Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres)

A total of 449 barley accessions were phenotyped for Pyrenophora teres f. teres resistance at three locations and in greenhouse trials. Genome-wide association studies identified 254 marker-trait associations corresponding to 15 QTLs. Net form of net blotch is one of the most important diseases of barley and is present in all barley growing regions. Under optimal conditions, it causes high yield losses of 10-40% and reduces grain quality. The most cost-effective and environmentally friendly way to prevent losses is growing resistant cultivars, and markers linked to effective resistance factors can accelerate the breeding process. Here, 449 barley accessions expressing different levels of resistance comprising landraces and commercial cultivars from the centres of diversity were selected. The set was phenotyped for seedling resistance to three isolates in controlled-environment tests and for adult plant resistance at three field locations (Belarus, Germany and Australia) and genotyped with the 50 k iSelect chip. Genome-wide association studies using 33,818 markers and a compressed mixed linear model to account for population structure and kinship revealed 254 significant marker-trait associations corresponding to 15 distinct QTL regions. Four of these regions were new QTL that were not described in previous studies, while a total of seven regions influenced resistance in both seedlings and adult plants.

An Improved Detached-Leaf Assay for Phenotyping Net Blotch of Barley Caused by Pyrenophora teres

Net blotch, caused by Pyrenophora teres, is a major barley (Hordeum vulgare) leaf disease worldwide. P. teres occurs as two forms-P. teres f. teres, and P. teres f. maculata-inducing net and spot-like symptoms, respectively. An intact-seedling assay, where entire seedlings are inoculated by spraying with a conidial suspension, is frequently used for phenotyping net blotch. However, this presents a biosecurity risk in the glasshouse when nonlocal isolates are being screened. Alternatively, a detached-leaf assay (DLA-droplet method) can be used in which leaf segments laid out in a covered tray are inoculated with droplets of a conidial suspension, confining the inoculum. However, using this method, net and spot form symptoms cannot be distinguished from each other. We have developed an improved DLA (DLA-spray method) in which detached whole leaves are sprayed with the inoculum to produce distinct lesions. We compare the results for the three phenotyping methods above using four isolates from both net and spot forms of the disease to inoculate a standard set of eight barley genotypes. Results indicate that the DLA-spray method is a functional, informative and rapid test that readily differentiates the two forms of the pathogen in a biosecure environment.

Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection

Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen. Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at seedling and adult plant growth stages using three P. triticina pathotypes prevalent in Australia. GWAS was applied to 11 phenotypic data sets which identified a total of 52 significant marker-trait associations representing 31 quantitative trait loci (QTL). Among them, 29 QTL were associated with adult plant resistance (APR). Of the 31 QTL, 13 were considered potentially new loci, whereas 4 co-located with previously catalogued Lr genes and 14 aligned to regions reported in other GWAS and genomic prediction studies. One seedling LR resistance QTL located on chromosome 3A showed pronounced levels of linkage disequilibrium among markers (r ² = 0.7), suggested a high allelic fixation. Subsequent haplotype analysis for this region found seven haplotype variants, of which two were strongly associated with LR resistance at seedling stage. Similarly, analysis of an APR QTL on chromosome 7B revealed 22 variants, of which 4 were associated with resistance at the adult plant stage. Furthermore, most of the tested lines in the diversity panel carried 10 or more combined resistance-associated marker alleles, highlighting the potential of allele stacking for long-lasting resistance.

Investigating successive Australian barley breeding populations for stable resistance to leaf rust

Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.

Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley

We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F₂ were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F_2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.

Spot form of net blotch resistance in barley is under complex genetic control

Evaluation of resistance to Pyrenophora teres f. maculata in barley breeding populations via association mapping revealed a complex genetic architecture comprising a mixture of major and minor effect genes. In the search for stable resistance to spot form of net blotch (Pyrenophora teres f. maculata, SFNB), association mapping was conducted on four independent barley (Hordeum vulgare L.) breeding populations comprising a total of 898 unique elite breeding lines from the Northern Region Barley Breeding Program in Australia for discovery of quantitative trait loci (QTL) influencing resistance at seedling and adult plant growth stages. A total of 29 significant QTL were validated across multiple breeding populations, with 22 conferring resistance at both seedling and adult plant growth stages. The remaining 7 QTL conferred resistance at either seedling (2 QTL) or adult plant (5 QTL) growth stages only. These 29 QTL represented 24 unique genomic regions, of which five were found to co-locate with previously identified QTL for SFNB. The results indicated that SFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H. A large proportion of the QTL acted in the same direction for both seedling and adult responses, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance. However, the accumulation of specific resistance alleles on several chromosomes must be considered in molecular breeding selection strategies.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

"To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants." Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Mapping Rph20: a gene conferring adult plant resistance to Puccinia hordei in barley

A doubled haploid (DH) barley (Hordeum vulgare L.) population of 334 lines (ND24260 × Flagship) genotyped with DArT markers was used to map genes for adult plant resistance (APR) to leaf rust (Puccinia hordei Otth) under field conditions in Australia and Uruguay. The Australian barley cultivar Flagship carries an APR gene (qRphFlag) derived from the cultivar Vada. Association analysis and composite interval mapping identified two genes conferring APR in this DH population. qRphFlag was mapped to the short arm of chromosome 5H (5HS), accounting for 64-85% of the phenotypic variation across four field environments and 56% under controlled environmental conditions (CEC). A second quantitative trait locus (QTL) from ND24260 (qRphND) with smaller effect was mapped to chromosome 6HL. In the absence of qRphFlag, qRphND conferred only a low level of resistance. DH lines displaying the highest level of APR carried both genes. Sequence information for the critical DArT marker bPb-0837 (positioned at 21.2 cM on chromosome 5HS) was used to develop bPb-0837-PCR, a simple PCR-based marker for qRphFlag. The 245 bp fragment for bPb-0837-PCR was detected in a range of barley cultivars known to possess APR, which was consistent with previous tests of allelism, demonstrating that the qRphFlag resistant allele is common in leaf rust resistant cultivars derived from Vada and Emir. qRphFlag has been designated Rph20, the first gene conferring APR to P. hordei to be characterised in barley. The PCR marker will likely be effective in marker-assisted selection for Rph20.

Mating type locus-specific polymerase chain reaction markers for differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of barley net blotch

Fourteen single nucleotide polymorphisms (SNPs) were identified at the mating type (MAT) loci of Pyrenophora teres f. teres (Ptt), which causes net form (NF) net blotch, and P. teres f. maculata (Ptm), which causes spot form (SF) net blotch of barley. MAT-specific SNP primers were developed for polymerase chain reaction (PCR) and the two forms were differentiated by distinct PCR products: PttMAT1-1 (1,143 bp) and PttMAT1-2 (1,421 bp) for NF MAT1-1 and MAT1-2 isolates; PtmMAT1-1 (194 bp) and PtmMAT1-2 (939 bp) for SF MAT1-1 and MAT1-2 isolates, respectively. Specificity was validated using 37 NF and 17 SF isolates collected from different geographic regions. Both MAT1-1 and MAT1-2 SNP primers retained respective specificity when used in duplex PCR. No cross-reactions were observed with DNA from P. graminea, P. tritici-repentis, or other ascomycetes, or barley. Single or mixed infections of the two different forms were also differentiated. This study provides the first evidence that the limited SNPs at the MAT locus are sufficient for distinguishing closely related heterothallic ascomycetes at subspecies levels, thus allowing pathogenicity and mating type characteristics of the fungus to be determined simultaneously. Methods presented will facilitate pathogen detection, disease management, and epidemiological studies.

Effects of leaf rust on selected Australian barleys

The effects of epidemics of leaf rust (Puccinia hordei Otth.) on grain size and yield of some commercial Australian barley cultivars were determined in 3 field experiments at or near Toowoomba in 1985, 1989 and 1990. Yield was reduced by 38% for the highly susceptible cultivar, Gus, in a mild to moderate epidemic in 1985; cvv. Prior, Schooner, Clipper, Lara and Stirling lost between 10 and 20% yield and cvv. Corvette and Grimmett were unaffected. In a mild to moderate epidemic in 1989, leaf rust reduced the yield of Gus by 40%, and of Grimmett and Clipper by 17 and 12%, respectively, while Prior and Corvette were unaffected. In a moderate to severe epidemic in 1990, yield losses were 62% in Gus, 26% in Grimmett, 31% in Skiff and 14% in the slow-rusting cultivar, Athos. No losses were detected for Corvette or the slow-rusting cultivar, Koru. Loss of yield was largely attributable to reduction in grain size.

Effectiveness of incomplete resistance to Pyrenophora tritici-repentis in wheat

Severe epidemics of yellow spot (Pyrenophora tritici-repentis) reduced grain yield by c. 60% in the highly susceptible wheat cv. Banks in two experiments. About two-thirds of the yield loss was associated with reduced grain size. Milder epidemics developed in cultivars with incomplete resistance and resulted in substantially smaller effects on grain yield. The value of the resistance in a high-yielding background was illustrated by yield advantages over Banks of c. 230% for Genaro 8 1 and c. 190% for Vicam 7 1, under heavy disease pressure. Lines selected from crosses of Genaro 81/2*Banks and Vicam 7!/2*Banks had less disease than Banks and only small to moderate yield losses occurred in the best selections under heavy disease pressure. This illustrates that the resistance from these sources can be transferred readily into adapted Australian wheats and should greatly reduce yield losses from yellow spot.

Susceptibility of Australian wheats to Pyrenophora tritici-repentis

The response of Australian wheats to yellow spot caused by Pyrenophora tritici-repentis has been examined under controlled conditions with a juvenile-plant screening system. About three-quarters of contemporary Australian wheats are highly susceptible to the disease and very few cultivars possess useful levels of resistance. Also, the majority of Australian wheats now undergoing final evaluation before releasing are highly susceptible to yellow spot. Modern wheats grown in Queensland and northern New South Wales are, as a group, more susceptible than those they replaced, and this may have contributed to the upsurge in yellow spot in the region. In two comparisons between ratings on juvenile plants under controlled conditions with field disease assessments and yield measures, the juvenile plant ratings and field disease assessments explained similar proportions of the variation in yield measures.

Effects of yellow spot on wheat: comparison of epidemics at different stages of crop development

Effects of yellow spot (Pyrenophoua tuitici-repentis) on two cultivars (Banks and Olympic) of wheat have been examined in a field experiment where distinctly different epidemics were produced in various treatments. Severe yellow spot before jointing reduced production of both tillers and dry matter, and substantially lowered leaf area index at jointing. Severe disease after jointing reduced leaf area index at flowering, dry weight of plants at maturity and harvest index. Crop phenology was also modified, with flowering being delayed by early disease and crop maturity hastened by late disease. Where yellow spot was severe throughout, the grain-filling period was greatly reduced. Grain yield of Banks was reduced by c. 13 % by early disease, c. 35 % by late disease, and c. 48 % by disease throughout the crop season. Most of the loss was in reduced grain size. Although yield loss in Olympic was less than in Banks, the resistance of Olympic was shown to be inadequate.

Yield losses in wheat from yellow spot: comparison of estimates derived from single tillers and plots

Losses in wheat yield associated with yellow spot (Pyrenophora tritici-repentis) have been examined in a field experiment where development of crop and disease were promoted with sprinkler irrigation. Different amounts of infected wheat stubble were applied to initiate epidemics in four treatments, while fungicide sprays were used to reduce the severity of yellow spot in a fifth treatment. The relationship between severity of yellow spot and the amount of infected stubble at first appeared to be linear but became more noticeably logarithmic as the epidemics progressed. Under conditions favouring disease development, a loss in grain yield of c. 49% was measured in the most severely diseased treatment relative to the sprayed treatment, with grain number per unit area and grain size both being reduced. The percentage loss in grain yield was less for main stems than for later heads. Regression analyses of disease severity with grain yield and its components using 50 main stems in each plot gave different estimates of yield loss, depending on the growth stage at which disease severity was assessed. These estimates of yield loss and those provided by a previously developed disease-loss relationship severely underestimated the overall loss in grain yield. However, there was better agreement between estimates derived from the regressions and loss in grain yield on main stems. Possible reasons for the discrepancies in estimates of loss in grain yield are discussed.

The epidemiology of yellow spot of wheat in southern Queensland

Aspects of the epidemiology of yellow spot of wheat, caused by Pyrenophovu tritici-repentis, have been examined in southern Queensland. Ascospores of the fungus were detected In the air above wheat stubble between March and October, but numbers at any one time were small. Small numbers of conidia trapped between late February and May apparently originated on the stubble. Large numbers of conidia in late October-November were produced predominantly on old lesions and dead tissues in a wheat crop planted through the stubble During late spring, numbers of air-borne conidia increased markedly the day after rain or irrigation. The results suggest that epidemics of yellow spot in southern Queensland are mainly initiated by ascospores and possibly conidia produced on stubble from the preceding diseased wheat crop. Large numbers of conidia produced on a diseased crop result in rapid development of the epidemic under favourable conditions and permit spread of the pathogen to other crops or localities.

The occurrence and control of yellow spot of wheat in north-eastern Australia

Explanations were sought for the increased severity of yellow spot of wheat (Pyrenophora tritici-repentis) in the north-eastern wheat growing areas of Australia. A close association between the severity of yellow spot and stubble management practices was found in a field experiment. There was less disease in plots where stubble had been burned (0.83 lesions per leaf) or burned and cultivated (0.62) than in plots which were mechanically cultivated (2.43) or untreated (11.75). In another study severe yellow spot developed as early as in the second wheat crop in a rotation. Differences in susceptibility to the disease were found among 11 wheat cultivars and lines. Vigorous development of the pathogen occurred on cereal rye and triticale while the fungus was isolated from small lesions on barley and four common grasses. Avoidance of planting wheat into infected wheat stubble, either by crop rotation or removal of surface stubble by incorporation or burning, should provide effective control of the disease in most situations.