Partial Resistance Genes Research Articles

Diversity of new Russian bread wheat cultivars according to leaf rust resistance genes

Background. Cultivation of resistant cultivars is an effective method of wheat protection against leaf rust. The purpose of this work was to characterize the juvenile leaf rust resistance of bread wheat cultivars listed in the State Register for Selection Achievements in 2021 and identify their Lr genes using molecular markers.Materials and methods. The material included 18 cultivars of winter bread wheat and nine spring ones. Juvenile resistance in the seedling phase was assessed with two test clones (kLr9 и kLr19) and the Krasnodar population of Puccinia triticina Erikss. Molecular markers were used to identify 18 Lr genes.Results and discussion. A high level of resistance (score 0 or 0;) was shown by cvs. ‘Khamdan’, ‘Sharm’ and ‘Omskaya 44’; moderate resistance (score 2, 2+) by ‘Albidum 2030’. Reactions of ‘Polina’, ‘Rossyp’, ‘Status’, ‘Balkysh’ and ‘Bogema’ were variable. The studied cultivars did not contain juvenile genes Lr9, Lr24, Lr25, Lr28, Lr29, Lr39, Lr47 or Lr66 and adult plant resistance genes Lr21 and Lr35. Markers of identifiable genes were not detected in cv. ‘Sharm’, highly resistant to leaf rust. ‘Khamdan’ had an ineffective Lr10 gene and a partial resistance gene Lr34, which offered no protection in the seedling stage. These cultivars seem to contain additional resistance genes. A high level of resistance to leaf rust in ‘Omskaya 44’ is provided by a combination of the Lr19, Lr26, Lr1 and Lr3 genes. In ‘Nemchinovskaya 85’, the partially effective adult plant resistance gene Lr37 was identified. In other tested cultivars, Lr1, Lr3, Lr10, Lr26 and Lr34 were widely represented.

Characterization of Six Partial Resistance Genes and One Quantitative Trait Locus to Blast Disease Using Near Isogenic Lines with a Susceptible Genetic Background of Indica Group Rice (Oryza sativa)

Seven near isogenic lines (NILs) for six partial blast-resistance genes— Pi35, pi21, Pi37(t)( Pi37-KRIL17), Pb1, and Pi34 (two: Pi34-Chubu32 and Pi34-Chugoku40, originating from different Japonica Group rice lines, ‘Chubu 32’ and ‘Chugoku 40’, respectively)—and one quantitative trait locus (QTL), PiPHL9, derived from Japonica Group line ‘Hokkai PL9’, were developed in rice ( Oryza sativa L.). These NILs have the genetic background of an Indica Group susceptible line ‘US-2’, which does not harbor complete resistance genes and can clarify the effects of partial resistance genes and the QTL. These NILs and US-2 were used to determine the effects of the partial resistance genes and the QTL based on the results of an inoculation test for leaf blast using international standard differential blast isolates in the young seedling stage and a natural infection test in the mature stage after heading at a blast field. The NILs produced mainly moderate reactions in the inoculation test and rarely exhibited “resistant” and “susceptible” reactions. Each of the partial resistance genes and the QTL had different effects in panicle blast. Two genes, Pi35 and Pb1, were the most effective with respect to resistance, followed by Pi37-KRIL17. Pi34-Chugoku40 was the weakest. The effects of pi21, Pi34-Chubu32, and PiPHL9 varied among cultivation seasons and could be easily affected by environmental conditions. This is the first report clarifying the effects of partial resistance genes without the major complete genes, which will be helpful for advanced genetic and pathological studies and as a source of genes for rice breeding. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Adult Genes Evaluation of Ethiopian Durum Accessions for Resistance to Stem Rust (Puccinia graminis f.sp. tritici)

The horizontal resistance is effective against broad range of pathogen races and even reduces the costs of fungicides for controlling.The objective of present study is based on the field assesment of adult resistance genes in Ethiopia durum wheat accessions for resistance to stem rust (Puccinia graminis f.sp. tritici). The 142 durum wheat accessions were obtained from the Ethiopian Biodiversity Institute and screening for stem rust in Debrezeit agricultural research experimental fields using alpha lattice design. The bulk of races (TTKSK (Ug99), TTTTF, TTRTF, JRCQC, TKTTF) inoculated during stem elongation stage. The disease assessment started the first symptom of seen in infector rows. In the field, durum accessions were examined utilizing for slow rust parameters. Accordingly, to that the 23 accessions were identified having low value of terminal rust resistance, low average coefficient of infection and low area under disease progress curve. The grain yield is negative and highly siginificant associated with slow rusting parameters. These accessions considered as having adult resistance genes with high partial resistance genes and important for further resistance breeding. Keywords: Accessions, Area under disease progress curve, Average cofficient of infection, Puccinia graminis f.sp. tritici, Terminal rust resistance DOI: 10.7176/JBAH/12-17-02 Publication date: September 30 th 2022

High-resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is responsible for significant yield losses worldwide, which can be minimized by the deployment of Pst resistance genes. Yr78 is an adult plant partial-resistance gene that has remained effective against the post-2000 virulent Pst races. In this study, we generated a high-resolution map of Yr78 based on 6,124 segregating chromosomes. We mapped Yr78 within a 0.05-cM interval on the short arm of chromosome 6B, which corresponds to an 11.16 Mb region between TraesCS6B02G116200 and TraesCS6B02G118000 in the 'Chinese Spring' Ref Seq. v1.1 genome. This interval is likely larger because it includes the unassembled NOR-B2 region, which may have contributed to the low recombination rate detected in this region. The Yr78 candidate region includes 15 genes that were prioritized for future functional studies based on their annotated function and polymorphisms between susceptible and resistant genotypes. Using exome capture data, we identified five major haplotypes in the candidate gene region, with the H1 haplotype associated with Yr78. The H1 haplotype was not detected in tetraploid wheat (Triticum turgidum L.) but was found in ∼30% of the common wheat cultivars (Triticum aestivum L.), suggesting that the associated resistance to stripe rust may have favored the selection of this haplotype. We developed two diagnostic molecular markers for the H1 haplotype that will facilitate the deployment of Yr78 in wheat breeding programs.

High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis

High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis

Distribution and Nucleotide Diversity of Yr15 in Wild Emmer Populations and Chinese Wheat Germplasm.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat. The wild emmer gene, Yr15 (Wtk1), which confers a strong broad-spectrum resistance to Pst isolates, is composed of kinase and pseudokinase domains. The analysis of 361 wild emmer accessions from a wide range of natural habitats confirms that functional Wtk1 is distributed mainly along a narrow axis from Mt. Carmel to Mt. Hermon regions, in the northern part of Israel, where environmental conditions are favorable to the onset of stripe rust. An analysis of full-length Wtk1 DNA sequences from 49 wild emmer accessions identified three haplotypes and extremely low nucleotide diversity (π = 0.00002). The sequence diversity of Wtk1 is 9.5 times lower than that of broad-spectrum partial resistance gene Yr36 (π = 0.00019), and both are in sharp contrast to the high level of nucleotide diversity previously reported for race-specific resistance genes (e.g., Lr10 and Pm3). However, the nonfunctional wtk1 sequences possess high level of nucleotide diversity (π = 0.07). These results may reflect the different resistance mechanisms and the different evolutionary processes that shaped these resistance genes. Yr15 was absent in 189 Chinese wheat landraces and was present in only 1.02% of the 583 tested modern Chinese wheat cultivars. These results corroborate our previous results showing that Yr15 was absent in 94% of a worldwide collection of 513 wheat cultivars, therefore indicating the importance of Yr15 in wheat stripe rust resistance breeding programs in China and elsewhere around the globe.

Genome-wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice.

SummaryBecause of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C‐RDP‐II), which contains 584 rice accessions and are genotyped with 700 000 single‐nucleotide polymorphism (SNP) markers. The C‐RDP‐II accessions were inoculated with three blast strains collected from different rice‐growing regions in China. Genome‐wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide‐binding site leucine‐rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up‐regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR‐Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non‐strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.

Genetic variation of blast (Pyricularia oryzae Cavara) resistance in rice (Oryza sativa L.) accessions widely used in Kenya.

A total of 47 rice accessions collected from Kenya were investigated the genetic variations and classified into two cluster groups, A and B, by polymorphism data of 65 simple sequence repeat (SSR) markers. Clusters A and B corresponded to Japonica and Indica Groups, respectively. The number of Japonica Group accessions was limited in comparison with those of the Indica Group. Based on their patterns of reaction to standard differential blast isolates (SDBIs), these accessions and 57 control cultivars including differential varieties and several accessions harboring partial resistance genes were classified again into three cluster groups: Ia (high resistance), Ib (intermediate resistance) and II (susceptible). The rice accessions from Kenya were classified only into groups Ia and Ib. The accessions from Kenya were finally classified into three categories, A-Ia, B-Ia and B-Ib, based on the two classifications of polymorphism of SSR markers and resistance. The Indica Group accessions had wider genetic variation for blast resistance than did the Japonica Group accessions. The three leading cultivars (Basmati 217, Basmati 370 and ITA 310) categorized into Cluster group Ia were susceptible to some SDBIs from Kenya. The genetic variation for blast resistance in Kenya was demonstrated as the first report using SDBIs.

Relationship between the number of partial resistance genes and the response to leaf rust in wheat genotypes

Relationship between the number of partial resistance genes and the response to leaf rust in wheat genotypes

Review of combinations of experimental and computational techniques to identify and understand genes involved in innate immunity and effector-triggered defence.

The innate immune system includes a first layer of defence that recognises conserved pathogen-associated molecular patterns that are essential for microbial fitness. Resistance (R) gene-based recognition of pathogen effectors, which function in modulation or avoidance of host immunity, activates a second layer of plant defence. In this review, experimental and computational techniques are considered to improve understanding of the plant immune system. Biocomputation contributes to discovery of the molecular genetic basis of host resistance against pathogens. Sequenced genomes have been used to identify R genes in plants. Resistance gene enrichment sequencing based on conserved protein domains has increased the number of R genes with nucleotide-binding site and leucine-rich repeat domains. Network analysis will contribute to an improved understanding of the innate immune system and identify novel genes for partial disease resistance. Machine learning algorithms are expected to become important in defining aspects of the immune system that are less well characterised, including identification of R genes that lack conserved protein domains.

Characterization of Lr75: a partial, broad-spectrum leaf rust resistance gene in wheat.

Here, we describe a strategy to improve broad-spectrum leaf rust resistance by marker-assisted combination of two partial resistance genes. One of them represents a novel partial adult plant resistance gene, named Lr75. Leaf rust caused by the fungal pathogen Puccinia triticina is a damaging disease of wheat (Triticum aestivum L.). The combination of several, additively-acting partial disease resistance genes has been proposed as a suitable strategy to breed wheat cultivars with high levels of durable field resistance. The Swiss winter wheat cultivar 'Forno' continues to show near-immunity to leaf rust since its release in the 1980s. This resistance is conferred by the presence of at least six quantitative trait loci (QTL), one of which is associated with the morphological trait leaf tip necrosis. Here, we used a marker-informed strategy to introgress two 'Forno' QTLs into the leaf rust-susceptible Swiss winter wheat cultivar 'Arina'. The resulting backcross line 'ArinaLrFor' showed markedly increased leaf rust resistance in multiple locations over several years. One of the introgressed QTLs, QLr.sfr-1BS, is located on chromosome 1BS. We developed chromosome 1B-specific microsatellite markers by exploiting the Illumina survey sequences of wheat cv. 'Chinese Spring' and mapped QLr.sfr-1BS to a 4.3cM interval flanked by the SSR markers gwm604 and swm271. QLr.sfr-1BS does not share a genetic location with any of the described leaf rust resistance genes present on chromosome 1B. Therefore, QLr.sfr-1BS is novel and was designated as Lr75. We conclude that marker-assisted combination of partial resistance genes is a feasible strategy to increase broad-spectrum leaf rust resistance. The identification of Lr75 adds a novel and highly useful gene to the small set of known partial, adult plant leaf rust resistance genes.

The Nitrogen Induced Sensitivity to Rice Blast Disease Depends on Partial Resistance Genes

The Nitrogen Induced Sensitivity to Rice Blast Disease Depends on Partial Resistance Genes

Genetics of Partial Resistance to Leaf Rust (Puccinia triticina) in Bread Wheat (Triticum aestivum)

The genetics of partial resistance to leaf rust (Puccinia triticina Erikss. & Henn.) in bread wheat (Triticum aestivum L. em Thell) was investigated in a nine-parent diallel (excluding reciprocals) using area under disease progress curve (AUDPC) and final disease severity (FDS) in the F1 and F2 generations. Test material consisted of slow rusting and susceptible lines. The Vr–Wr graphs exhibited partial dominance for FDS and complete dominance for AUDPC (F1 and F2 generations). Parents CPAN1796, HD2329, NW1014 and MACS2496 had preponderance of minor genes for partial resistance, whereas susceptible parents SONALIKA and HS1138-6-4 showed the absence of minor genes for both AUDPC and FDS (F1 and F2 generations). Variations due to additive and dominance genetic variances were significant for both AUDPC and FDS (F1 and F2 generations). The estimate of 1–3 minor gene(s) in the slow rusting parents may be responsible for race non-specific adult plant resistance. Since narrow-sense heritability for both AUDPC and FDS was moderate in both F1 and F2, success in selecting desirable lines with partial resistance to leaf rust in early segregating generations can easily be achieved. The parents CPAN1796, NW1014, HD2329, PBW373 and RAJ3077 with low AUDPC and FDS having partial resistance either due to Lr34 and/or minor genes were identified as good general combiners. The parents identified in the study can be used in breeding program for developing high-yielding cultivars with durable leaf rust resistance.

The cytochrome P450 CYP6P4 is responsible for the high pyrethroid resistance in knockdown resistance-free Anopheles arabiensis

Pyrethroid insecticides are the front line vector control tools used in bed nets to reduce malaria transmission and its burden. However, resistance in major vectors such as Anopheles arabiensis is posing a serious challenge to the success of malaria control.Herein, we elucidated the molecular and biochemical basis of pyrethroid resistance in a knockdown resistance-free Anopheles arabiensis population from Chad, Central Africa. Using heterologous expression of P450s in Escherichia coli coupled with metabolism assays we established that the over-expressed P450 CYP6P4, located in the major pyrethroid resistance (rp1) quantitative trait locus (QTL), is responsible for resistance to Type I and Type II pyrethroid insecticides, with the exception of deltamethrin, in correlation with field resistance profile. However, CYP6P4 exhibited no metabolic activity towards non-pyrethroid insecticides, including DDT, bendiocarb, propoxur and malathion. Combining fluorescent probes inhibition assays with molecular docking simulation, we established that CYP6P4 can bind deltamethrin but cannot metabolise it. This is possibly due to steric hindrance because of the large vdW radius of bromine atoms of the dihalovinyl group of deltamethrin which docks into the heme catalytic centre.The establishment of CYP6P4 as a partial pyrethroid resistance gene explained the observed field resistance to permethrin, and its inability to metabolise deltamethrin probably explained the high mortality from deltamethrin exposure in the field populations of this Sudano-Sahelian An. arabiensis. These findings describe the heterogeneity in resistance towards insecticides, even from the same class, highlighting the need to thoroughly understand the molecular basis of resistance before implementing resistance management/control tools.

Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei.

Key messageRphq2, a minor gene for partial resistance toPuccinia hordei, was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes ofrphq2andRphq2barley 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.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2627-5) contains supplementary material, which is available to authorized users.

Genome-Wide Association Mapping for Leaf Tip Necrosis and Pseudo-black Chaff in Relation to Durable Rust Resistance in Wheat.

The partial rust resistance genes Lr34 and Sr2 have been used extensively in wheat (Triticum aestivum L.) improvement, as they confer exceptional durability. Interestingly, the resistance of Lr34 is associated with the expression of leaf tip necrosis (LTN) and Sr2 with pseudo-black chaff (PBC). Genome-wide association mapping using CIMMYT's stem rust resistance screening nursery (SRRSN) wheat lines was done to identify genotyping-by-sequencing (GBS) markers linked to LTN and PBC. Phenotyping for these traits was done in Ithaca, New York (fall 2011); Njoro, Kenya (main and off-seasons, 2012), and Wellington, India (winter, 2013). Using the mixed linear model (MLM), 18 GBS markers were significantly associated with LTN. While some markers were linked to loci where the durable leaf rust resistance genes Lr34 (7DS), Lr46 (1BL), and Lr68 (7BL) were mapped, significant associations were also detected with other loci on 2BL, 5B, 3BS, 4BS, and 7BS. Twelve GBS markers linked to the Sr2 locus (3BS) and loci on 2DS, 4AL, and 7DS were significantly associated with PBC. This study provides insight into the complex genetic control of LTN and PBC. Further efforts to validate and study these loci might aid in determining the nature of their association with durable resistance.

Genetics of Partial Resistance to Leaf Rust (<i>Puccinia triticina</i> Erikss. & Henn.) in Bread Wheat (<i>Triticum aestivum</i> L. em Thell)

The genetics of partial resistance to leaf rust ( Puccinia triticina Erikss. & Henn.) in bread wheat ( Triticum aestivum L. em Thell) was investigated in a nine-parent diallel (excluding reciprocals) using area under disease progress curve (AUDPC) and final disease severity (FDS) in the F 1 and F 2 generations. Test material consisted of slow rusting and susceptible lines. The Vr-Wr graphs exhibited partial dominance for FDS and complete dominance for AUDPC (F 1 and F 2 generations). Parents CPAN1796, HD2329, NW1014 and MACS2496 had preponderance of minor genes for partial resistance, whereas, susceptible parents SONALIKA and HS1138-6-4 showed absence of minor genes for both AUDPC and FDS (F 1 and F 2 generations). Variations due to additive and dominance genetic variances were significant for both AUDPC and FDS (F 1 and F 2 generations). The estimate of 1-3 minor gene(s) in the slow rusting parents may be responsible for race non-specific adult plant resistance. Since narrow sense heritability for both AUDPC and FDS, was moderate in both F 1 and F 2 , success in selecting desirable lines with partial resistance to leaf rust in early segregating generations can easily be achieved. The parents CPAN1796, NW1014, HD2329, PBW373 and RAJ3077 with low AUDPC and FDS having partial resistance either due to Lr34 and/ or minor genes were identified as good general combiners. The parents identified in the study can be used in breeding program for developing high yielding cultivars with durable leaf rust resistance.

Pyramiding of partial disease resistance genes has a predictable, but diminishing, benefit to efficacy

Partial resistance genes often need to be ‘pyramided’ into a crop cultivar to obtain commercially acceptable levels of disease resistance. Analysis of data from four different wheat mapping populations, segregating for partial resistance to four contrasting foliar pathogens, showed a diminishing benefit to disease control from increasing the numbers of resistance loci in wheat lines. To test whether a general function could describe the efficacy benefit from pyramiding, a simple multiplicative survival model (MSM) was used to predict disease severities on mapping population lines carrying various combinations of two, three or four resistance loci. The effectiveness of each resistance locus was expressed as the disease severity in lines carrying resistance alleles at one locus, as a proportion of the severity in lines carrying no detectable resistance alleles. The predicted severity from any given combination of multiple resistance loci was calculated as the product of the proportional severities for the relevant single loci. A regression line fitted to transformed observed against predicted values explained 93% of the variation, with a slope and intercept not significantly different from 1 and 0, respectively. MSM may therefore provide a simple method to test contrasting types of partial resistance and search for synergistic combinations. The analysis suggests that diminishing returns are a general feature of partial resistance to foliar pathogens in wheat, a finding that is likely to apply to other crop pathosystems. Identifying and combining ever more QTL is likely to provide limited gains. The consequences of these findings for QTL analysis are described.

Attenuated colicin-based screening to discover and create novel resistance genes

I formulated a systematic approach to screen for colicin resistance-associated genes by using an attenuated colicin mutant and demonstrated its utility in a screen of genes related to colicin E5 resistance. Screening of an Escherichia coli genome library revealed rstA as a partial resistance gene to colicin E5. Transcript expression of BtuB and OmpF, proteins responsible for translocation of nuclease E colicins, was clearly inhibited in an rstA-overexpressing strain. In addition, the tatA::recN fusion gene provides resistance to an attenuated colicin E5 mutant. Improving tatA::recN by directed coevolution, I created a novel gene with enhanced resistance to colicin E5 and concluded that attenuated colicin-based screening is useful for the discovery and creation of novel colicin resistance-associated genes.

Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of 'Président Roulin' against Venturia inaequalis.

BackgroundScab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple. While a few scab resistance genes (R genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance, supposed to be more durable, are still unknown. This study aims to investigate the molecular mechanisms involved in the partial resistance of the old Belgian apple cultivar ‘Président Roulin’ against V. inaequalis.ResultsA global gene expression analysis was conducted in ‘Président Roulin’ (partially resistant) and in ‘Gala’ (susceptible) challenged by V. inaequalis by using the cDNA-AFLP method (cDNA-Amplified Fragment Length Polymorphism). Transcriptome analysis revealed significant modulation (up- or down-regulation) of 281 out of approximately 20,500 transcript derived fragments (TDFs) in ‘Président Roulin’ 48 hours after inoculation. Sequence annotation revealed similarities to several genes encoding for proteins belonging to the NBS-LRR and LRR-RLK classes of plant R genes and to other defense-related proteins. Differentially expressed genes were sorted into functional categories according to their gene ontology annotation and this expression signature was compared to published apple cDNA libraries by Gene Enrichment Analysis. The first comparison was made with two cDNA libraries from Malus x domestica uninfected leaves, and revealed in both libraries a signature of enhanced expression in ‘Président Roulin’ of genes involved in response to stress and photosynthesis. In the second comparison, the pathogen-responsive TDFs from the partially resistant cultivar were compared to the cDNA library from inoculated leaves of Rvi6 (HcrVf2)-transformed ‘Gala’ lines (complete disease resistance) and revealed both common physiological events, and notably differences in the regulation of defense response, the regulation of hydrolase activity, and response to DNA damage. TDFs were in silico mapped on the ‘Golden Delicious’ apple reference genome and significant co-localizations with major scab R genes, but not with quantitative trait loci (QTLs) for scab resistance nor resistance gene analogues (RGAs) were found.ConclusionsThis study highlights possible candidate genes that may play a role in the partial scab resistance mechanisms of ‘Président Roulin’ and increase our understanding of the molecular mechanisms involved in the partial resistance against apple scab.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1043) contains supplementary material, which is available to authorized users.