Rients E. Niks

Identification of QTLs for partial resistance to leaf rust (Puccinia hordei) in barley.

Abstract The partial resistance to leaf rust in barley is a quantitative resistance that is not based on hypersensitivity. To map the quantitative trait loci (QTLs) for partial resistance to leaf rust, we obtained 103 recombinant inbred lines (RILs) by single-seed descent from a cross between the susceptible parent L94 and the partially resistant parent Vada. These RILs were evaluated at the seedling and adult plant stages in the greenhouse for the latent period (LP) of the rust fungus, and in the field for the level of infection, measured as area under the disease progress curve (AUDPC). A dense genetic map based on 561 AFLP markers had been generated previously for this set of RILs. QTLs for partial resistance to leaf rust were mapped using the “Multiple Interval Mapping” method with the putative QTL markers as cofactors. Six QTLs for partial resistance were identified in this population. Three QTLs, Rphq1, Rphq2 and Rphq3, were effective at the seedling stage and contributed approximately 55% to the phenotypic variance. Five QTLs, Rph2, Rphq3, Rphq4, Rphq5, and/or Rphq6 contributed approximtely. 60% of the phenotypic variance and were effective at the adult plant stage. Therefore, only the QTLs Rphq2 and Rhpq3 were not plant-stage dependent. The identified QTLs showed mainly additive effects and only one significant interaction was detected, i.e. between Rphq1 and Rphq2. The map positions of these QTLs did not coincide with those of the race-specific resistance genes, suggesting that genes for partial resistance and genes for hypersensitive resistance represent entirely different gene families. Also, three QTLs for days to heading, of which two were also involved in plant height, were identified in the present recombinant inbred population. These QTLs had been mapped previously on the same positions in different populations. The perspectives of these results for breeding for durable resistance to leaf rust are discussed.

Characterization of Lr34, a major gene conferring nonhypersensitive resistance to wheat leaf rust.

Wheat leaf rust resistance gene Lr34 is claimed to contribute to durability of resistance in wheat cultivars in combination with other genes for resistance. We compared the effect of Lr34 with that of Lr12 and Lr13 (all in Thatcher background) and with the partial resistance of Akabozu and BH1146. Seedlings of all lines displayed a compatible infection type. Lr34 increased latency period and decreased infection frequency, especially at low temperature. The gene caused a small but significant increase in early abortion of sporelings. The number of haustoria per sporeling 42 h after inoculation was reduced significantly, but this was not associated with papilla formation. In adult plants the effect of Lr34 was much clearer. In the flag leaf Lr34 decreased infection frequency and increased latency period. Many infection units did not develop further than the stage in which they caused pale (nonhypersensitive) flecks. Also at the microscopic level we found no increased hypersensitivity due to Lr34. Lr34 shared features both with Lr13 and with the genes for partial resistance in Akabozu and BH1146. The main difference with Lr13 was the association of the latter with chlorosis at the macroscopic level and cell necrosis at the microscopic level. Lr34 and the partial resistance in Akabozu and BH1146 are based on reduced rates of haustorium formation in the early stages of infection, in association with no or relatively little plant cell necrosis. However, the reduction of haustorium formation in Thatcher-Lr34 appeared to be due to a low rate of intercellular hyphal development and not to papilla formation as in Akabozu and BH1146. We argue that Lr34 should be considered a major gene conferring partial resistance sensu Parlevliet.

Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars

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.

Potentially durable resistance mechanisms in plants to specialised fungal pathogens

Specialised plant pathogens are in many ways adapted to exploit their host plants. Infective propagules should reach the appropriate plant tissue, gain access to the tissue and negate or suppress various kinds of constitutive and inducible resistance mechanisms. The resistance type most frequently deployed in plant breeding is the race-specific resistance, where a hypersensitive response of plant tissue is elicited by an avirulence factor produced by the pathogen. The great disadvantage of this type of resistance is, that it is often ephemeral. Detailed screening of germplasm may result in the discovery of alternative defence mechanisms not associated with hypersensitivity, that may be durable. Avoidance mechanisms may reduce the chance of infection. Upright plant habit has been reported to decrease spore deposition in cereals. Crop architecture may also affect aspects such as humidity and aeration in the crop, and hence the chances for successful infection by pathogen propagules. Other examples of avoidance are leaf surface properties that interfere with leaf wettability, germ tube orientation and finding of stomata to enter the leaf. Stomata in some accessions of Hordeum chilense are excessively covered by cuticular wax that prevent rust fungal germ tubes from perceiving the stomata, resulting in failure of penetration of the pathogen into the leaf. There is evidence that incompatible host species, biotrophic pathogenic fungi induce basic compatibility by suppressing defence mechanisms. Failure of this induction results in abortion of the infection attempt. Several cases of apparently durable resistance are discussed that are based on failure of haustorium formation, and are not associated with hypersensitivity. They may represent cases where the pathogen has problems in establishing basic compatibility.

Nonhost and basal resistance: how to explain specificity?

Nonhost resistance to plant pathogens can be constitutive or induced by microbes. Successful pathogens suppress microbe-induced plant defences by delivering appropriate effectors, which are apparently not sufficiently effective on nonhost plant species, as can be concluded from the strong host specificity of many biotroph plant pathogens. Such effectors act on particular plant targets, such as promoters or motifs in expressed sequences. Despite much progress in the elucidation of the molecular aspects of nonhost resistance to plant pathogens, very little is known about the genes that determine whether effectors can or cannot suppress the basal defence. In hosts they can, in nonhosts they cannot. The targets determining the host status of plants can be identified in inheritance studies. Recent reports have indicated that nonhost resistance is inherited polygenically, and exhibits strong similarity and association with the basal resistance of plants to adapted pathogens.

Rin4 Causes Hybrid Necrosis and Race-Specific Resistance in an Interspecific Lettuce Hybrid

Some inter- and intraspecific crosses may result in reduced viability or sterility in the offspring, often due to genetic incompatibilities resulting from interactions between two or more loci. Hybrid necrosis is a postzygotic genetic incompatibility that is phenotypically manifested as necrotic lesions on the plant. We observed hybrid necrosis in interspecific lettuce (Lactuca sativa and Lactuca saligna) hybrids that correlated with resistance to downy mildew. Segregation analysis revealed a specific allelic combination at two interacting loci to be responsible. The allelic interaction had two consequences: (1) a quantitative temperature-dependent autoimmunity reaction leading to necrotic lesions, lethality, and quantitative resistance to an otherwise virulent race of Bremia lactucae; and (2) a qualitative temperature-independent race-specific resistance to an avirulent race of B. lactucae. We demonstrated by transient expression and silencing experiments that one of the two interacting genes was Rin4. In Arabidopsis thaliana, RIN4 is known to interact with multiple R gene products, and their interactions result in hypersensitive resistance to Pseudomonas syringae. Site-directed mutation studies on the necrosis-eliciting allele of Rin4 in lettuce showed that three residues were critical for hybrid necrosis.

Isolate-specific QTLs for partial resistance to Puccinia hordei in barley

Abstract By using a high-density AFLP marker linkage map, six QTLs for partial resistance to barley leaf rust (Puccinia hordei) isolate 1.2.1. have been identified in the RIL offspring of a cross between the partially resistant cultivar ’Vada’ and the susceptible line L94. Three QTLs were effective at the seedling stage, and five QTLs were effective at the adult plant stage. To study possible isolate specificity of the resistance, seedlings and adult plants of the 103 RILs from the cross L94×’Vada’ were also inoculated with another leaf rust isolate, isolate 24. In addition to the two QTLs that were effective against isolate 1.2.1. at the seedling stage, an additional QTL for seedling resistance to isolate 24 was identified on the long arm of chromosome 7. Of the eight detected QTLs effective at the adult plant stage, three were effective in both isolates and five were effective in only one of the two isolates. Only one QTL had a substantial effect at both the seedling and the adult plant stages. The expression of the other QTLs was developmental-stage specific. The isolate specificity of the QTLs supports the hypothesis of Parlevliet and Zadoks (1977) that partial resistance may be based on a minor-gene-for-minor-gene interaction.

Failure of haustorial development as a factor in slow growth and development of Puccinia hordei in partially resistant barley seedlings.

Observations on six barley lines differing for partial resistance, at 44 h and 6·5 days after inoculation with Puccinia hordei, indicated that a proportion of colonies fail to form haustoria, the proportion failing being related to the level of partial resistance. Following the formation of the first hauslorium, the rate of formation of further haustoria was reduced for some time in lines with high levels of partial resistance. Failed haustorium formation was quantified by determining the number of induced papillae. When colonies reach a certain size, the host-colony interaction appears to change abruptly towards high compatibility, since the hyphae formed from then on induce fewer papillae than before. Indications were found for differences in resistance levels between epidermal and mesophyll cells. Differences in size and phase of development of colonies at 6·5 days after inoculation both within and between barley lines were connected with differences in the degree of formation of wall appositions (papillae formation) around the point of entry into the leaf. The results are likely to have importance for understanding the mechanisms that determine basic compatibility.

Tomato Defense to Oidium neolycopersici: Dominant Ol Genes Confer Isolate-Dependent Resistance Via a Different Mechanism Than Recessive ol-2

Tomato powdery mildew caused by Oidium neolycopersici has become a globally important disease of tomato (Lycopersicon esculentum). To study the defense responses of tomato triggered by tomato powdery mildew, we first mapped a set of resistance genes to O. neolycopersici from related Lycopersicon species. An integrated genetic map was generated showing that all the dominant resistance genes (Ol-1, Ol-3, Ol-4, Ol-5, and Ol-6) are located on tomato chromosome 6 and are organized in three genetic loci. Then, near-isogenic lines (NIL) were produced that contain the different dominant Ol genes in a L. esculentum genetic background. These NIL were used in disease tests with local isolates of O. neolycopersici in different geographic locations, demonstrating that the resistance conferred by different Ol genes was isolate-dependent and, hence, may be race-specific. In addition, the resistance mechanism was analyzed histologically. The mechanism of resistance conferred by the dominant Ol genes was associated with hypersensitive response, which varies in details depending on the Ol-gene in the NIL, while the mechanism of resistance governed by the recessive gene ol-2 on tomato chromosome 4 was associated with papillae formation.

The RPi-mcd1 Locus from Solanum microdontum Involved in Resistance to Phytophthora infestans, Causing a Delay in Infection, Maps on Potato Chromosome 4 in a Cluster of NBS-LRR Genes

The distinction between field resistance and resistance based on resistance (R) genes has been proven valid for many plant-pathogen interactions. This distinction does not seem to be valid for the interaction between potato and late blight. In this study, a locus involved in late blight resistance, derived from Solanum microdontum, provides additional evidence for this lack of distinction. The resistance is associated with a hypersensitive response and results in a delay of infection of approximately 1 to 2 weeks. Both a quantitative as well as a qualitative genetic approach were used, based on data from a field assay. Quantitative trait locus (QTL) analysis identified a QTL on chromosome 4 after correction of the resistance data for plant maturity. A qualitative genetic analysis resulted in the positioning of this locus on the short arm of chromosome 4 in between amplified fragment length polymorphism marker pCTmACG_310 and cleaved amplified polymorphic sequence markers TG339 and T0703. This position coincides with a conserved Phytophthora R gene cluster which includes R2, R(2-like), R(Pi-blb3), and R(Pi-abpt). This implies that R(Pi-mcd1) is the fifth R gene of this nucleotide-binding site leucine-rich repeat cluster. The implications of our results on R-gene-based and field resistance are discussed.