and all detected polymorphisms between the races and formae speciales of P. graminis that were tested. Seven detected polymorphisms between P. graminis and P. recondita; the remaining two probes showed no detectable homology to P. recondita genomic DNA. The potential applications of RFLP markers to study the origin of genetic variability in P. graminis tritici are discussed.