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Extensive research in the area of plant innate immunity has increased considerably our understanding of the molecular mechanisms associated with resistance controlled by a dominant resistance gene. In contrast, little is known about the molecular basis underlying the resistance conferred by quantitative trait loci (QTLs). In this study, using the interaction of tomato (Solanum lycopersicum) with Oidium neolycopersici, we compared the cytological, biochemical and molecular mechanisms involved in both monogenic and polygenic resistances conferred by a dominant gene (Ol-1) and three QTLs (Ol-qtls), respectively. Our results showed that the three Ol-qtls jointly confer a very high level of broad-spectrum resistance and that the resistance is associated with both the hypersensitive response and papillae formation, with the hypersensitive response being prevalent. Both H2O2 and callose accumulation, which are coupled with Ol-1-mediated resistance, are also associated with the resistance conferred by Ol-qtls. Further, we analysed the pathogen-induced transcript profiles of near-isogenic lines carrying the three Ol-qtls and the Ol-1 gene. Transcript profiles obtained by cDNA-amplified fragment length polymorphism analysis showed that, on fungal challenge, about 70% of the transcript-derived fragments are up-regulated in both susceptible and resistant genotypes. Most of the sequenced transcript-derived fragments showed homology to genes with functions in defence responses, suggesting that defence-responsive genes responsible for basal defence are involved in both monogenic and polygenic resistances conferred by Ol-1 and Ol-qtls, respectively. Although about 18% of the identified transcript-derived fragments are specific for either monogenic or polygenic resistance, their expression patterns need to be further verified by quantitative reverse transcriptase-polymerase chain reaction

Basal resistance of barley to powdery mildew is a quantitatively inherited trait that limits the growth and sporulation of barley powdery mildew pathogen by a non-hypersensitive mechanism of defense. Two experimental barley lines were developed with a very high (ErBgh) and low (EsBgh) level of basal resistance to powdery mildew by cycles of convergent crossing and phenotypic selection between the most resistant and between the most susceptible lines, respectively, from four mapping populations of barley. Phenotypic selection in convergent crossing was highly effective in producing contrasting phenotypes for basal resistance and susceptibility. In ErBgh, almost 90% of infection units failed to form a primary haustorium in the epidermal cells in association with papilla formation, but in EsBgh only 33% of infection units failed to form a primary haustorium. The contrast between ErBgh and EsBgh for successful formation of secondary and subsequent haustoria was much less obvious (69% versus 79% successful secondary haustorium formation). In an earlier investigation, we determined seven QTLs for basal resistance in the four mapping populations. Checking the peak markers of these QTLs indicated that only four out of seven QTLs were confirmed to be present in the selected resistant lines and only four QTLs for susceptibility were confirmed to be present in the selected susceptible lines. Surprisingly, none of the expected QTLs could be detected in the resistant line ErBgh. We discuss some reasons why marker aided selection might be less efficient in raising levels of basal resistance than phenotypic selection. The very resistant and susceptible lines developed here are valuable material to be used in further experiments to characterize the molecular basis of basal resistance to powdery mildew.

This study used the pathosystem of lettuce (Lactuca spp.) and downy mildew (Bremia lactucae) as a model to investigate the inheritance of nonhost resistance, and focused on the contribution of quantitative trait loci (QTLs) to nonhost resistance at various developmental stages in the lettuce life cycle. A set of 28 backcross inbred lines (BILs) of L. saligna CGN05271 (nonhost) introgressions in a L. sativa cv. Olof (host) background identified 16 introgressions that contributed to resistance at various plant developmental stages: seedlings, young plants, adult plants in the greenhouse and adult plants in the field. This paper provisionally considered these introgressions to be 16 QTLs. Of these 16 QTLs, seven were identified previously and nine were new. For 15 QTLs (Rbq1, Rbq2, rbq3–7 and Rbq8–15), the resistance alleles were derived from the nonhost L. saligna; the resistance allele of the other QTL (Rbq16) was from the susceptible L. sativa cv. Olof. Of the 15 QTLs in L. saligna, only two, rbq5 and rbq7, were found to be effective at every plant developmental stage; the other 13 QTLs were only effective at certain developmental stages. Experiments with seven B. lactucae races did not provide evidence that any QTL was race-specific. The data suggest that nonhost resistance in L. saligna is the result of cumulative effects of many resistance QTLs operating at various developmental stages.

Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 × ‘Vada’ mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei.

Isolate-specific aspect of non-hypersensitive resistance in wheat to wheat leaf rust was studied at seedling stage in the green house. Isolate-specific response of non-hypersensitive resistance was assessed from latency period (LP) and infection frequency (IF) of two single-pustule isolates of Puccinia triticina in 26 spring wheat cultivars/lines. Small but significant cultivar x isolate interactions were observed for LP and IF in seedlings of host genotypes. Isolate specific effect for LP at seedling stage was consistent and reproduced in a repeated experiment; however, the interaction for IF was inconsistent and was not reproducible. The inconsistency in cultivar x isolate interaction may be due to some non-genetic origin. The result suggested that a gene-for-gene relationship could exist between non-hypersensitive resistance genes in the host and genes in pathogen.

A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus (BYD)), and morphological traits (rachilla hair length, lodicule size) with AFLP markers and SSR markers were found. Known major genes and QTLs were confirmed, but also new putative QTLs were found. The LD mapping clearly indicated the common occurrence of Rph3, a gene for hypersensitivity resistance against Puccinia hordei, and also confirmed the QTL Rphq2 for prolonging latency period of P. hordei in seedlings. We also found strong indication for a hitherto not reported gene for resistance or tolerance to BYD on chromosome 2, linked to SSR marker HVM054. Our conclusion is that LD mapping is a valuable additional tool in the search for applicable marker associations with major genes and QTLs.

Full nonhost resistance can be defined as immunity, displayed by an entire plant species against all genotypes of a plant pathogen. Interesting biological questions are, whether the genes responsible for the nonhost status of a plant species have a general or a specific effectiveness to heterologous (“nonhost”) pathogens? Is the nonhost resistance to pathogens of plant species that are related to the nonhost based on R-genes or on other types of genes? We study this question in barley (Hordeum vulgare L.), which is a near-nonhost to several rusts (Puccinia) of cereals and grasses. By crosses and selection we accumulated susceptibility and developed an experimental line, SusPtrit, with high susceptibility to at least nine different heterologous rust taxa such as the wheat and Agropyron leaf rusts (P. triticina and P. persistens, respectively). At the microscopic level there is also some variation among barley accessions in the degree that the heterologous wheat powdery mildew (Blumeria graminis f.sp. tritici) is able to form haustoria in epidermal cells. So, also the genetics of the variation in level of nonhost resistance to heterologous mildew fungi can be studied in barley. Our data obtained on mapping populations involving three regular nonhost-immune accessions (Vada, Cebada Capa and Golden Promise) suggest that nonhost resistance is the joined effect of multiple, quantitative genes (QTLs) and very occasionally a major gene (R-gene?) is involved. Most QTLs have effect to only one or two heterologous rusts, but some have a wider spectrum. This was confirmed in a set of QTL-NILs. Those QTL-NILs are used to fine-map the effective genes. In some cases, a QTL region with effectiveness to several heterologous rusts might be a cluster of genes with a more narrow spectrum of effectiveness. Our evidence suggests that nonhost resistance in barley to rust and powdery mildew fungi of related Gramineae is not due to R-genes, but to pathogen species-specific quantitative resistance genes.

International audience; Key message We developed 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. Nonhost and partial resistance to Puccinia rust fungi in barley are polygenically inherited. These types of resistance are principally prehaustorial, show high diversity between accessions of the plant species and are genetically associated. To study nonhost and partial resistance, as well as their association, candidate gene(s) for resistance must be cloned and tested in susceptible material where SusPtrit would be the line of choice. Unfortunately, SusPtrit is not amenable to Agrobacterium-mediated transformation. Therefore, a doubled haploid (DH) mapping population (n = 122) was created by crossing SusPtrit with Golden Promise to develop a 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. We identified nine genomic regions occupied by resistance quantitative trait loci (QTLs) against four non-adapted rust fungi and P. hordei isolate 1.2.1 (Ph.1.2.1). Four DHs were selected for an Agrobacterium-mediated transformation efficiency test. They were among the 12 DH lines most susceptible to the tested non-adapted rust fungi. The most efficiently transformed DH line was SG062N (11-17 transformants per 100 immature embryos). The level of non-adapted rust infection on SG062N is either similar to or higher than the level of infection on SusPtrit. Against Ph.1.2.1, the latency period conferred by SG062N is as short as that conferred by SusPtrit. SG062N, designated 'Golden SusPtrit', will be a valuable experimental line that could replace SusPtrit in nonhost and partial resistance studies, especially for stable transformation using candidate genes that may be involved in rust-resistance mechanisms.

A resistance gene (Rph22) to barley leaf rust caused by Puccinia hordei was introgressed from the non-host species Hordeum bulbosum into cultivated barley. The H. bulbosum introgression in line ‘182Q20’ was located to chromosome 2HL using genomic in situ hybridisation (GISH). Using molecular markers it was shown to cover approximately 20 % of the genetic length of the chromosome. The introgression confers a very high level of resistance to P. hordei at the seedling stage that is not based on a hypersensitive reaction. The presence of the resistance gene increased the latency period of the leaf rust fungus and strongly reduced the infection frequency relative to the genetic background cultivar ‘Golden Promise’. An F2 population of 550 individuals was developed and used to create a genetic map of the introgressed region and to determine the map position of the underlying resistance gene(s). The resistance locus, designated Rph22, was located to the distal portion of the introgression, co-segregating with markers H35_26334 and H35_45139. Flanking markers will be used to reduce the linkage drag, including gene(s) responsible for a yield penalty, around the resistance locus and to transfer the gene into elite barley germplasm. This genetic location is also known to harbour a QTL (Rphq2) for non-hypersensitive leaf rust resistance in the barley cultivar ‘Vada’. Comparison of the ‘Vada’ and H. bulbosum resistances at this locus may lead to a better understanding of the possible association between host and non-host resistance mechanisms.

Extensive research in the area of plant innate immunity has increased considerably our understanding of the molecular mechanisms associated with resistance controlled by a dominant resistance gene. In contrast, little is known about the molecular basis underlying the resistance conferred by quantitative trait loci (QTLs). In this study, using the interaction of tomato (Solanum lycopersicum) with Oidium neolycopersici, we compared the cytological, biochemical and molecular mechanisms involved in both monogenic and polygenic resistances conferred by a dominant gene (Ol‐1) and three QTLs (Ol‐qtls), respectively. Our results showed that the three Ol‐qtls jointly confer a very high level of broad‐spectrum resistance and that the resistance is associated with both the hypersensitive response and papillae formation, with the hypersensitive response being prevalent. Both H(2)O(2) and callose accumulation, which are coupled with Ol‐1‐mediated resistance, are also associated with the resistance conferred by Ol‐qtls. Further, we analysed the pathogen‐induced transcript profiles of near‐isogenic lines carrying the three Ol‐qtls and the Ol‐1 gene. Transcript profiles obtained by cDNA‐amplified fragment length polymorphism analysis showed that, on fungal challenge, about 70% of the transcript‐derived fragments are up‐regulated in both susceptible and resistant genotypes. Most of the sequenced transcript‐derived fragments showed homology to genes with functions in defence responses, suggesting that defence‐responsive genes responsible for basal defence are involved in both monogenic and polygenic resistances conferred by Ol‐1 and Ol‐qtls, respectively. Although about 18% of the identified transcript‐derived fragments are specific for either monogenic or polygenic resistance, their expression patterns need to be further verified by quantitative reverse transcriptase‐polymerase chain reaction.

Partial resistance is a quantitative type of resistance that, by definition of Parlevliet, is not based on hypersensitivity. It is largely pathotype nonspecific, although some minor isolate-specific responses have been reported. In order to elucidate the isolate specificity of individual genes for partial resistance, three barley recombinant inbred line mapping populations were analyzed for resistance to the leaf rust fungus Puccinia hordei. The mapping populations were inoculated with one isolate avirulent and two isolates virulent to resistance gene Rph7g. Six significant quantitative trait loci (QTLs) were detected. Of these, two (Rphq3 and Rphq11) were detected with only the avirulent isolate (1.2.1.) and one (Rphq18) only with both virulent isolates (CO-04 and 28.1). The effectiveness of these QTLs was tested with 14 isolates, using a tester set of genotypes containing alleles for resistance or susceptibility for these QTLs. QTL Rphq18 was effective to only two isolates, CO-04 and 28.1, whereas Rphq3 and Rphq11 were ineffective to CO-04 and 28.1 but effective to all other isolates, except one. This resulted in a significant Person's differential interaction, which is a hallmark of a gene¿for¿gene interaction. The minor gene¿for¿minor gene interaction is not based on hypersensitivity and there is no evidence that the resistance is based on genes belonging to the nucleotide-binding leucine-rich repeat class., Support for this research was provided by Fundación Pedro Barrie de la Maza to A. M. González (http://www.fbarrie.org).

The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of fungal haustoria. It is not known which of these candidate genes have allelic variation that contributes to the natural variation in powdery mildew resistance, because many of them may be highly conserved within the barley species and may act downstream of the basal resistance reaction. Twenty-two expressed sequence tag or cDNA clone sequences that are likely to play a role in the barley–Blumeria interaction based on transcriptional profiling, gene silencing, or overexpression data, as well as mlo, Ror1, and Ror2, were mapped and considered candidate genes for contribution to basal resistance. We mapped the quantitative trait loci (QTL) for powdery mildew resistance in six mapping populations of barley at seedling and adult plant stages and developed an improved high-density integrated genetic map containing 6,990 markers for comparing QTL and candidate gene positions over mapping populations. We mapped 12 QTL at seedling stage and 13 QTL at adult plant stage, of which four were in common between the two developmental stages. Six of the candidate genes showed coincidence in their map positions with the QTL identified for basal resistance to powdery mildew. This co-localization justifies giving priority to those six candidate genes to validate them as being responsible for the phenotypic effects of the QTL for basal resistance.

International audience; Abstract Partial resistance is generally considered to be a durable form of resistance. In barley, Rphq2, Rphq3 and Rphq4 have been identiWed as consistent quantitative trait loci (QTLs) for partial resistance to the barley leaf rust pathogen Puccinia hordei. These QTLs have been incorporated separately into the susceptible L94 and the partially resistant Vada barley genetic backgrounds to obtain two sets of near isogenic lines (NILs). Previous studies have shown that these QTLs are not eVective at conferring disease resistance in all stages of plant development. In the present study, the two sets of QTL–NILs and the two recurrent parents, L94 and Vada, were evaluated for resistance to P. hordei isolate 1.2.1 simultaneously under greenhouse conditions from the Wrst leaf to the Xag leaf stage. EVect of the QTLs on resistance was measured by development rate of the pathogen, expressed as latency period (LP). The data show that Rphq2 prolongs LP at the seedling stage (the Wrst and second leaf stages) but has almost no eVect on disease resistance in adult plants. Rphq4 showed no eVect on LP until the third leaf stage, whereas Rphq3 is consistently eVective at prolonging LP from the Wrst leaf to the Xag leaf. The changes in the eVectiveness of Rphq2 and Rphq4 happen at the barley tillering stage (the third to fourth leaf stages). These results indicate that multiple disease evaluations of a single plant by repeated inoculations of the fourth leaf to the Xag leaf should be conducted to precisely estimate the eVect of Rphq4. The present study conWrms and describes in detail the plant development-dependent eVectiveness of partial resistance genes and, consequently, will enable a more precise evaluation of partial resistance regulation during barley development

Background: Higher plants possess a large multigene family encoding secreted class III peroxidase (Prx) proteins. Peroxidases appear to be associated with plant disease resistance based on observations of induction during disease challenge and the presence or absence of isozymes in resistant vs susceptible varieties. Despite these associations, there is no evidence that allelic variation of peroxidases directly determines levels of disease resistance. Methodology/Principal Findings: The current study introduces a new strategy called Prx-Profiling. We showed that with this strategy a large number of peroxidase genes can be mapped on the barley genome. In order to obtain an estimate of the total number of Prx clusters we followed a re-sampling procedure, which indicated that the barley genome contains about 40 peroxidase gene clusters. We examined the association between the Prxs mapped and the QTLs for resistance of barley to homologous and heterologous rusts, and to the barley powdery mildew fungus. We report that 61% of the QTLs for partial resistance to P. hordei, 61% of the QTLs for resistance to B. graminis and 47% of the QTLs for non-host resistance to other Puccinia species co-localize with Prx based markers. Conclusions/Significance: We conclude that Prx-Profiling was effective in finding the genetic location of Prx genes on the barley genome. The finding that QTLs for basal resistance to rusts and powdery mildew fungi tend to co-locate with Prx clusters provides a base for exploring the functional role of Prx-related genes in determining natural differences in levels of basal resistance. © 2010 González et al.

Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley–Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes.

The ability of plant cells to resist invasion by pathogenic fungi at the cell periphery (pre-invasion resistance) differs from other types of resistance that are generally triggered after parasite entry and during differentiation of specialised intracellular feeding structures. Genetic sources of pre-invasion resistance such as mlo for barley powdery mildew and Lr34 for resistance to wheat leaf rust have proven to be broad-spectrum in effect and durable in the field. Continued breeding for this type of resistance (often quantitative in effect) is therefore considered an important strategy to protect cereal crops long-term against potentially devastating fungal diseases such as rusts. Considerable progress has been made in characterising genes and processes underlying pre-invasion resistance using mutant analysis, molecular genetics, gene cloning, and the model plant Arabidopsis, as well as comparative functional analysis of genes in Arabidopsis and cereals. This review summarises the current knowledge in this field, and discusses several aspects of pre-invasion resistance potentially pertinent to use in breeding; namely, biological cost of the resistance and effectiveness of individual resistance genes against multiple pathogen types. We show that mutations in Mlo, Ror1, and Ror2 genes known to affect powdery mildew pre-invasion resistance have no detectable effect on partial resistance to barley leaf rust as measured by latency period.

Isolate-specific aspect of non-hypersensitive resistance in wheat to wheat leaf rust was studied at seedling stage in the green house. Isolate-specific response of non-hypersensitive resistance was assessed from latency period (LP) and infection frequency (IF) of two single-pustule isolates of Puccinia triticina in 26 spring wheat cultivars/lines. Small but significant cultivar x isolate interactions were observed for LP and IF in seedlings of host genotypes. Isolate specific effect for LP at seedling stage was consistent and reproduced in a repeated experiment; however, the interaction for IF was inconsistent and was not reproducible. The inconsistency in cultivar x isolate interaction may be due to some non-genetic origin. The result suggested that a gene-for-gene relationship could exist between non-hypersensitive resistance genes in the host and genes in pathogen.

We developed an evolutionary relevant model system, barley-Puccinia [corrected] rust fungi, to study the inheritance and specificity of plant factors that determine to what extent innate nonhost immunity can be suppressed. A mapping population was developed from a cross between an experimental barley line (SusPtrit) [corrected] with exceptional susceptibility to several heterologous [corrected] (nonhost) rust fungi and regular, immune, cv. Vada [corrected] Seedlings were inoculated with five heterologous [corrected] and two homologous (host) species of rust fungi. Resistance segregated quantitatively for each of the rust fungi. In total, 18 chromosomal regions were implicated. For each rust species, a different set of genes was effective. Of the 18 chromosomal regions, 11 were significantly effective to only one rust species and 7 were effective to more than one rust species, implying genetic linkage or pleiotropy. One resistance (R) gene for hypersensitive resistance to Puccinia hordei-secalini was mapped, suggesting occasional contribution of R genes to nonhost resistance in barley. Quantitative trait loci (QTLs) with effects to multiple rust fungi did not tend to be particularly effective to rust species that were phylogenetically related, as determined from their internal transcribed spacer sequence. We suggest that the QTLs described here play a role as specific and quantitative recognition factors that are specifically negated by the rust to successfully suppress innate immunity.

In a mapping population derived from the Ethiopian barley line L94 x Vada, natural infection by barley yellow dwarf virus (BYDV) occurred. While line L94 hardly showed symptoms, Vada was severely affected. The 103 recombinant inbred lines segregated bimodally. The major gene responsible for this resistance mapped to chromosome 6H. We propose to name the locus Ryd3. A subset of recombinant inbred lines, L94, and Vada were planted in a subsequent field test which confirmed the previous field observations. Double antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) indicated that the epidemic was due to a combination of the serotypes BYDV-PAV and BYDV-MAV. In the accessions with the least BYDV symptoms no virus was detected, justifying the consideration of the gene as conferring true resistance rather than tolerance to these viruses. In a laboratory/gauze house trial a near-isogenic line carrying the Vada chromosome 6H fragment in an L94 background was affected as much as Vada. The effect of Ryd3 was quantified, and compared with that of the only other known major gene for resistance to BYDV, Ryd2, which is also of Ethiopian origin and is located on chromosome 3H. Both genes seemed to reduce the chance of the viral isolate used in this study to establish infection. In plants in which it became established, the virus concentration reached a similar level as in susceptible accessions, but with less dramatic symptom development. Inoculated plants in which the virus failed to multiply tended to show an increase in the number of ears per plant, resulting in higher grain yield per plant. Ryd3 co-segregates with several PCR-based molecular markers that may serve for marker assisted selection.

Nonhost resistance is the most common type of resistance in plants. Understanding the factors that make plants susceptible or resistant may help to achieve durably effective resistance in crop plants. Screening of 109 barley (Hordeum vulgare L.) accessions in the seedling stage indicated that barley is a complete nonhost to most of the heterologous rust fungi studied, while it showed an intermediate status with respect to Puccinia triticina, P. hordei-murini, P. hordei-secalini, P. graminis f. sp. lolii and P. coronata ff. spp. avenae and holci. Accessions that were susceptible to a heterologous rust in the seedling stage were much more or completely resistant at adult plant stage. Differential interaction between barley accessions and heterologous rust fungi was found, suggesting the existence of rust-species-specific resistance. In particular, many landrace accessions from Ethiopia and Asia, and naked-seeded accessions, tended to be susceptible to several heterologous rusts, suggesting that some resistance genes in barley are effective against more than one heterologous rust fungal species. Some barley accessions had race-specific resistance against P. hordei-murini. We accumulated genes for susceptibility to P. triticina and P. hordei-murini in two genotypes called SusPtrit and SusPmur, respectively. In the seedling stage, these accessions were as susceptible as the host species to the target rusts. They also showed unusual susceptibility to other heterologous rusts. These two lines are a valuable asset to further experimental work on the genetics of resistance to heterologous rust fungi.

Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, efficient exploitation of conservation of synteny requires ‘homology bridges’ between the model genome and the target region that contains a gene of interest. As effective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a specific region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe × Morex doubled haploid population and showed a strong association between differential gene expression and cis-regulation, with 83% of differentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-specific pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identified a total of 411 genes as differentially expressed, including HvPHGPx, a gene previously identified as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identification of differential expression by BSA constitutes a novel method to identify genes located in specific regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species. Electronic supplementary material The online version of this article (doi:10.1007/s00122-011-1538-3) contains supplementary material, which is available to authorized users.