Resistance to <Emphasis Type="Italic">Rhynchosporium commune</Emphasis> in a collection of European spring barley germplasm

Key message

Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1.

Abstract

Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars.

     

Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

Key message

In two Spanish barley landraces with outstanding resistance to scald, the Rrs1 _Rh4 locus was fine mapped including all known markers used in previous studies and closely linked markers were developed.

Abstract

Scald, caused by Rhynchosporium commune, is one of the most prevalent barley diseases worldwide. A search for new resistance sources revealed that Spanish landrace-derived lines SBCC145 and SBCC154 showed outstanding resistance to scald. They were crossed to susceptible cultivar Beatrix to create large DH-mapping populations of 522 and 416 DH lines that were scored for disease resistance in the greenhouse using two R. commune isolates. To ascertain the pattern of resistance, parents and reference barley lines with known scald resistance were phenotyped with a panel of differential R. commune isolates. Subpopulations were genotyped with the Illumina GoldenGate 1,536 SNP Assay and a large QTL in the centromeric region of chromosome 3H, known to harbour several scald resistance genes and/or alleles, was found in both populations. Five SNP markers closest to the QTL were converted into CAPS markers. These CAPS markers, together with informative SSR markers used in other scald studies, confirmed the presence of the Rrs1 locus. The panel of differential scald isolates indicated that the allele carried by both donors was Rrs1 _Rh4 . The genetic distance between Rrs1 and its flanking markers was 1.2 cM (11_0010) proximally and 0.9 cM (11_0823) distally, which corresponds to a distance of just below 9 Mbp. The number and nature of scald resistance genes on chromosome 3H are discussed. The effective Rrs1 allele found and the closely linked markers developed are already useful tools for molecular breeding programs and provide a good step towards the identification of candidate genes.     

Fine mapping,physical mapping and development of diagnostic markers for the <Emphasis Type="Italic">Rrs2</Emphasis> scald resistance gene in barley

The Rrs2 gene confers resistance to the fungal pathogen Rhynchosporium secalis which causes leaf scald, a major barley disease. The Rrs2 gene was fine mapped to an interval of 0.08 cM between markers 693M6_6 and P1D23R on the distal end of barley chromosome 7HS using an Atlas (resistant) × Steffi (susceptible) mapping population of 9,179 F₂-plants. The establishment of a physical map of the Rrs2 locus led to the discovery that Rrs2 is located in an area of suppressed recombination within this mapping population. The analysis of 58 barley genotypes revealed a large linkage block at the Rrs2 locus extending over several hundred kb which is present only in Rrs2 carrying cultivars. Due to the lack of recombination in the mapping population and the presence of a Rrs2-specific linkage block, we assume a local chromosomal rearrangement (alien introgression or inversion) in Rrs2 carrying varieties. The variety analysis led to the discovery of eight SNPs which were diagnostic for the Rrs2 phenotype. Based on these SNPs diagnostic molecular markers (CAPS and pyrosequencing markers) were developed which are highly useful for marker-assisted selection in resistance gene pyramiding programmes for Rhynchosporium secalis resistance in barley.     

Inheritance and chromosome locations of scald-resistance genes derived from Iranian and Turkish wild barleys

 A set of advanced backcross barley lines derived from crosses between cv Clipper and different Iranian and Turkish wild barleys, which are homozygous for particular isozyme-marked donor intervals, was screened for resistance to barley scald. Eight lines that consistently exhibited scald resistance were identified, and genetic analysis indicated that single dominant genes encoded resistance in five of the lines, single recessive genes were present in two lines, and a pair of unlinked, dominant genes encoded the resistance in the last line. Linkage between the scald-resistance gene and the isozyme marking the introgressed donor chromosome interval was detected in four lines, allowing the chromosome locations of these resistance genes to be determined. One such resistance gene resides on barley chromosome 5, to which no other scald-resistance genes have been mapped; this gene has been designated Rrs14. A survey of the effectiveness of the eight resistance genes against a set of virulent pathotypes of the scald pathogen revealed that four of the lines were completely resistant to all of them. In two instances, the recovery of more than one scald-resistance gene from a single original donor parent could be demonstrated. These scald-resistance genes should provide additional opportunities for breeding programs that aim to develop scald-resistant barley cultivars. Received: 8 August 1996/Accepted: 27 September 1996     

Research advances in the Pyrenophora teres–barley interaction

Pyrenophora teres f. teres and P. teres f. maculata are significant pathogens that cause net blotch of barley. An increased number of loci involved in P. teres resistance or susceptibility responses of barley as well as interacting P. teres virulence effector loci have recently been identified through biparental and association mapping studies of both the pathogen and host. Characterization of the resistance/susceptibility loci in the host and the interacting effector loci in the pathogen will provide a path for targeted gene validation for better-informed release of resistant barley cultivars. This review assembles concise consensus maps for all loci published for both the host and pathogen, providing a useful resource for the community to be used in pathogen characterization and barley breeding for resistance to both forms of P. teres.     

AB-QTL analysis in spring barley. I. Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley

The objective of this study was to map new resistance genes against powdery mildew (Blumeria graminis f. sp. hordei L.), leaf rust (Puccinia hordei L.) and scald [Rhynchosporium secalis (Oud.) J. Davis] in the advanced backcross doubled haploid (BC₂DH) population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). Using field data of disease severity recorded in eight environments under natural infestation and genotype data of 98 SSR loci, we detected nine QTL for powdery mildew, six QTL for leaf rust resistance and three QTL for scald resistance. The presence of the exotic QTL alleles reduced disease symptoms by a maximum of 51.5, 37.6 and 16.5% for powdery mildew, leaf rust and scald, respectively. Some of the detected QTL may correspond to previously identified qualitative (i.e. Mla) and to quantitative resistance genes. Others may be newly identified resistance genes. For the majority of resistance QTL (61.0%) the wild barley contributed the favourable allele demonstrating the usefulness of wild barley in the quest for resistant cultivars.     

QTL analysis of resistance to the rice blast pathogen in barley (Hordeum vulgare)

Barley is compatible with the rice blast pathogen (Pyricularia oryzae Cav.). Fiftyfour barley cultivars of diverse geographic origin and pedigree were inoculated with three isolates of the rice blast pathogen. All barley genotypes showed blast disease symptoms when inoculated at the seedling stage with each of the three isolates. However, one genotype showed quantitative resistance to all three isolates and three genotypes showed quantitative resistance to one or two of the isolates. By inoculating a set of doubled-haploid lines derived from the cross ’Harrington’ (susceptible) and ’TR306’ (resistant) with isolate Ken 54–20, we mapped quantitative trait loci (QTLs) determining seedling stage blast resistance. At all QTLs, TR306 contributed the resistance alleles. The four QTLs, when considered jointly, explained 43.6% of the phenotypic variation in blast symptom expression. A comparison of the blast resistance QTLs with other disease resistance QTLs reported in this population revealed a region on chromosome 4 (4H) with multiple disease resistance loci. It will be useful to capitalize on the syntenic relationship of rice and barley and to integrate information on species-specific resistance genes with information on the reaction of the two species to the same pathogen. Received: 7 January 2000 / Accepted: 22 September 2000     

Invasion of <Emphasis Type="Italic">Rhynchosporium commune</Emphasis> onto wild barley in the Middle East

Rhynchosporium commune was recently introduced into the Middle East, presumably with the cultivated host barley (Hordeum vulgare). Middle Eastern populations of R. commune on cultivated barley and wild barley (H. spontaneum) were genetically undifferentiated and shared a high proportion of multilocus haplotypes. This suggests that there has been little selection for host specialization on H. spontaneum, a host population often used as a source of resistance genes introduced into its domesticated counterpart, H. vulgare. Low levels of pathogen genetic diversity on H. vulgare as well as on H. spontaneum, indicate that the pathogen was introduced recently into the Middle East, perhaps through immigration on infected cultivated barley seeds, and then invaded the wild barley population. Although it has not been documented, the introduction of the pathogen into the Middle East may have a negative influence on the biodiversity of native Hordeum species.     

Genetic and molecular analyses of resistance to a variant of Puccinia striiformis in barley

Seedlings of 62 Australian barley cultivars and two exotic barley genotypes were assessed for resistance to a variant of Puccinia striiformis, referred to as “Barley Grass Stripe Rust” (BGYR), first detected in Australia in 1998, which is capable of infecting wild Hordeum species and some genotypes of cultivated barley. Fifty-three out of 62 cultivated barley cultivars tested were resistant to the pathogen. Genetic analyses of seedling resistance to BGYR in six Australian barley cultivars and one Algerian barley landrace indicated that they carried either one or two major resistance genes to the pathogen. A single recessive seedling resistance gene, rpsSa3771, identified in Sahara 3771, was located on the long arm of chromosome 1 (7 H), flanked by the restriction fragment length polymorphism (RFLP) markers Xwg420 and Xcdo347 at genetic distances of 12.8 and 21.9 cM, respectively. Mapping resistance to BGYR at adult plant growth stages using the doubled haploid (DH) population Clipper × Sahara 3771 identified two major quantitative trait loci (QTL), one on the long arm of chromosome 3 (3 H) and the second on the long arm of chromosome 1 (7 H), accounting for 26 % and 18 % of the total phenotypic variation, respectively. The QTL located on chromosome 7HL corresponded to seedling resistance gene rpsSa3771 and the second QTL was concluded to correspond to a single APR gene, designated rpsCl, contributed by cultivar Clipper.     

Pyramiding of <Emphasis Type="Italic">Ryd2</Emphasis> and <Emphasis Type="Italic">Ryd3</Emphasis> conferring tolerance to a German isolate of <Emphasis Type="Italic">Barley yellow dwarf virus</Emphasis>-PAV (BYDV-PAV-ASL-1) leads to quantitative resistance against this isolate

Barley yellow dwarf virus (BYDV) is an economically important pathogen of barley, which may become even more important due to global warming. In barley, several loci conferring tolerance to BYDV-PAV-ASL-1 are known, e.g. Ryd2, Ryd3 and a quantitative trait locus (QTL) on chromosome 2H. The aim of the present study was to get information whether the level of tolerance against this isolate of BYDV in barley can be improved by combining these loci. Therefore, a winter and a spring barley population of doubled haploid (DH) lines were genotyped by molecular markers for the presence of the susceptibility or the resistance encoding allele at respective loci (Ryd2, Ryd3, QTL on chromosome 2H) and were tested for their level of BYDV-tolerance after inoculation with viruliferous (BYDV-PAV-ASL-1) aphids in field trials. In DH-lines carrying the combination Ryd2 and Ryd3, a significant reduction of the virus titre was detected as compared to lines carrying only one of these genes. Furthermore, spring barley DH-lines with this allele combination also showed a significantly higher relative grain yield as compared to lines carrying only Ryd2 or Ryd3. The QTL on chromosome 2H had only a small effect on the level of tolerance in those lines carrying only Ryd2, or Ryd3 or a combination of both, but the effect in comparison to lines carrying no tolerance allele was significant. Overall, these results show that the combination of Ryd2 and Ryd3 leads to quantitative resistance against BYDV-PAV instead of tolerance.     

Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA

We used a well-characterized barley mapping population (BCD 47 × Baronesse) to determine if barley stripe rust (BSR) resistance quantitative trait loci (QTL) mapped in Mexico and the USA were effective against a reported new race in Peru. Essentially the same resistance QTL were detected using data from each of the three environments, indicating that these resistance alleles are effective against the spectrum of naturally occurring races at these sites. In addition to the mapping population, we evaluated a germplasm array consisting of lines with different numbers of mapped BSR resistance alleles. A higher BSR disease severity on CI10587, which has a single qualitative resistance gene, in Peru versus Mexico suggests there are differences in pathogen virulence between the two locations. Confirmation of a new race in Peru will require characterization using a standard set of differentials, an experiment that is underway. The highest levels of resistance in Peru were observed when the qualitative resistance gene was pyramided with quantitative resistance alleles. We also used the mapping population to locate QTL conferring resistance to barley leaf rust and barley powdery mildew. For mildew, we identified resistance QTL under field conditions in Peru that are distinct from the Mla resistance that we mapped using specific isolates under controlled conditions. These results demonstrate the long-term utility of a reference mapping population and a well-characterized germplasm array for locating and validating genes conferring quantitative and qualitative resistance to multiple pathogens.     

Molecular marker analyses of powdery mildew resistance in barley

Powdery mildew, caused byEryisphe graminis f. sp.hordei, is one of the most important diseases of barley (Hordeum vulgare). A number of loci conditioning resistance to this disease have been reported previously. The objective of this study was to use molecular markers to identify chromosomal regions containing genes for powdery mildew resistance and to estimate the resistance effect of each locus. A set of 28 F₁ hybrids and eight parental lines from a barley diallel study was inoculated with each of five isolates ofE. graminis. The parents were surveyed for restriction fragment length polymorphisms (RFLPs) at 84 marker loci that cover about 1100 cM of the barley genome. The RFLP genotypes of the F₁s were deduced from those of the parents. A total of 27 loci, distributed on six of the seven barley chromosomes, detected significant resistance effects to at least one of the five isolates. Almost all the chromosomal regions previously reported to carry genes for powdery mildew resistance were detected, plus the possible existence of 1 additional locus on chromosome 7. The analysis indicated that additive genetic effects are the most important component in conditioning powdery mildew resistance. However, there is also a considerable amount of dominance effects at most loci, and even overdominance is likely to be present at a number of loci. These results suggest that quantitative differences are likely to exist among alleles even at loci which are considered to carry major genes for resistance, and minor effects may be prevalent in cultivars that are not known to carry major genes for resistance.     

Interaction between Rhynchosporium secalis and Pyrenophora teres in the Field and Identification of Genotypes with Double Resistance in a Doubled-haploid Barley Population

Net blotch [Pyrenophora teres (Died.) Drechsl.] and scald [Rhynchosporium secalis (Oudem.) J.J. Davis] are the two most important foliar diseases of barley (Hordeum vulgare L.) in Tunisia. The use of cultivars with double resistance is the most effective method in controlling both diseases. A doubled‐haploid barley population derived from Tunisian cultivars was evaluated to both net blotch and scald during two growing seasons in the field. Mass disease index (MDI), area under the disease progress curve (AUDPC) and apparent infection type (r) were used to assess disease reaction. MDI of net blotch and scald reached up to 65% and 90% respectively. Least significant difference (LSD) test and comparison of the reaction of the doubled haploid (DH) lines to the overall population mean value were efficient in identifying lines with double resistance to both diseases. From the 59 DH lines screened, lines 21, 33, 37, 46 and 47 showed the best level of adult plant resistance to both diseases and may be used in a breeding program for diseases resistance. Interactions between R. secalis and P. teres were investigated at the level of the whole plant under variable epidemic conditions. Under low epidemic conditions, net blotch and scald developments were usually independent, but positively associated for tolerant lines for both diseases. Under high epidemic conditions, competition effects were obtained for susceptible and resistant genotypes. This competition seems to be an exploitation competition that is associated with decreasing resource availability as it occurs only with high levels of infestation or/and when susceptible lines are infected. This study demonstrates the variability of net blotch and scald interaction with epiphytotic conditions and group of resistance.     

A single binding site mediates resistance- and disease-associated activities of the effector protein NIP1 from the barley pathogen Rhynchosporium secalis

The effector protein NIP1 from the barley (Hordeum vulgare) pathogen Rhynchosporium secalis specifically induces the synthesis of defense-related proteins in cultivars of barley expressing the complementary resistance gene, Rrs1. In addition, it stimulates the activity of the barley plasma membrane H(+)-ATPase in a genotype-unspecific manner and it induces necrotic lesions in leaf tissues of barley and other cereal plant species. NIP1 variants type I and II, which display quantitative differences in their activities as elicitor and H(+)-ATPase stimulator, and the inactive mutant variants type III* and type IV*, were produced in Escherichia coli. Binding studies using (125)I-NIP1 type I revealed a single class of binding sites with identical binding characteristics in microsomes from near-isogenic resistant (Rrs1) and susceptible (rrs1) barley. Binding was specific, reversible, and saturable, and saturation ligand-binding experiments yielded a K(d) of 5.6 nm. A binding site was also found in rye (Secale cereale) and the nonhost species wheat (Triticum aestivum), oat (Avena sativa), and maize (Zea mays), but not in Arabidopsis (Arabidopsis thaliana). For NIP1 types I and II, equilibrium competition-binding experiments revealed a correlation between the difference in their affinities to the binding site and the differences in their elicitor activity and H(+)-ATPase stimulation, indicating a single target molecule to mediate both activities. In contrast, the inactive proteins type III* and type IV* are both characterized by high affinities similar to type I, suggesting that binding of NIP1 to this target is not sufficient for its activities.     

Genetics of seedling and adult plant resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley

Net blotch (caused by Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) are important foliar diseases of barley in the midwestern region of the USA. To determine the number and chromosomal location of Mendelian and quantitative trait loci (QTL) controlling resistance to these diseases, a doubled haploid population (Steptoe/Morex) was evaluated to the pathogens at the seedling stage in the greenhouse and at the adult plant stage in the field. Alleles at two or three unlinked loci were found to confer resistance to the net blotch pathogen at the seedling stage depending on how progeny exhibiting an intermediate infection response were classified. This result was corroborated in the quantitative analysis of the raw infection response data as 2 major QTL were identified on chromosomes 4 and 6M. A third QTL was also identified on chromosome 6P. Seven QTL were identified for net blotch resistance at the adult plant stage and mapped to chromosomes 1P, 2P, 3P, 3M, 4, 6P, and 7P. The 7 QTL collectively accounted for 67.6% of the phenotypic variance under a multiple QTL model. Resistance to the spot blotch pathogen was conferred by a single gene at the seedling stage. This gene was mapped to the distal region of chromosome 1P on the basis of both qualitative and quantitative data analyses. Two QTL were identified for spot blotch resistance at the adult plant stage: the largest QTL effect mapped to chromosome 5P and the other mapped to chromosome 1P near the seedling resistance locus. Together, the 2 QTL explained 70.1% of the phenotypic variance under a multiple QTL model. On the basis of the chromosomal locations of resistance alleles detected in this study, it should be feasible to combine high levels of resistance to both P. teres f. teres and C. sativus in barley cultivars.     

Quantitative trait loci controlling barley powdery mildew and scald resistances in two different barley doubled haploid populations

Powdery mildew and scald can cause significant yield loss in barley. In order to identify new resistance genes for powdery mildew and scald in barley, two barley doubled haploid (DH) populations were screened for adult plant resistance in the field and glasshouse under natural infection. The mapping populations included 92 DH lines from the cross of TX9425 × Franklin and 177 DH lines from the cross of Yerong × Franklin. Two quantitative trait loci (QTL) for resistance to powdery mildew were identified in the TX9425 × Franklin population. These QTL were mapped to chromosomes 7H and 5H, respectively. The phenotypic variation explained by the two QTL detected in this population was 22 and 17%, respectively. Three significant QTL were identified from the Yerong × Franklin population for the resistance to powdery mildew; the major one, detected on the short arm of chromosome 1H, explained 66% of phenotypic variation. The major QTL for scald resistance, identified from two different populations which shared a common parent, Franklin, were mapped in the similar position on 3H. However, the Franklin allele provided resistance to one population but susceptibility to the other population. The Yerong allele on 3H showed much better resistance to scald than the Franklin allele, which has not been reported before. Using high-density maps for both populations, some markers which were very close to the resistance genes were identified. Transgression beyond the parents in disease resistances of the DH populations indicates that both small-effect QTLs and genetic background may also have significant contributions towards the resistance.     

QTL analysis of root-lesion nematode resistance in barley: 1. Pratylenchus neglectus

The root-lesion nematode Pratylenchus neglectus can cause severe losses in barley cultivation. Multiplication rates had been found to vary greatly between different barley accessions. Two winter barley cultivars, Igri and Franka, had been found to differ in their ability to resist this parasite. An existing Igri?×?Franka doubled haploid population was chosen to genetically map resistance genes after artificial inoculation with P. neglectus in the greenhouse and climate chamber. A continuous phenotypic variation was found indicating a quantitative inheritance of P. neglectus resistance. An existing map was enriched by 527 newly developed Diversity Array Technology markers (DArTs). The new genetic linkage map was comprised of 857 molecular markers that cover 1,157?cM on seven linkage groups. Using phenotypic data collected from four different experiments in 3?years, five quantitative trait loci were mapped by composite interval mapping on four (3H, 5H, 6H and 7H) linkage groups. A quantitative trait locus with a large phenotypic effect of 16% and likelihood of odds (LOD) score of 6.35 was mapped on linkage group 3H. The remaining four QTLs were classified as minor or moderate with LOD scores ranging from 2.71 to 3.55 and R ² values ranging from 8 to 10%. The DNA markers linked to the resistance QTLs should be quite useful for marker-assisted selection in barley breeding because phenotypic selection is limited due to time constraints and labor costs.     

The race-specific elicitor, NIP1, from the barley pathogen, Rhynchosporium secalis, determines avirulence on host plants of the Rrs1 resistance genotype.

NIP1, a small phytotoxic protein secreted by the barley pathogen Rhynchosporium secalis, is a race-specific elicitor of defense responses in barley cultivars carrying the resistance gene, Rrs1. Co-inoculation employing spores from a virulent fungal race together with the NIP1 protein converted the phenotype of the interaction from compatible to incompatible only on Rrs1-containing plants. In addition, transformation of a virulent fungal race with the nip1 gene yielded avirulent transformants. This demonstrated that the protein is the product of a fungal avirulence gene. The fungal genome was found to contain a single copy of the nip1 gene. Sequence analysis of nip1 cDNA and genomic clones revealed that the gene consists of two exons and one intron. The derived amino acid sequence comprised a secretory signal peptide of 22 amino acids and a cysteine-rich mature protein of 60 amino acids. All fungal races that were avirulent on barley cultivars of the Rrs1 resistance genotype carry and express the nip1 gene and secrete an elicitor-active NIP1 polypeptide. In contrast, races lacking this gene were virulent. In addition, single nucleotide exchanges were detected in the coding region of the nip1 alleles in one virulent fungal race and in a race whose interaction with barley is not controlled by the Rrs1 gene. The resulting exchanges of single amino acids render the gene products elicitor-inactive. Thus, the R.secalis-barley interaction provides the first example of a pathosystem conforming to the gene-for-gene hypothesis in which a plant with a particular resistance gene recognizes a pathogen by a virulence factor, i.e. one of its offensive weapons. On the fungal side, in turn, recognition by the host plant is eluded by either deletion of the encoding gene or alteration of the primary structure of the gene product.