Characterisation of barley resistance to rhynchosporium on chromosome 6HS

An island of receptor-like genes at the Rrs13 locus on barley chromosome 6HS co-locate with three novel sources of scald resistance

Three Hordeum spontaneum-derived resistances (referred to as 145L2, 41T1 and 40Y5) have demonstrated long-term effectiveness against barley scald, caused by Rhynchosporium commune, in western Canada. Genetic mapping of these resistances in three populations, and the use of five barley genome assemblies, revealed they co-located to a narrowly defined 0.58-1.2 Mbp region of chromosome 6HS containing the Rrs13 scald resistance gene. Differential disease reactions among the three resistances and a Rrs13 carrier (AB6) to a panel of 24 scald isolates indicated that the four resistances were unique from one another. A marker created to target the 6HS scald locus was screened across a panel of barley germplasm that included H. vulgare, H. spontaneum and H. bulbosum lines. The marker showed specificity to H. vulgare lines known to carry the 6HS scald resistances and to two H. spontaneum lines that trace their origins to Jordan. Within the 0.58-1.2 Mbp region were 2-7 tandemly repeated leucine-rich repeat receptor-like proteins (LRR-RLP) and one lectin receptor-like kinase (Lec-RLK) genes with abundant sequence variation between them. The well-defined role that RLP and RLK genes play in plant defense responses make them logical candidate resistance genes, with one possible hypothesis being that each unique scald resistance may be encoded by a different RLP that interacts with a common RLK. It is suggested the three scald resistances be temporarily named Rrs13145L2, Rrs1341T1 and Rrs1340Y5 to recognize their co-location to the Rrs13 locus until it is determined whether these resistances represent unique genes or alleles of the same gene.

Genome-Wide Association Study for Identification of Marker-Trait Associations Conferring Resistance to Scald from Globally Collected Barley Germplasm

Scald is one of the major economically important foliar diseases in barley, causing up to 40% yield loss in susceptible varieties. The identification of quantitative trait loci and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies were conducted using a panel of 697 barley genotypes to identify quantitative trait loci for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for genome-wide association studies analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations related to scald resistance were identified across six different chromosomes. Eleven of these marker-trait associations correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel marker-trait associations were identified in this study, with the candidate genes encoding a diverse class of proteins, including region leucine-rich repeats, AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinase family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.

Reviews of taxonomy, epidemiology, and management practices of the barley scald (Rhynchosporium graminicola) disease

Barley scald is very important in temperate and wet regions worldwide and has become one of the most important foliar diseases. Before the development of recent technologies, several scientists had argued that Rhynchosporium secalis is the causal agent of scald disease. However, the causal agent of this disease was revised and recognized as Rhynchosporium commune. Again recently, Rhynchosporium graminicola was suggested to be replaced as the causal agent of R. commune. The disease outbreak is depending on cool and frequent rainfall. Because of scald disease significance, numerous management practices have been advocated. Then, resistance materials, and mixing of resistant and susceptible cultivars have been used as the best management methods. Several studies have demonstrated that some cultivars and landraces of barley are resistant to scald disease during the seedling and adult growth stages. The first cultivar is "Atlas 46″ which was created from the cultivar "Turk". From biological method: Bacillus polymyxa, Paenibacillus polymyxa KaI245, and Bacillus subtilis are very effective in treating this disease. Finally, as a last option, different fungicides have been suggested. Pathogenicity testing, seed treatments, tillage, cultivar mixtures, and biological control are all commonly overlooked in developing countries. Cultural practices such as times of fungicide application, appropriate time of sowing to scape disease, and tillage practices which are adopted for other diseases are greatly missed for scald disease. Then, we are intended to assess the various findings available on barley scald biology, taxonomy, and management.

Wild barley (Hordeum spontaneum) and landraces (Hordeum vulgare) from Turkey contain an abundance of novel Rhynchosporium commune resistance loci

Rhynchosporium commune is a globally devastating pathogen of barley. Wild and landrace barley are underutilized, however, contain an abundance of loci that can be used as potential sources of resistance. Rhynchosporium commune, the causal agent of the disease scald or leaf blotch of barley, is a hemibiotrophic fungal pathogen of global importance, responsible for yield losses ranging from 30 to 40% on susceptible varieties. To date, over 150 resistance loci have been characterized in barley. However, due to the suspected location of the R. commune host jump in Europe, European germplasm has been the primary source used to screen for R. commune resistance leaving wild (Hordeum spontaneum) and landrace (H. vulgare) barley populations from the center of origin largely underutilized. A diverse population consisting of 94 wild and 188 barley landraces from Turkey were genotyped using PCR-GBS amplicon sequencing and screened with six Turkish R. commune isolates. The isolates were collected from distinct geographic regions of Turkey with two from the Aegean region, two from central Turkey and two from the Fertile Crescent region. The data set was utilized for association mapping analysis with a total of 21 loci identified, of which 12 were novel, indicating that these diverse primary barley gene pools contain an abundance of novel R. commune resistances that could be utilized for resistance breeding.

Pyramiding of scald resistance genes in four spring barley MAGIC populations

Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public-Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.

Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

BACKGROUND

Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke.

RESULTS

In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected.

CONCLUSIONS

To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.

Recent insights into barley and Rhynchosporium commune interactions

Rhynchosporium commune is the causal pathogen of scald in barley (Hordeum vulgare), a foliar disease that can reduce yield by up to 40% in susceptible cultivars. R. commune is found worldwide in all temperate growing regions and is regarded as one of the most economically important barley pathogens. It is a polycyclic pathogen with the ability to rapidly evolve new virulent strains in response to resistance genes deployed in commercial cultivars. Hence, introgression and pyramiding of different loci for resistance (qualitative or quantitative) through marker-assisted selection is an effective way to improve scald resistance in barley. This review summarizes all 148 resistance quantitative trait loci reported at the date of submission of this review and projects them onto the barley physical map, where it is clear many loci co-locate on chromosomes 3H and 7H. We have summarized the major named resistance loci and reiterated the renaming of Rrs15 (CI8288) to Rrs17. This review provides a comprehensive resource for future discovery and breeding efforts of qualitative and quantitative scald resistance loci.

Fine mapping QSc.VR4, an effective and stable scald resistance locus in barley (Hordeum vulgare L.), to a 0.38-Mb region enriched with LRR-RLK and GLP genes

An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance.

Characterisation of barley landraces from Syria and Jordan for resistance to rhynchosporium and identification of diagnostic markers for Rrs1Rh4

Diagnostic markers for Rrs1_Rh4 have been identified by testing for associations between SNPs within the Rrs1 interval in 150 barley genotypes and their resistance to Rhynchosporium commune isolates recognised by lines containing Rrs1. Rhynchosporium or barley scald, caused by the destructive fungal pathogen Rhynchosporium commune, is one of the most economically important diseases of barley in the world. Barley landraces from Syria and Jordan demonstrated high resistance to rhynchosporium in the field. Genotyping of a wide range of barley cultivars and landraces, including known sources of different Rrs1 genes/alleles, across the Rrs1 interval, followed by association analysis of this genotypic data with resistance phenotypes to R. commune isolates recognised by Rrs1, allowed the identification of diagnostic markers for Rrs1_Rh4. These markers are specific to Rrs1_Rh4 and do not detect other Rrs1 genes/alleles. The Rrs1_Rh4 diagnostic markers represent a resource that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars. Thirteen out of the 55 most resistant Syrian and Jordanian landraces were shown to contain markers specific to Rrs1_Rh4. One of these lines came from Jordan, with the remaining 12 lines from different locations in Syria. One of the Syrian landraces containing Rrs1_Rh4 was also shown to have Rrs2. The remaining landraces that performed well against rhynchosporium in the field are likely to contain other resistance genes and represent an important novel resource yet to be exploited by European breeders.

Bivariate analysis of barley scald resistance with relative maturity reveals a new major QTL on chromosome 3H

The disease scald of barley is caused by the pathogen Rhynchosporium commune and can cause up to 30–40% yield loss in susceptible cultivars. In this study, the Australian barley cultivar ‘Yerong’ was demonstrated to have resistance that differed from Turk (Rrs1 (Rh3 type)) based on seedling tests with 11 R. commune isolates. A doubled haploid population with 177 lines derived from a cross between ‘Yerong’ and the susceptible Australian cultivar ‘Franklin’ was used to identify quantitative trait loci (QTL) for scald resistance. A QTL on chromosome 3H was identified with large effect, consistent with a major gene conferring scald resistance at the seedling stage. Under field conditions, a bivariate analysis was used to model scald percentage of infected leaf area and relative maturity, the residuals from the regression were used as our phenotype for QTL analysis. This analysis identified one major QTL on chromosome 3H, which mapped to the same position as the QTL at seedling stage. The identified QTL on 3H is proposed to be different from the Rrs1 on the basis of seedling resistance against different R. commune isolates and physical map position. This study increases the current understanding of scald resistance and identifies genetic material possessing QTLs useful for the marker-assisted selection of scald resistance in barley breeding programs.