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Global food security depends on cereal crops with durable disease resistance. Most cereals are colonized by rust fungi, which are pathogens of major significance for global agriculture1. Cereal rusts display a high degree of host specificity and one rust species or forma specialis generally colonizes only one cereal host2. Exploiting the non-host status and transferring non-host resistance genes between cereal crop species has been proposed as a strategy for durable rust resistance breeding. The molecular determinants that define the host status to rusts, however, are largely unknown. Here, we show that orthologous genes at the Rphq2 locus for quantitative leaf rust resistance from cultivated barley3 and Rph22 from wild bulbous barley4 affect the host status to leaf rusts. Both genes encode lectin receptor-like kinases. We transformed Rphq2 and Rph22 into an experimental barley line that has been bred for susceptibility to non-adapted leaf rusts, which allowed us to quantify resistance responses against various leaf rust species. Rphq2 conferred a much stronger resistance to the leaf rust of wild bulbous barley than to the leaf rust adapted to cultivated barley, while for Rph22 the reverse was observed. We hypothesize that adapted leaf rust species mitigate perception by cognate host receptors by lowering ligand recognition. Our results provide an example of orthologous genes that connect the quantitative host with non-host resistance to cereal rusts. Such genes provide a basis to exploit non-host resistance in molecular breeding.

Three barley mapping populations sharing the parental line SusPtrit suffered from an unknown condition affecting grain quality and germination. Grains showed dark blotches or even whole-grain discoloration and shrivelling. Symptoms were similar to kernel discoloration as reported in wheat and barley. Some covered-seed lines affected by this quality condition produced grains that were either not covered at all or in which partial hull loss was observed, a phenotype that resembles that of grain skinning. No fungal or bacterial agent was identified as causal organism, and we demonstrate that the poor quality phenotype is not transmitted to the next generation – therefore unlikely due to a seed borne pathogen. A major effect QTL on chromosome 6H was mapped independently in all three populations, with the poor quality allele contributed by SusPtrit. A second, minor effect QTL, was mapped on chromosome 2H in the SusPtrit x Golden Promise population, with Golden Promise as the parent donor of the allele conferring poor quality. The grain quality disorder is not linked to the nud gene on chromosome 7H for the naked/covered seed trait.

Key message The nonhost resistance of wild lettuce to lettuce downy mildew seems explained by four components of a putative set of epistatic genes. Abstract The commonplace observation that plants are immune to most potential pathogens is known as nonhost resistance (NHR). The genetic basis of NHR is poorly understood. Inheritance studies of NHR require crosses of nonhost species with a host, but these crosses are usually unsuccessful. The plant-pathosystem of lettuce and downy mildew, Bremia lactucae, provides a rare opportunity to study the inheritance of NHR, because the nonhost wild lettuce species Lactuca saligna is sufficiently cross-compatible with the cultivated host Lactuca sativa. Our previous studies on NHR in one L. saligna accession led to the hypothesis that multi-locus epistatic interactions might explain NHR. Here, we studied NHR at the species level in nine accessions. Besides the commonly used approach of studying a target trait from a wild donor species in a cultivar genetic background, we also explored the opposite, complementary approach of cultivar introgression in a wild species background. This bidirectional approach encompassed (1) nonhost into host introgression: identification of L. saligna derived chromosome regions that were overrepresented in highly resistant BC1 plants (F1 × L. sativa), (2) host into nonhost introgression: identification of L. sativa derived chromosome regions that were overrepresented in BC1 inbred lines (F1 × L. saligna) with relatively high infection levels. We demonstrated that NHR is based on resistance factors from L. saligna and the genetic dose for NHR differs between accessions. NHR seemed explained by combinations of epistatic genes on three or four chromosome segments, of which one chromosome segment was validated by the host into nonhost approach. Electronic supplementary material The online version of this article (10.1007/s00122-018-3112-8) contains supplementary material, which is available to authorized users.

Key message Resistance factors against non-adapted powdery mildews were mapped in barley. Some QTLs seem effective only to non-adapted mildews, while others also play a role in defense against the adapted form. The durability and effectiveness of nonhost resistance suggests promising practical applications for crop breeding, relying upon elucidation of key aspects of this type of resistance. We investigated which genetic factors determine the nonhost status of barley (Hordeum vulgare L.) to powdery mildews (Blumeria graminis). We set out to verify whether genes involved in nonhost resistance have a wide effectiveness spectrum, and whether nonhost resistance genes confer resistance to the barley adapted powdery mildew. Two barley lines, SusBgtSC and SusBgtDC, with some susceptibility to the wheat powdery mildew B. graminis f.sp. tritici (Bgt) were crossed with cv Vada to generate two mapping populations. Each population was assessed for level of infection against four B. graminis ff.spp, and QTL mapping analyses were performed. Our results demonstrate polygenic inheritance for nonhost resistance, with some QTLs effective only to non-adapted mildews, while others play a role against adapted and non-adapted forms. Histology analyses of nonhost interaction show that most penetration attempts are stopped in association with papillae, and also suggest independent layers of defence at haustorium establishment and conidiophore formation. Nonhost resistance of barley to powdery mildew relies mostly on non-hypersensitive mechanisms. A large-effect nonhost resistance QTL mapped to a 1.4 cM interval is suitable for map-based cloning. Electronic supplementary material The online version of this article (10.1007/s00122-018-3055-0) contains supplementary material, which is available to authorized users.

The new phytologist 213(3), 1346-1362 (2017). doi:10.1111/nph.14220, Published by Wiley-Blackwell, Oxford [u.a.]

The main objective of this research was to analyze whether selection under conventional conditions (indirect selection) is as effective as selection under organic conditions (direct selection) to develop varieties suitable for organic farming systems. Two F3 barley (Hordeum vulgare L.) populations ‘Primus’/‘Idumeja’ (P/I) and ‘Anni’/‘Dziugiai’ (A/Dz) targeted for organic variety development were selected in two organically and two conventionally managed environments during F3 to F3:6. From there, the performance of the five best F3:6 lines selected in each of the four environments from each cross (in total, 40 lines) were compared at all four sites during two years. For obtaining varieties adapted to organic conditions for the P/I cross, it did not matter at which condition the selection was performed. For A/Dz, the best selection results in terms of yield, combined with other traits included for an organic ideotype, were achieved under well-managed organic conditions. We conclude that direct and indirect selection in early breeding stages are equally suitable for the development of cultivars for organic conditions if (i) care is taken that selection considers not only yield, but also other traits important for organic growing conditions, (ii) selection is not performed under too stressful conditions, and (iii) testing in later stages of the breeding program is conducted under various organic farming conditions for the best recommended varieties for organic agriculture.

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce worldwide. Breeding for resistance to this disease is a major priority for most lettuce breeding programs. Many genes and factors for resistance to B. lactucae have been reported by multiple researchers over the past ~50 years. Their nomenclature has not been coordinated, resulting in duplications and gaps in nominations. We have reviewed the available information and rationalized it into 51 resistance genes and factors and 15 quantitative trait loci along with supporting documentation as well as genetic and molecular information. This involved multiple rounds of consultation with many of the original authors. This paper provides the foundation for naming additional genes for resistance to B. lactucae in the future as well as for deploying genes to provide more durable resistance.

Key message QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Abstract Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes. Electronic supplementary material The online version of this article (10.1007/s00122-018-3239-7) contains supplementary material, which is available to authorized users.

Western flower thrips [Frankliniella occidentalis (Pergande)] is a worldwide pest insect that causes damage in pepper cultivation, so growers would benefit from host plant resistance. The objectives of this study were (1) to evaluate the effect of plant age on thrips resistance using nine Capsicum accessions with different levels of thrips resistance at three different plant ages, and (2) to study the effect of leaf age on thrips resistance in a resistant and a susceptible pepper accession. The fraction of first instar larvae that did not develop into second instar was used as a measure for thrips resistance. Our results show that plants start to develop thrips resistance when they are between 4 and 8 weeks old. This transition was most marked on the resistant accession CGN16975, on which about 50% of the L1 larvae developed into the next stage on 4-week-old plants, whereas none of them developed beyond the L1 stage on 8- or 12-week-old plants. Furthermore, it is shown that youngest fully opened leaves of the resistant accession CGN16975 are significantly more resistant to thrips than older leaves; 89% of the L1 larvae did not develop into the next stage on the youngest leaves, whereas 57% did not develop beyond the L1 stage on the oldest leaves. Young leaves of the susceptible accession CGN17219 are more susceptible than older leaves; 9 versus 52% of the L1 larvae did not develop into the next stage on young and old leaves, respectively. These findings can be used to improve integrated pest management strategies.

Phytochemicals not only determine the taste and smell of plants and their products, they also play a crucial role in resistance against pests and pathogens. In previous work, we identified a form of resistance to thrips (Frankliniella occidentalis) expressed in leaves of pepper (Capsicum annuum). In the current study, we characterized leaves of an interspecific C. annuum × C. chinense F2 population for variation in their global phytochemical composition by an untargeted metabolomics approach. Quantitative trait locus (QTL) mapping resulted in metabolite QTLs (mQTLs) for 304 of the 674 metabolites detected. We compared the QTL mapping results to those obtained earlier on fruits in the same population. Very different QTL hotspots were found, suggesting that the metabolite composition of leaves and fruits is regulated independently. Six leaf mQTLs co-located with the major QTL for resistance to thrips, which we previously identified in the same F2 population. Four of them were significantly correlated to thrips resistance, including two diterpene glycosides and a flavonoid compound which may indicate a possible role of these metabolites in thrips resistance. If a causal role of some of these metabolites in resistance can be proven this will help in the identification of the causal gene(s) and it may provide leads for the identification of other sources of thrips resistance in Capsicum and in other species.

Background The green peach aphid (GPA), Myzus persicae, is economically one of the most threatening pests in pepper cultivation, which not only causes direct damage but also transmits many viruses. Breeding aphid resistant pepper varieties is a promising and environmentally friendly method to control aphid populations in the field and in the greenhouse. Until now, no strong sources of resistance against the GPA have been identified. Therefore the main aims of this study were to identify pepper materials with a good level of resistance to GPA and to elucidate possible resistance mechanisms. Results We screened 74 pepper accessions from different geographical areas for resistance to M. persicae. After four rounds of evaluation we identified one Capsicum baccatum accession (PB2013071) as highly resistant to M. persicae, while the accessions PB2013062 and PB2012022 showed intermediate resistance. The resistance of PB2013071 resulted in a severely reduced uptake of phloem compared to the susceptible accession, as determined by Electrical Penetration Graph (EPG) studies. Feeding of M. persicae induced the expression of callose synthase genes and resulted in callose deposition in the sieve elements in resistant, but not in susceptible plants. Conclusions Three aphid resistant pepper accessions were identified, which will be important for breeding aphid resistant pepper varieties in the future. The most resistant accession PB2013071 showed phloem-based resistance against aphid infestation. Electronic supplementary material The online version of this article (10.1186/s12870-018-1340-3) contains supplementary material, which is available to authorized users.

The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect. Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whitefly-resistance related traits and associated biochemical traits in this species. Minor quantitative trait loci (QTLs) for whitefly adult survival (AS) and oviposition rate (OR) were identified and some were confirmed in an F2BC1 population, where they showed increased percentages of explained variance (more than 30%). Bulked segregant analyses on pools of whitefly-resistant and -susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whitefly-resistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or susceptibility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correlation between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.

Cultivation of spinach requires high amounts of nitrogen (N), which puts a strain on the environment. A sustainable solution to this problem is to breed for crops with higher N use efficiency (NUE). The aim of this study was to provide tools for molecular breeding and to elucidate the genetic variation of factors contributing to NUE in spinach. A cross was made between two F1 hybrid cultivars contrasting in NUE. Several F1 progeny were self-pollinated and based on evaluation of the F2 generation, a mapping F2 population (335 individuals) of a single F1 was selected. SNP markers for the genetic map were discovered by RNA sequencing of the two parent cultivars, and 283 SNP markers were used to produce a genetic map comprising of six linkage groups (P01–P06), ranging in size from 46 to 116 cM. NUE related traits were determined for a set of F2:3 families grown under low and high N conditions in a hydroponics system under an Ingestad N-addition model. Interval mapping analysis detected 39 trait-specific QTLs, with several QTLs accumulating on P01 and P02 of the linkage map. The QTLs and in particular the P01 and P02 regions provide potential targets for the improvement of NUE in spinach.

Quantitative resistance (QR) refers to a resistance that is phenotypically incomplete and is based on the joined effect of several genes, each contributing quantitatively to the level of plant defense. Often, QR remains durably effective, which is the primary driver behind the interest in it. The various terms that are used to refer to QR, such as field resistance, adult plant resistance, and basal resistance, reflect the many properties attributed to it. In this article, we discuss aspects connected to those attributions, in particular the hypothesis that much of the QR to biotrophic filamentous pathogens is basal resistance, i.e., poor suppression of PAMP-triggered defense by effectors. We discuss what role effectors play in suppressing defense or improving access to nutrients. Based on the functions of the few plant proteins identified as involved in QR, vesicle trafficking and protein/metabolite transportation are likely to be common physiological processes relevant to QR.

Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays and comprehensive metabolite profiling. Broad spectrum resistance was found in Solanum galapagense and a few accessions of S. pimpinellifolium. Resistance to the sap sucking insects may be based on the same mechanism, but different from the caterpillar resistance. Large and highly significant differences in the leaf metabolomes were found between S. galapagense, containing type IV trichomes, and its closest relative S. cheesmaniae, which lacks type IV trichomes. The most evident differences were the relatively high levels of different methylated forms of the flavonoid myricetin and many acyl sucrose structures in S. galapagense. Possible candidate genes regulating the production of these compounds were identified in the Wf-1 QTL region of S. galapagense, which was previously shown to confer resistance to the whitefly B. tabaci. The broad spectrum insect resistance identified in S. galapagense will be very useful to increase resistance in cultivated tomato.

Background The green peach aphid (GPA), Myzus persicae, is economically one of the most threatening pests in pepper cultivation, which not only causes direct damage but also transmits many viruses. Breeding aphid resistant pepper varieties is a promising and environmentally friendly method to control aphid populations in the field and in the greenhouse. Until now, no strong sources of resistance against the GPA have been identified. Therefore the main aims of this study were to identify pepper materials with a good level of resistance to GPA and to elucidate possible resistance mechanisms. Results We screened 74 pepper accessions from different geographical areas for resistance to M. persicae. After four rounds of evaluation we identified one Capsicum baccatum accession (PB2013071) as highly resistant to M. persicae, while the accessions PB2013062 and PB2012022 showed intermediate resistance. The resistance of PB2013071 resulted in a severely reduced uptake of phloem compared to the susceptible accession, as determined by Electrical Penetration Graph (EPG) studies. Feeding of M. persicae induced the expression of callose synthase genes and resulted in callose deposition in the sieve elements in resistant, but not in susceptible plants. Conclusions Three aphid resistant pepper accessions were identified, which will be important for breeding aphid resistant pepper varieties in the future. The most resistant accession PB2013071 showed phloem-based resistance against aphid infestation.

Whiteflies are among the world's most significant agricultural pests and chemical insecticides are extensively used to reduce crop damage to acceptable levels. However, nearly all insecticides pose a threat to the environment and alternative control methods, such as breeding of crop varieties that are inherently insect-resistant, are needed. Previously, a strong source of plant-age dependent resistance to the cabbage whitefly (Aleyrodes proletella) has been identified in the modern white cabbage (Brassica oleracea var. capitata) variety Rivera. However, nothing is known about the molecular mechanisms or the genes involved in this resistance. In the present study, a multidisciplinary approach combining transcriptome and metabolome profiling with genetic mapping was used to identify the molecular players of whitefly resistance in cabbage. Transcriptome profiles of young (susceptible) and older (resistant) Rivera plants were analyzed using RNA sequencing. While many genes involved in general processes were differentially expressed between both ages, several defense-related processes were overrepresented in the transcriptome profile of older plants. Hormone measurements revealed that jasmonic acid (JA) levels decreased upon whitefly infestation at both plant ages. Interestingly, abscisic acid (ABA) levels showed contrasting effects in response to whitefly infestation: ABA levels were reduced in young plants but induced in older plants upon whitefly feeding. Auxin levels were significantly lower in older plants compared with young plants, independent of whitefly presence, while glucosinolate levels were higher. Additionally, whitefly performance was monitored in an F2 population derived from a cross between Rivera and the susceptible white cabbage variety Christmas Drumhead. Significant QTL intervals were mapped on chromosome 2 and 9 for oviposition rate and whitefly adult survival, respectively. Several genes that were higher expressed in older plants and located in the identified QTL intervals were orthologous to Arabidopsis genes that have been related to ABA signaling, suggesting a role for ABA in the regulation of resistance towards whiteflies. Our results show that combining different omics approaches is a useful strategy to identify candidate genes underlying insect resistance.

A QTL for thrips resistance on pepper chromosome 6 was identified and validated. This QTL affects thrips larval development and explains 50 % of the variation. Thrips is one of the most damaging pests in pepper (Capsicum). Resistance to thrips was identified in Capsicum annuum. This study was aimed at the elucidation of the genetic background of thrips resistance in Capsicum through QTL mapping. The QTL analysis was carried out for Frankliniella occidentalis resistance in an F2 population consisting of 196 plants derived from an interspecific cross between the highly resistant C. annuum AC 1979 as female parent and the highly susceptible C. chinense 4661 as male parent. Fifty-seven SSR, 109 AFLP, and 5 SNP markers were used to construct a genetic map with a total length of 1636 cM. Damage caused by larvae and the survival of first and second instar larval stages observed in a no-choice test were used as parameters of resistance. Interval mapping detected one QTL for each of these parameters, all co-localizing near the same marker on chromosome 6. Use of this marker as co-factor in a multiple-QTL mapping analysis failed to uncover any additional QTLs. This QTL explained about 50 % of the genetic variation, and the resistance allele of this QTL was inherited from the resistant parent. Thrips resistance was not linked to trichome density.

Barley (Hordeum vulgare L.) mapping populations have been developed that are useful to study the inheritance of quantitative resistance to adapted and unadapted rust fungi. In a recent host range study, we found that the parents of those mapping populations also differed in their resistance to the crown rust Puccinia coronata (PcE) of couch grass (Elymus repens), as well as three isolates of P. striiformis, representing formae speciales hordei (Psh), tritici (Pst) and bromi (Psb). Available mapping populations were phenotyped at the seedling stage to map the genes conferring resistance to these rust isolates. Resistances to PcE, Psb and Pst inherit quantitatively. This contrasted with reports that barley nonhost resistance to unadapted formae speciales of P. striiformis is based on major genes. We mapped QTLs effective against PcE using relative latency period and relative infection frequency. Some QTLs for resistance were contributed by ‘Vada’ and ‘Cebada Capa’, others by SusPtrit. One PcE-resistance QTL on 3H, contributed by ‘Cebada Capa’, co-localised with a QTL effective against four unadapted grass rust species, indicating either a single gene with broad-spectrum effectiveness or a cluster of rather specific genes. Chromosome arm 7HL from Vada seems particularly rich in genes for resistance to rust fungi. Resistance to Pst and Psb, measured as the number of uredinia, tended to co-localise with each other and mapped to 1HS, 2HL and 7HL. The nearly complete resistance of Ethiopian line L94 to Psh was due to a major gene mapped on chromosome 4H. That gene is likely the recessive gene rpsGZ, which was previously reported in the Ethiopian line Grannenlose Zweizeilige.

Summary Candidate effectors from lettuce downy mildew (Bremia lactucae) enable high‐throughput germplasm screening for the presence of resistance (R) genes. The nonhost species Lactuca saligna comprises a source of B. lactucae R genes that has hardly been exploited in lettuce breeding. Its cross‐compatibility with the host species L. sativa enables the study of inheritance of nonhost resistance (NHR).We performed transient expression of candidate RXLR effector genes from B. lactucae in a diverse Lactuca germplasm set. Responses to two candidate effectors (BLR31 and BLN08) were genetically mapped and tested for co‐segregation with disease resistance.BLN08 induced a hypersensitive response (HR) in 55% of the L. saligna accessions, but responsiveness did not co‐segregate with resistance to Bl:24. BLR31 triggered an HR in 5% of the L. saligna accessions, and revealed a novel R gene providing complete B. lactucae race Bl:24 resistance. Resistant hybrid plants that were BLR31 nonresponsive indicated other unlinked R genes and/or nonhost QTLs.We have identified a candidate avirulence effector of B. lactucae (BLR31) and its cognate R gene in L. saligna. Concurrently, our results suggest that R genes are not required for NHR of L. saligna.

The cabbage whitefly (Aleyrodes proletella) is a phloem-feeding insect that is a serious problem in Brassica oleracea crops like Brussels sprouts, kale and savoy cabbage. In order to develop whitefly-resistant varieties it is essential to identify effective sources of resistance. In this study, we screened a large collection of 432 accessions, including wild material and landraces of Brassica oleracea as well as crop wild relatives, to determine whitefly performance in a no-choice field experiment. Putatively resistant accessions were further tested under greenhouse conditions. Resistant accessions were identified among B. oleracea var. capitata (cabbage) landraces and in the species B. villosa, B. incana and B. montana. Whereas resistance in cabbage is only expressed in plants of at least 12 weeks old, some wild relatives were already starting to express resistance at 6 weeks. This could open up possibilities for breeding cabbages that are resistant at a young(er) plant age. Our research also shows again the importance of crop wild relatives for finding pest resistances.

Background Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. Results In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. Conclusions Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.

Big Data has been seen as a remedy for the efficient management of the ever-increasing genomic data. In this paper, we investigate the use of Apache Spark to store and process Variant Calling Files (VCF) on a Hadoop cluster. We demonstrate Tomatula, a software tool for converting VCF files to Apache Parquet storage format, and an application to query variant calling datasets. We evaluate how the wall time (i.e. time until the query answer is returned to the user) scales out on a Hadoop cluster storing VCF files, either in the original flat-file format, or using the Apache Parquet columnar storage format. Apache Parquet can compress the VCF data by around a factor of 10, and supports easier querying of VCF files as it exposes the field structure. We discuss advantages and disadvantages in terms of storage capacity and querying performance with both flat VCF files and Apache Parquet using an open plant breeding dataset. We conclude that Apache Parquet offers benefits for reducing storage size and wall time, and scales out with larger datasets.

Barley is a near-nonhost to numerous heterologous (nonadapted) rust pathogens because a small proportion of genotypes are somewhat susceptible. We assessed 66 barley accessions and three mapping populations (Vada × SusPtrit, Cebada Capa × SusPtrit, and SusPtrit × Golden Promise) for response to three Swedish oat stem rust (Puccinia graminis f. sp. avenae) fungal isolates and determined that barley is a near-nonhost to P. graminis f. sp. avenae and that resistance was polygenically inherited. The parental genotypes Vada and Golden Promise were immune to all three isolates, whereas Cebada Capa was immune to two isolates and moderately resistant to the third. Phenotypic data from the Vada × SusPtrit mapping population and the barley accessions tested also demonstrated isolate-specific resistance. In particular, the SusPtrit parent and several other accessions allowed sporulation by isolate Ingeberga but were resistant to isolate Evertsholm. Nine chromosomal regions carried quantitative trait loci (QTL) (Rpgaq1 to Rpgaq9) of varying effect, most of which colocated to previously identified QTL for resistance to other heterologous rust pathogens. Rpgaq1 on chromosome 1H (Vada and Golden Promise) was effective toward all isolates tested. Microscopic examination indicated that resistance was prehaustorial in Vada whereas, in SusPtrit, both pre- and posthaustorial mechanisms play a role.

The cabbage whitefly [Aleyrodes proletella L. (Hemiptera: Aleyrodidae)] is becoming a serious pest in Brassica oleracea L. (Brassicaceae) crops. However, almost nothing is known about the interaction of this insect with its host plants. Previous studies have shown differences in the natural occurrence of adults, eggs, and nymphs on the closely related B. oleracea cultivars Christmas Drumhead and Riviera grown in the field. In this study, we aimed to identify the nature of these differences and to gain insight into the resistance mechanisms against A. proletella. We used no-choice experiments on field- and greenhouse-grown plants to show that the differences between the two cultivars are mainly based on antibiosis (traits that reduce herbivore performance) and not on antixenosis (traits that deter herbivory). This was further supported by laboratory choice experiments that indicated little or no discrimination between the two cultivars based on plant volatiles. We showed that resistance is dependent on plant age, that is, resistance increased during plant development, and is mainly independent of environmental factors. Analysis of probing behaviour revealed that the resistance trait affects A. proletella at the phloem level and that morphological differences between the two cultivars are most likely not involved. We suggest that compounds present in the phloem reduce sap ingestion by the whitefly and that this explains the observed resistance

1. Plants face threats from a variety of herbivorous insects and can use induced responses to defend themselves against these attackers. Induced responses are mediated by signal transduction involving phytohormones, such as jasmonic acid (JA) and salicylic acid (SA). Cross-talk between signal transduction pathways triggered by attackers with contrasting feeding styles allows plants to fine-tune defences. A central question in this emerging field is to understand how responses to single attackers interfere with responses to other attackers, especially by integratively addressing molecular and ecological aspects. 2. We examined the plant-mediated interactions between the leaf-chewing Pieris brassicae and the phloem-sucking Brevicoryne brassicae, and their respective parasitoids Cotesia glomerata and Diaeretiella rapae, when feeding simultaneously, sequentially or in isolation on the brassicaceous ecological model plant Brassica oleracea. We analysed the underlying defence mechanisms in the plant. Levels of the phytohormones JA and SA transcriptional responses of a number of selected defence-related genes and secondary plant compounds were quantified at different time points during the single and multiple infestations. 3. The caterpillars developed faster and reached a larger body mass on plants previously attacked by aphids. Aphids initially developed faster on plants with caterpillars, although the moment of moulting to adults was independent of the presence of caterpillars. Both parasitoid species performed better under multiple-infestation scenarios than in single-herbivore situations. 4. On plants attacked by aphids, the JA levels were tenfold lower than on undamaged plants or plants with caterpillars. Additionally, the low transcript levels of LOX and MYC, genes coding for a JA biosynthesis-related enzyme and a transcription factor, respectively, in aphid-infested plants, suggest that the facilitation of the caterpillar performance was mediated by interference in signal transduction. Levels of carbon and nitrogen and secondary plant compounds (glucosinolates) did not differ significantly between treatments, suggesting that these compounds did not mediate the facilitation. 5. Our data show that the leaf chewer and phloem feeder asymmetrically interact not via competition as would be expected from interspecific herbivores but instead via facilitation; the phloem feeder attenuated JA-related plant defences, thus facilitating the growth and development of the leaf chewers. In linear bitrophic systems, interactions between JA and SA signalling pathways have been proposed to allow plants to fine-tune their defences, but if facilitation frequently occurs in interspecific interguild interactions among herbivores this may represent an important constraint for plant defences. Such a constraint might be reduced if, as in our model system, parasitoids also benefit from interactions between interguild hosts and nonhosts, but parasitoids are rarely considered in model molecular systems to assess the impact of herbivore-induced plant defences.

Plants show phenotypic changes when challenged with herbivorous insects. The mechanisms underlying these changes include the activation of transcriptional responses, which are dependent on the attacking insect. Most transcriptomic studies on crucifer–insect interactions have focused on the model plant Arabidopsis thaliana, a species that faces low herbivore pressure in nature. Here, we study the transcriptional responses of plants from a wild black mustard (Brassica nigra) population to herbivores of different feeding guilds using an A. thaliana-based whole-genome microarray that has previously been shown to be suitable for transcriptomic analyses in Brassica. Transcriptional responses of B. nigra after infestation with either Pieris rapae caterpillars or Brevicoryne brassicae aphids are analyzed and compared. Additionally, the insect-induced expression changes of some individual genes are analyzed through quantitative real-time polymerase chain reaction. The results show that feeding by both insect species results in the accumulation of transcripts encoding proteins involved in the detoxification of reactive oxygen species, defensive proteins and glucosinolates and this is correlated with experimental evidence in the literature on such biochemical effects. Although genes encoding proteins involved in similar processes are regulated by both insects, there was little overlap in the induction or repression of individual genes. Furthermore, P. rapae and B. brassicae seem to affect different phytohormone signaling pathways. In conclusion, our results indicate that B. nigra activates several defense-related genes in response to P. rapae or B. brassicae feeding, but that the response is dependent on the attacking insect species.

The jasmonic acid (JA) pathway is the main signal-transduction pathway induced by insect folivory. Mutant plants affected in the jasmonate pathway (18:0 and/or 16:0-oxylipin routes) were studied to assess the effects of JA and its oxylipin intermediates 12-oxophytodienoic acid (OPDA) and dinor-OPDA (dnOPDA) on interconnected signal-transduction pathways that underlie induced defenses in Arabidopsis. Our data show that the oxylipin jasmonates dnOPDA, OPDA and JA have different roles in defense signaling induced after feeding by the chewing-biting caterpillar Pieris rapae. Jasmonic acid, and not OPDA or dnOPDA, is the major signaling compound required for the induction of the defense-related genes LOX2 (Lipoxygenase 2), OPR3 (12-Oxophytodienoate reductase 3), ACX1 (Acyl-CoA oxidase 1) and PAL1 (Phenylalanine ammonia-lyase 1). Monitoring PAL1 transcript levels clearly showed that accumulation of JA upon P. rapae feeding results in the induction of the salicylic acid pathway. Furthermore, JA is the major signaling compound required for the P. rapae-induced expression of the defense-related gene HPL1 (Hydroperoxide lyase 1). The jasmonate dnOPDA influences the induction of the HPL-branch as well, yet its effect is antagonistic to the effect of JA. Our data show that these jasmonates may be used to fine-tune Arabidopsis’ herbivore-induced responses in terms of the HPL-branch from the oxylipin pathway.

1. Arthropod communities are structured by complex interactions between bottom-up (resource-based) and top-down (natural enemy-based) forces. Their relative importance in shaping arthropod communities, however, continues to be under debate. Bottom-up and top-down forces can be affected by intraspecific plant variation, for example by differences in concentrations of secondary metabolites that affect herbivore abundance through plant quality (bottom-up) or attract natural enemies of these herbivores (top-down). 2. Our objective was to investigate whether herbivore abundance is more strongly affected by plant-mediated bottom-up or top-down forces. 3. We used a model system of four cultivars of Brassica oleracea that show a high degree of variation in several plant traits, resistance to herbivores and attraction of natural enemies. During two field seasons, we recorded the abundance of several herbivorous and carnivorous insect species. To assess the relative importance of bottom-up and top-down forces, we quantified chemical and morphological traits of the cultivars (bottom-up) and assessed parasitization of herbivores and predator oviposition on plants inoculated with a controlled number of herbivores (top-down). 4. We show that intraspecific variation in plant chemistry and morphology consistently affects the abundance of insect herbivores and their natural enemies, resulting in cascading effects on tritrophic interactions in the associated insect community. Foliar profiles of glucosinolates and leaf toughness appeared most important for these effects. Brassica oleracea cultivars that harboured the largest numbers of herbivores also harboured the largest numbers of natural enemies. Differences in the fraction of herbivores parasitized and in predator oviposition on plants inoculated with a controlled number of herbivores could not explain the differences in natural abundance of herbivores. 5. Although abundance of herbivores is most likely influenced by a combination of bottom-up and top-down forces, it appears that in the tritrophic system investigated, bottom-up forces (plant chemistry and morphology) were more important for herbivore abundance than plant-mediated top-down forces (attraction and arrestment of natural enemies).

Herbivorous insects are widespread and often serious constraints to crop production. The use of insect-resistant crops is a very effective way to control insect pests in agriculture, and the development of such crops can be greatly enhanced by knowledge on plant resistance mechanisms and the genes involved. Plants have evolved diverse ways to cope with insect attack that has resulted in natural variation for resistance towards herbivorous insects. Studying the molecular genetics and transcriptional background of this variation has facilitated the identification of resistance genes and processes that lead to resistance against insects. With the development of new technologies, molecular studies are not restricted to model plants anymore. This review addresses the need to exploit natural variation in resistance towards insects to increase our knowledge on resistance mechanisms and the genes involved. We will discuss how this knowledge can be exploited in breeding programmes to provide sustainable crop protection against insect pests. Additionally, we discuss the current status of genetic research on insect-resistance genes. We conclude that insect-resistance mechanisms are still unclear at the molecular level and that exploiting natural variation with novel technologies will contribute greatly to the development of insect-resistant crop varieties.

Cabbage root flies (Delia radicum) are a major threat to cabbage production in Western Europe and North America. Host plant resistance is the most promising option in controlling cabbage root fly damage. In a no-choice field test, we evaluated 94 accessions belonging to 16 Brassica-species for antibiosis resistance against the larvae. Thirteen accessions were selected as putatively resistant, which were subsequently re-tested in the greenhouse. The proportion of eclosed flies was introduced as the main parameter to assess antibiosis in the greenhouse, together with other insect and plant parameters. High levels of antibiosis resistance were identified in B. fruticulosa PI663081 and B. spinescens BRA2994, with significantly lower proportions of eclosed flies (1 % of the number of eggs used for infestation) compared to other accessions. Both species are difficult to cross with B. oleracea. Plants with a high level of antibiosis and medium to high tolerance were found in several accessions of other Brassica species (B. villosa BRA2922, B. montana BRA2950, B. hilarionis HRIGU12483, B. macrocarpa BRA2944) which are more amenable for crossing with B. oleracea. Selection of the most resistant plants belonging to these accessions may yield promising candidates for breeding cabbages resistant to Delia radicum.

Rphq2 , a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43 %, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.

Phosphorus (P) is often an important limiting factor for crop yields, but rock phosphate as fertilizer is a non-renewable resource and expected to become scarce in the future. High P input levels in agriculture have led to environmental problems. One of the ways to tackle these issues simultaneously is improving phosphorus use efficiency (PUE) of the crops through breeding. In this review, we describe plant architectural and physiological traits important for PUE. Subsequently, we discuss efficient methods of screening for PUE traits. We address targeted cultivation methods, including solid and hydroponic systems, as well as testing methods, such as image analysis systems, and biomass and photosynthesis measurements. Genetic variation for PUE traits has been assessed in many crops, and genetics of PUE has been studied by quantitative trait loci (QTL) analyses and genome-wide association study. A number of genes involved in the plant’s response to low P have been characterized. These genes include transcription factors, and genes involved in signal transduction, hormonal pathways, sugar signalling, P saving metabolic pathways, and in P scavenging, including transporters and metabolites and/or ATP-ases mobilizing P in the soil. In addition, the role of microorganisms promoting PUE of plants, particularly arbuscular mycorrhizal fungi is discussed. An overview is given of methods for selecting for optimal combinations of plant and fungal genotypes, and their genetics, incl. QTLs and genes involved. In conclusion, significant progress has been made in selecting for traits for PUE, developing systems for the difficult but highly relevant root phenotyping, and in identifying QTLs and genes involved.

Background Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. Results Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. Conclusions Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0879-0) contains supplementary material, which is available to authorized users.

The whitefly Bemisia tabaci is a serious threat in tomato cultivation worldwide as all varieties grown today are highly susceptible to this devastating herbivorous insect. Many accessions of the tomato wild relative Solanum pennellii show a high resistance towards B. tabaci. A mapping approach was used to elucidate the genetic background of whitefly-resistance related traits and associated biochemical traits in this species. Minor quantitative trait loci (QTLs) for whitefly adult survival (AS) and oviposition rate (OR) were identified and some were confirmed in an F2BC1 population, where they showed increased percentages of explained variance (more than 30%). Bulked segregant analyses on pools of whitefly-resistant and -susceptible F2 plants enabled the identification of metabolites that correlate either with resistance or susceptibility. Genetic mapping of these metabolites showed that a large number of them co-localize with whitefly-resistance QTLs. Some of these whitefly-resistance QTLs are hotspots for metabolite QTLs. Although a large number of metabolite QTLs correlated to whitefly resistance or susceptibility, most of them are yet unknown compounds and further studies are needed to identify the metabolic pathways and genes involved. The results indicate a direct genetic correlation between biochemical-based resistance characteristics and reduced whitefly incidence in S. pennellii.

Herbivory contributes substantially to plant functional diversity and in ways that move far beyond direct defence trait patterns, as effective growth strategies under herbivory require modification of multiple functional traits that are indirectly related to defence. In order to understand how herbivory has shaped plant functional diversity, we need to consider the physiology and architecture of the herbivores and how this constrains effective defence strategies. Here we consider herbivory by mammals in savanna communities that range from semi-arid to humid conditions. We posited that the saplings of savanna trees can be grouped into two contrasting defence strategies against mammals, namely architectural defence versus low nutrient defence. We provide a mechanistic explanation for these different strategies based on the fact that plants are under competing selection pressures to limit herbivore damage and outcompete neighbouring plants. Plant competitiveness depends on growth rate, itself a function of leaf mass fraction (LMF) and leaf nitrogen per unit mass (Nm). Architectural defence against vertebrates (which includes spinescence) limits herbivore access to plant leaf materials, and partly depends on leaf-size reduction, thereby compromising LMF. Low nutrient defence requires that leaf material is of insufficient nutrient value to support vertebrate metabolic requirements, which depends on low Nm. Thus there is an enforced tradeoff between LMF and Nm, leading to distinct trait suites for each defence strategy. We demonstrate this tradeoff by showing that numerous traits can be distinguished between 28 spinescent (architectural defenders) and non-spinescent (low nutrient defenders) of Fabaceae tree species from savannas, where mammalian herbivory is an important constraint on plant growth. Distributions of the strategies along an LMF-Nm tradeoff further provides a predictive and parsimonious explanation for the uneven distribution of spinescent and non-spinescent species across water and nutrient gradients.

This chapter discusses some of the activities and achievements of the Plant Genetic Resources (PGR) Secure project, which aims to: (i) identify host plant resistance to the cabbage whitefly (Aleyrodes proletella) and cabbage aphid (Brevicoryne brassicae) via a germplasm screen where both are specialist phloem-feeding insects that feed only on members of the Brassicaceae family; (ii) elucidate the resistance mechanism; and (iii) provide tools to breeders that will facilitate resistance breeding. It is shown that the PGR Secure project has delivered valuable information on the extent of whitefly and aphid resistance in landrace accessions of Brassica oleracea var. capitata, as well as in wild relatives of B. oleracea. The whitefly resistance present in Brassica villosa, B. incana and B. montana is expressed both in 6- and 12-week-old plants, which indicates that this form of resistance is probably different from that already present in B. oleracea. These sources can be used in breeding resistant varieties. By combining novel phenomics, genomics and transcriptomics technologies, resistance breeding can be speeded up significantly. The developed and publicly available 90 k Affymetrix Axiom Brassica array can play an important role in this. The single nucleotide polymorphism markers linked to the resistance quantitative trait loci (QTLs) will facilitate an efficient introgression of the QTLs into high-yielding varieties.

Cell walls and cellular turgor pressure shape and suspend the bodies of all vascular plants. In response to attack by fungal and oomycete pathogens, which usually breach their host's cell walls by mechanical force or by secreting lytic enzymes, plants often form local cell wall appositions (papillae) as an important first line of defence. The involvement of cell wall biosynthetic enzymes in the formation of these papillae is still poorly understood, especially in cereal crops. To investigate the role in plant defence of a candidate gene from barley (Hordeum vulgare) encoding cellulose synthase-like D2 (HvCslD2), we generated transgenic barley plants in which HvCslD2 was silenced through RNA interference (RNAi). The transgenic plants showed no growth defects but their papillae were more successfully penetrated by host-adapted, virulent as well as avirulent nonhost isolates of the powdery mildew fungus Blumeria graminis. Papilla penetration was associated with lower contents of cellulose in epidermal cell walls and increased digestion by fungal cell wall degrading enzymes. The results suggest that HvCslD2-mediated cell wall changes in the epidermal layer represent an important defence reaction both for nonhost and for quantitative host resistance against nonadapted wheat and host-adapted barley powdery mildew pathogens, respectively.

Aphids are a problem in pepper cultivation, causing direct damage as well as acting as vectors for viruses. Resistance to aphids is therefore a desired trait in pepper varieties, but resistant varieties are not available yet. Our research is focused on finding sources of aphid resistance and elucidation of the genetics and mechanism of resistance. In our poster we present some of our results: an efficient bioassay with Myzus persicae and a comparison of the performance of a collection of Capsicum accessions in this biotest.

Mitogen-activated protein kinases (MAPKs) have been shown to act as key regulators of stress responses in model plant and crop species. So far, however, the MAPK family has not been systematically studied in barley. Herein, we identified 16 HvMAPKs (Hv—Hordeum vulgare) based on computational analysis of barley transcriptomics and genomics databases. HvMAPKs contain all canonical MAPK domains, except for HvMPK2, which lacks a MAPK domain signature. In addition, five HvMAPKs harbor TEY and ten HvMAPKs harbor TDY dual phosphorylation motif in the activation loop. Interestingly, HvMPK2 contains a MEY instead of TEY phosphorylation motif. We classified HvMAPKs into four major plant MAPK clades based on phylogeny reconstruction and anchored all HvMAPK genes to five out of seven barley chromosomes. Furthermore, we inoculated seedlings of susceptible barley line L94 and its isolines L94-Rph3 and L94-Rph7 with rust fungus Pucciniahordei and analyzed the expression of 16 HvMAPK genes using qRT-PCR at 1–4.5 days post inoculation. In total, six HvMAPK genes exhibited significantly altered expression by P. hordei infection. The expression of HvMPK5, HvMPK6, HvMPK7 and HvMPK12 (set one genes) was strongly induced especially during effector-triggered immunity (ETI), whereas the expression of HvMPK2 and HvMPK17 (set two genes) was specifically downregulated during ETI. Yet the expression of HvMPK8 was also specifically but weakly downregulated during ETI. Overall, the expression patterns suggest that set one genes positively regulate ETI in barley–P. hordei pathosystem, whereas set two genes negatively regulate ETI and/or programmed cell death in this pathosystem.

Foraging success of predators profoundly depends on reliable and detectable cues indicating the presence of their often inconspicuous prey. Carnivorous insects rely on chemical cues to optimize foraging efficiency. Hyperparasitoids that lay their eggs in the larvae or pupae of parasitic wasps may find their parasitoid hosts developing in different herbivores. They can use herbivore-induced plant volatiles (HIPVs) to locate parasitized caterpillars. Because different herbivore species induce different HIPV emission from plants, hyperparasitoids may have to deal with large variation in volatile information that indicates host presence. In this study, we used an ecogenomics approach to first address whether parasitized caterpillars of two herbivore species (Pieris rapae and P. brassicae) induce similar transcriptional and metabolomic responses in wild Brassica oleracea plants and, second, whether hyperparasitoids Lysibia nana are able to discriminate between these induced plant responses to locate their parasitoid host in different herbivores under both laboratory and field conditions. Our study revealed that both herbivore identity and parasitism affect plant transcriptional and metabolic responses to herbivory. We also found that hyperparasitoids are able to respond to HIPVs released by wild B. oleracea under both laboratory and field conditions. In addition, we observed stronger attraction of hyperparasitoids to HIPVs when plants were infested with parasitized caterpillars. However, hyperparasitoids were equally attracted to plants infested by either herbivore species. Our results indicate that parasitism plays a major role in HIPV-mediated plant–hyperparasitoid interactions. Furthermore, these findings also indicate that plant trait-mediated indirect interaction networks play important roles in community-wide species interactions.

Spathoglottis is a native terrestrial orchid that attracting horticultural interest as a landscaping plant. Distinguishing orchid at species level based on morphological characteristics is unconvincing as some characteristic may sensitive to environmental. Therefore, molecular characterization could be an alternative method in characterizing Spathoglottis species. Amplified Fragment Length Polymorphism (AFLP) marker was selected to characterize the Spathoglottis species. Among 56 AFLP primer combinations tested on Spathoglottis plicata, only eight primer combinations gave clear scorable polymorphic bands. A total of 60 accessions of Spathoglottis species, hybrid and outgroup (Dendrobium) were analysed using the eight primer combinations and generated 891 polymorphic bands with 98.41% in average. The AFLP patterns showed that the Spathoglottis species sampled were clearly different.

Background: Plants have developed a variety of mechanisms to counteract aphid attacks. They activate their defences by changing the expression of specific genes. Previously we identified an activation tag mutant of Arabidopsis thaliana on which Myzus persicae population development was reduced. Activation tag mutants are gain-of-function in which the expression of a gene is increased by the insertion of the Cauliflower mosaic virus 35S enhancer that acts on the natural promoter. By further characterizing this previously identified mutant we identified a gene that reduces performance of M. persicae and also provided clues about the mechanism involved. Results: We show that SKU5 SIMILAR 13 (SKS13), a gene whose expression in wild type plants is restricted to pollen and non-responsive to M. persicae attack, is overexpressed in the A. thaliana mutant showing reduced performance of M. persicae. Monitoring M. persicae feeding behaviour on SKS13 overexpressing plants indicated that M. persicae have difficulties feeding from the phloem. The constitutive expression of SKS13 results in accumulation of reactive oxygen species, which is possibly regulated through the jasmonic acid pathway. The enhanced resistance is not aphid species specific as also the population development of Brevicoryne brassicae was affected. Conclusions: We demonstrate that constitutive expression in leaves of the pollen-specific gene SKS13 can enhance plant defence, resulting in a reduction of M. persicae population development and also decreases the transmission of persistent viruses. Overexpression of SKS13 in A. thaliana also affects B. brassicae and possibly other phloem feeding insects as well. Identifying genes that can enhance plant defence against insects will be important to open up new avenues for the development of insect resistant crop plants.

Downy mildew (Bremia lactucae) in lettuce (Lactuca sativa) is a devastating foliar disease causing high losses in lettuce cultivation. The wild lettuce and nonhost species, Lactuca saligna, is absolute resistant to downy mildew and cross-fertile with L. sativa, albeit with a low success rate and occasional reduced fertility and/or vitality in later inbred generations. This exceptional availability of hybrid plant offsprings creates a unique opportunity to study nonhost resistance by a genetic approach. The L. saligna nonhost resistance genes might be more durable than the classical monogenic race-specific R genes that are mainly used in lettuce breeding. The identification of genes conferring nonhost resistance is a crucial step in its understanding and usage in breeding. In this thesis the quantitative resistances of three backcross introgression lines (BILs), carrying an individual 30 to 50 cM long introgression segment from L. saligna in a L. sativa background, were fine mapped. Disease evaluation of sub-BILs with smaller introgression segments revealed that the resistance of all three BILs was explained by 17 sub-QTLs with a smaller and plant stage dependent effect, some segments reducing, others even promoting downy mildew infection. Further the potential of stacking quantitative resistances of eight BILs per combinations of two was tested under field conditions. Only three out of ten double-combinations resulted in an increased resistance level compared to their parental individual lines, from which one had additive and two had epistatic interactions between the introgressions. As the studies on individual QTL effects of BILs did not reveal potential genetic interactions that could explain the complete resistance of L. saligna, a novel approach was set out to search for indications of epistatic interactions. ‘Selective genotyping’ was applied on the phenotypic disease extremes of large F2 offsprings, in which multi-locus interactions between L. saligna alleles are still prevalent. In a kind of bulked segregant analysis approach four major resistance regions were identified. Preliminary results showed epistatic interactions between the regions on Chromosome 6 and 1 and between Chromosome 6 and 7. During the development of sub-BILs, a digenic hybrid incompatibility was observed: plants carrying a L. saligna segment on Chromosome 6 always required a L. saligna segment on Chromosome 4. Segregation analysis suggested a prezygotic reproductive barrier by non-transmission of one specific hybrid gametophyte (male and female). In cooperation with the research group of Guido van den Ackerveken of University Utrecht a lettuce germplasm screening was conducted for candidate downy mildew effector proteins, which interact with resistance genes in lettuce and trigger a defence response. One of two responsive effector proteins, ‘BLG01’, triggered a hypersensitive cell death response in most tested L. saligna accessions and its response was mapped on Chromosome 9. Despite the complex interactions between resistance QTLs, this thesis research has delivered many insights that are important steps forward towards understanding the incompatible interaction between B. lactucae and L. saligna and its future application in resistance breeding.

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.