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Recently, Elsinoë piri has become an important pathogen in unsprayed and organic apple orchards. The increasing demand for organic apples as well as the limited use of fungicides imposed by European legislation has turned this pathogen, which has been known for over a century in Europe, into a resurgent phytosanitary threat. It also represents a new trait to be taken into account in apple breeding programmes. As E. piri is extremely difficult to isolate and causes symptoms that can be confused with those caused by other pathogens, a quantitative PCR (qPCR) test has been developed based on the internal transcribed spacer (ITS) region of the rDNA gene. This test, which displays a low limit of detection, allows the early detection of the fungus in apple leaves. As a quantitative method, it is a promising tool for breeding purposes as it can be used on leaves to assess the level of quantitative resistance of apple cultivars to the disease. The molecular test is also useful to gain knowledge on the epidemiology of this re-emerging fungal disease. Spore trapping conducted in 2015, 2016 and 2020 using Rotorod devices and the qPCR test showed that airborne inoculum is released at the end of the growing season. Tests were also carried out to demonstrate that the pathogen was detected in buds during winter. A comparison of 18 E. piri isolates based on the sequencing of five genome regions highlighted a high genotypic diversity. All these isolates were detected with the qPCR test developed in this study.

Despite the growing concerns over the damages and unsustainability of conventional agriculture, arable farmers struggle to convert to organic cropping practices. In wheat farming, the lack of cultivars adapted to organic cropping has prompted a search for alternatives to better cope with unpredictability and stress. In that respect, heterogeneous material (HM) has attracted a lot of attention for its good performances and yield stability across years and environments. These benefits are thought to arise from facilitative plant interactions brought forth by intraspecifc diversity, but much remains to be known about the mechanisms at play as well as their interactions with the other elements of the cropping system. Here, we review the literature on plant interactions within organic bread wheat crops through the successive scopes of (i) heterogeneous material, (ii) plant density, and (iii) their interaction. Our major findings are as follows: (1) optimizing heterogeneous material performance and evolutionary trajectories grossly amounts to tipping the balance between competitive and facilitative plant interactions toward the latter. (2) The stress gradient hypothesis applies to the competition/facilitation balance within HM: The more stressful the conditions, the more facilitation happens. (3) Plant density also affects this balance, and the relationship between net facilitation and plant density in HM follow a humped curve. (4) Therefore, the optimal plant density range for HM should be both narrower and lower than for pure lines, and also harder to predict. (5) High-tillering, high individual yielding plant types should probably be aimed for in HM, for two reasons: first, they perform better at the lower-than-the-recommendations plant densities at which HM are expected to best express their potential. Second, optimal plant densities of such plant types are more stable across environments, which should increase the probability of falling within the narrower optimal plant density range of HM, particularly in unpredictable and/or stressed environments.

In the framework of celiac disease, this research aims at evaluating the reactivity of 195 wheat accessions and 240 spelt accessions to A1 and G12 monoclonal antibodies. A great variability in reactivity was found among the accessions of both subspecies. On average, spelt showed very slightly higher reactivity than wheat but accessions with low reactivity were encountered in both subspecies. In both wheat and spelt, there was no significant difference in the level of reactivity between varieties and landraces. Similarly, there was no significant difference in reactivity between old, mid and new varieties of wheat. In contrast, new spelt varieties showed lower levels of reactivity than old and mid ones. No relationship could be established between level of reactivity, protein content and the Zeleny index. This research did not establish a link between the breeding strategies for baking quality improvement and A1-G12 antibodies reactivity.

The effects of drought on water relations, gas exchanges and epigenetic alterations were studied in two faba bean ( Vicia faba L.) genotypes with contrasting levels of drought tolerance. The drought-tolerant Bachar genotype was less affected by water deficit in comparison with the drought-sensitive F177 in terms of photosynthetic function and water status in plants as indicated by less reduction in net photosynthesis (A), transpiration rate (E), stomatal conductance (gs) and relative water content (RWC). In this study, the methylation-sensitive amplification polymorphism (MSAP) technique was used to profile the DNA methylation patterns of Bachar and F177 under drought and control conditions. Overall, the amount of methylation was higher in leaves than in roots and the contribution of fully methylated loci was always higher than that of hemimethylated loci. Under control and drought treatment, the total methylation level in leaf tissues was 37.43% and 30.62% in Bachar, 41.23% and 38.16% in F177, indicating a decrease of 6.81% and 3.07% in Bachar and F177 respectively, due to drought exposure. The results revealed that DNA methylation in root tissues was decreased by 3.63% (from 23.43% to 19.80%) in Bachar and increased by 0.66% (from 16.53% to 17.19%) in F177 under drought stress. Differentially displayed DNA fragments in MSAP profiles were cloned and sequenced. A sequence analysis identified six potentially drought stress-related differentially methylated regions (DMRs). Five of these have high homology to previously identified or putative proteins found in other plants, including lipoxygenase ( LOX ), calcium-dependent protein kinase ( CDPK ), ABC transporter family ( ABC ), glycosyl hydrolase ( GH ) and phosphoenolpyruvate carboxylase ( PEPC ) and were chosen for further characterization. Quantitative reverse transcription PCR analysis revealed that VfLOX , VfCDPK , VfABC and VfGH varied under drought stress; the expression level of these studied genes was higher in Bachar than in F177. This could suggest their possible role in faba bean drought stress tolerance. Overall, the genome-wide epigenetic changes are probably an important regulatory mechanism for faba bean response to drought and as well to other environmental stresses.

For the first time eight local tomato cultivars collected from four different regions of Morocco were assessed with RAPD and SSR methods. Most of RAPD markers give monomorphic banding profiles. Only OPU03 marker showed a total of 4 polymorphic amplicons out of 8 recorded in FIGUIG2 cultivar. The analysis with SSR markers gives more polymorphism. The number of alleles amplified assessed from 2 to 5 alleles among cultivars. The similarity matrix subjected by the unweighted pairgroup arithmetic method (UPGMA) clustering grouped the cultivars in four groups where FIGUIG2 cultivar formed a separate and more distant cluster. In addition this cultivar holds the very high percentage of uniformity (99%) indicating that is an homogeneous traditional cultivar with high purity. This genotype can be conserved and used in breeding programs. More traditional Moroccan cultivars must be collected in order to determine their genetic structure.

Drought is a major environmental stress that limits faba bean growth, leading to considerable reduction in their productivity. Two genotypes (Giza 3 and Hara) were evaluated under three water treatments (90%, 60% and 30% field capacity). The results showed that water stress affects negatively chlorophyll fluorescence parameters at different levels of water deficit and the variations of Fv/Fm, ΦPSII and electron transport rate in Giza 3 were largely higher than those in Hara. Drought preferentially enhanced the activities of superoxide dismutase, catalase and guaiacol peroxidase whereas it did not affect ascorbate peroxidase activity. Real-time reverse transcriptase-polymerase chain reaction results demonstrated that the expression of aquaporin (PIP), myeloblastosis (MYB), nine-cis-epoxycarotenoid dioxygenase, late embryogenesis abundant, dehydrins (Dhn), heat shock protein (HSP) and APETALA2/ethylene-responsive factor was modified in response to drought conditions and that all genes were different...

Assessment of genetic diversity is an essential component in germplasm characterization and utilization. Molecular markers serve as a valuable tool to assess the genetic variation and germplasm identification, which play a key role for faba (Vicia faba L.) bean breeding. In this study, we analyzed the genetic diversity of faba bean accessions based on simple sequence repeats (SSRs) and morphological traits. Forty-six faba bean accessions, originating from different countries and from the ICARDA breeding program, were evaluated by using 15 morphological and agronomic traits and 17 simple sequence repeat (SSR) loci. Significant differences among accessions for the 15 morphological descriptors were observed. Analysis by SSR markers showed a high genetic diversity among the accessions: All SSRs showed polymorphism, and 101 alleles were revealed for all accessions. The number of alleles at each locus ranged from 2 to 10, with an average of 5.94 alleles per marker, and the polymorphic information content (PIC) values ranged from 0.38 to 0.84 with a mean of 0.69. Expected heterozygosity (He), observed heterozygosity (Ho), unbiased expected heterozygosity (UHe), and Shannon’s information index (I) showed existence of high genetic variation between accessions from different pedigree. Analyses of genetic distance of the accessions separated the accessions into two groups and seven and five subgroups according to morphological and SSR analysis, respectively. Principal component analysis (PCA) of the SSR markers showed that the first two principal components (PCs) explained a total of 43.90 % of the genetic variation and allowed to distinguish three groups of accessions. Regardless of the method of analysis, Tunisian cultivars are grouped together. For the rest of the accessions, the geographical origin did not seem to be the main factor for structuring the variability of the studied accessions. Elite accessions from the ICARDA faba bean program differed from others and clustered together. The results obtained suggested that the faba bean microsatellite markers can be used to efficiently distinguish faba bean genotypes and to estimate their genetic diversity.

Faba bean (Vicia faba L.) ranks fourth in food legume crop production in the world. However, drought is a potential major constraint to faba bean production and improved faba bean cultivars and development of drought-resistant varieties play a key role in enhancing faba bean crop production. In this study, suppression subtractive hybridization (SSH) technique was used to study differential expression in response to water stress and to identify genes involved in molecular mechanism of drought tolerance. A forward subtractive cDNA library induced by water deficit conditions was constructed used Hara faba bean cultivar grown in pots and treated with either well-watered (WW) or water-stressed (WS). A total of 28 clones were identified as drought stress induced. After sequencing, ten unique expressed sequence tags (ESTs) were obtained by clustering and blast analysis which showed homology to known drought responsive genes including heat shock protein (HSP), late embryogenic abundant (LEA), zinc finger protein transcription factors (ZFP), lipid transfer protein (LTP), chlorophyll a/b-binding protein (ChlBP), thioredoxin h (Trx h), and ATP synthase as well as some functionally unknown transcripts. Their expression was characterized in Leaf, root, flower, cotyledon, and stem tissue. Quantitative RT-PCR analysis revealed that eight genes were consistently up-regulated in Hara compared to Giza3 cultivar, known as drought-tolerant and sensitive respectively under water deficit treatment. The expression of six genes was differentially expressed in different stages of water stress faba bean plant. Drought responsive genes showed changed expression patterns, indicating that they may play important roles in faba bean water stress response. Furthermore, these results indicate that drought-induced genes are related to metabolic pathways and genetic regulation of stress and development and can serve as a foundation for future studies to elucidate drought stress mechanisms of faba bean.

The gluten proteins of cereals such as bread wheat (Triticum aestivum ssp. aestivum) and spelt (T. aestivum ssp. spelta) are responsible for celiac disease (CD). The α-gliadins constitute the most immunogenic class of gluten proteins as they include four main T-cell stimulatory epitopes that affect CD patients. Spelt has been less studied than bread wheat and could constitute a source of valuable diversity. The objective of this work was to study the genetic diversity of spelt α-gliadin transcripts and to compare it with those of bread wheat. Genotyping data from 85 spelt accessions obtained with 19 simple sequence repeat (SSR) markers were used to select 11 contrasted accessions, from which 446 full open reading frame α-gliadin genes were cloned and sequenced, which revealed a high allelic diversity. High variations among the accessions were highlighted, in terms of the proportion of α-gliadin sequences from each of the three genomes (A, B and D), and their composition in the four T-cell stimulatory epitopes. An accession from Tajikistan stood out, having a particularly high proportion of α-gliadins from the B genome and a low immunogenic content. Even if no clear separation between spelt and bread wheat sequences was shown, spelt α-gliadins displayed specific features concerning e.g. the frequencies of some amino acid substitutions. Given this observation and the variations in toxicity revealed in the spelt accessions in this study, the high genetic diversity held in spelt germplasm collections could be a valuable resource in the development of safer varieties for CD patients. Electronic supplementary material The online version of this article (doi:10.1007/s11032-016-0569-5) contains supplementary material, which is available to authorized users.

In plants, the myo-inositol-1-phosphate synthase (EC 5.5.1.4; MIPS) is an evolutionarily conserved enzyme protein and catalyzes the synthesis of myo-inositol, which is a central molecule required for cell metabolism and plant growth. A full-length cDNA encoding common bean (Phaseolus vulgaris L.) MIPS (designated Pv_BAT93 MIPS) was isolated from seed of P. vulgaris (cv, BAT93) by rapid amplification of cDNA ends. The cDNA of Pv_BAT93 MIPS comprised 1,873 bp, which encodes 510 amino acids. The Pv_BAT93 MIPS gene was highly homologous with those of other plant species, such as P. vulgaris (cv, Taylor’s Horticultural), Arabidopsis thaliana, Medicago sativa and Glycine max. DNA blot analysis indicated that at least three copies of MIPS are present in the common bean genome. RT-PCR analysis indicated that the Pv_BAT93 MIPS transcripts existed in developing seeds and other common bean tissues, including leaves, flowers, and cotyledons but showed lower levels expression in roots and stems. Real-time quantitative PCR showed that Pv_BAT93 MIPS gene is differentially expressed during common bean seed development. In situ hybridization of developing seeds in the wild type and in the ethyl methanesulfonate mutant showed that expression of Pv_BAT93 MIPS was identified in the embryo tissues, from the globular to late cotyledon stages, confirming a possible involvement of Pv_BAT93 MIPS in common bean seed development.

Interspecific hybridization in the genus Phaseolus, conducted to introgress desired traits into common bean (Phaseolus vulgaris L.), leads to the abortion of immature embryos, usually at early developmental stages. Little is known about the physiological responses of embryo dysfunction in P. vulgaris during the early stages of embryogenesis and the genes that are involved in these responses. Identification of the genes involved in Phaseolus embryogenesis may provide information that will help to understand the molecular basis of Phaseolus embryo dysfunction. To investigate the genes expressed during Phaseolus seed development, we constructed a suppression subtractive hybridization (SSH) library using cDNA from abortive seed development as the driver and those from normal seed development as tester. The differentially expressed cDNA fragments were identified by differential screening. We identified 72 unique ESTs of which we selected 12 candidates on the basis of their redundancy. These candidates were subjected to a validation procedure based on the study of their expression level by real-time PCR. Sequence analysis revealed that most of the differentially expressed genes are related to metabolism and regulation such as protein synthesis. Some genes also encoded transcription factors. These genes showed high mRNA transcript levels in seed tissues and little or no expression in other tissues (root, stem, flower, leaf, and cotyledon). Seven genes were chosen and their expression profile during seed development in P. vulgaris was analyzed by real-time PCR using RNA preparations originating from different seed development stages. This study revealed hitherto unknown genes putatively involved in dicotyledonous embryogenesis, which serve as a starting point for understanding Phaseolus embryogenesis.

Two genotypes of common bean (Phaseolus vulgaris L.) were studied to determine the structural cause of seed abortion in this species. In the non-abortive control (wild-type, cultivar BAT93), the histological analysis revealed a classical pattern of seed development and showed coordinated differentiation of the embryo proper, suspensor, endosperm tissue and seed coat. In contrast, the ethyl methanesulfonate (EMS) mutant (cultivar BAT93) showed disruption in the normal seed development leading to embryo abortion. Aborted embryos from these degenerate seeds showed abnormalities in suspensor and cotyledons at the globular, heart, torpedo and cotyledon stages. Exploring the feasibility of incorporating the available online bioinformatics databases, we identified 22 genes revealing high homology with genes involved in Arabidopsis thaliana embryo development and expressed in common bean immature seeds. The expression patterns of these genes were confirmed by RT–PCR. All genes were highly expressed in seed tissues. To study the expression profiles of isolated genes during Phaseolus embryogenesis, six selected genes were examined by quantitative RT–PCR analysis on the developing embryos of wild-type and EMS mutant plants. All selected genes were expressed differentially at different stages of embryo development. These results could help to improve understanding of the mechanism of common bean embryogenesis.

Hybrid embryos resulting from crosses between Phaseolus species often fail to reach maturity and some combinations frequently abort at early developmental stages. The genetic or molecular basis for these consistent developmental defects is at present not clear. However, an extremely complex genetic system, thought to be caused by major epigenetic changes associated with gene expression changes, has been shown to be active in plant species. We have investigated DNA methylation in two interspecific hybrids, Phaseolus vulgaris × Phaseolus coccineus and its reciprocal crosses, using methylation sensitive amplification polymorphism (MSAP). The potential use of MSAP for detecting methylation variation during embryogenesis in interspecific hybrids is discussed. Significant differences in the DNA methylation patterns were observed in abortive (interspecific hybrids) and non abortive (parental) genotypes. Taken together, our results strongly suggest that generalized alterations in DNA methylation profiles could play a causative role in early interspecific embryo abortion in vivo. A considerable change in the methylation pattern during embryogenesis could be involved in the disruption of the regulation or maintenance of the embryogenesis process of Phaseolus interspecific hybrids. The results also support the earlier hypothesis that DNA methylation is critical for the regulation of plant embryogenesis and gene expression.

Chicory (Cichorium intybus) roots contain high amounts of inulin, a fructose polymer used as a storage carbohydrate by the plant and as a human dietary and prebiotic compound. We performed 2-D electrophoretic analysis of proteins from root material before the first freezing period. The proteins were digested with trypsin and the peptides analyzed by MS (MALDI-TOF/TOF). From the 881 protein spots analyzed, 714 proteins corresponded to a database accession, 619 of which were classified into functional categories. Besides expected proteins (e.g. related to metabolism, energy, protein synthesis, or cell structure), other well-represented categories were proteins related to folding and stability (49 spots), proteolysis (49 spots), and the stress response (67 spots). The importance of abiotic stress response was confirmed by the observation that 7 of the 21 most intense protein spots are known to be involved in cold acclimation. These results suggest a major effect of the low temperature period that preceded root harvesting.

Two dehydrin genes were identified from a Cichorium intybus EST database. They were among the most abundant sequences obtained from 10 cDNA libraries constructed from chicory roots grown under field conditions. The full length cDNA sequences, designated CiDHN1 and CiDHN2, were 1,176 and 1,055 bp long and encoded predicted polypeptides of 262 and 261 amino acids, respectively. The deduced CiDHN1 protein contains a S-segment and four lysine-rich consensus motifs (K-segments) which represent a typical SK(4) structure of dehydrins. The CiDHN2 sequence contains two Y motifs and two K-segments classifying CiDHN2 as Y(2)K(2)-type dehydrin. Southern-blotting analysis suggested that CiDHN1 and CiDHN2 are single copy genes. Northern-blotting analysis revealed that both CiDHN genes are expressed in roots and leaves, with seasonal variations in transcript accumulation. The effect of cold on the CiDHN1 and CiDHN2 transcript level was demonstrated. CiDHN1 and CiDHN2 promoter analysis revealed the presence of low temperature-responsive and ABA-responsive elements.

Due to its beneficial effects on river ecosystems, black alder (Alnus glutinosa) is one of the tree species selected for planting on riverbanks in the cross-border area encompassing Wallonia in Belgium, Lorraine in France, and Luxembourg. The preservation of this species, however, is threatened by an invasive pathogen that particularly targets and kills young alder individuals. The objectives of this study were to characterize the genetic diversity and the genetic structure of A. glutinosa at this local level with the aim of assisting the conservation and replanting strategies and to determine if a germplasm collection comprising individuals from the same cross-border area captures the diversity present in the region. Nuclear simple sequence repeat (SSR) and chloroplastic DNA (cpDNA) markers were used to analyze four local wild populations and the germplasm collection which is representative of two river catchments and six legal provenance regions. Three populations distant from the studied area were also included. A panel of 14 nuclear SSR loci revealed high allelic diversity and very low differentiation among wild populations (mean F ST = 0.014). The germplasm collection displayed a range of alleles that were representative of the different populations, and no significant differentiation between the germplasm collection and the local wild populations was observed, making this collection, as far as allelic diversity is concerned, suitable for providing trees for riverbank replanting programs. Using SSR markers, various statistical approaches consistently indicated the lack of a significant geographical structure at the level of the river catchments or provenance regions. In contrast, two cpDNA haplotypes were detected and displayed a cross-border geographically structured distribution that could be taken into account in defining new cross-border provenance regions.

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple. Although major scab resistance genes (R gene) have been widely studied, little is known about the molecular mechanisms underlying partial resistance, thought to be more durable. We used a candidate gene approach to decipher the genetic determinism of the durable partial resistance in ‘President Roulin’, an old Belgian apple cultivar. Pathological tests using monoconidial isolates of V. inaequalis on F1 ‘Gala’ x ‘President Roulin’ progeny suggested that partial resistance was broad spectrum but resulted from the combination of several race-specific interactions and was governed by at least five R genes. From an earlier transcript profiling study, we selected 13 pathogen-regulated genes in ‘President Roulin’ with a known role in plant defense and characterized their expression over a time-course experiment. These candidate defense genes (CDGs) were regulated between 6 and 120 h after inoculation. Most were significantly up- or downregulated in incompatible interactions only or were induced earlier compared with compatible interactions. Among them, eight were mapped in silico within chromosomal regions containing disease resistance factors (R gene analogues, major scab R genes or quantitative trait loci). We also investigated the extent of the correlation between CDG expression data and phenotypic variation in the progeny. We estimated that the induction of nine out of 10 CDGs accounted for up to 46 % of the phenotypic variance. Our study has improved the understanding of partial apple scab resistance and could be used in developing functional molecular markers for breeding new ‘spray-free’ cultivars with durable scab resistance.

Black alder (Alnus glutinosa Gaertn.) is an actinorhizal tree species that is becoming increasingly interesting as a pioneer species and a soil improvement species, as well as for its ecological benefits for river ecosystems and bank stabilisation. Little is known at the molecular level about its genetic variation and population structure. Microsatellite markers suitable for use for A. glutinosa were searched for by data mining the publicly available Alnus sequences and by testing cross-genera amplification of 26 available Corylus SSR markers. We report the characteristics of 11 microsatellite markers that are usable for A. glutinosa. The observed and expected heterozygosity ranged from 0.160 to 0.920 and 0.147 to 0.882, respectively. Two loci showed significant deviation from Hardy–Weinberg Equilibrium. This deviation is likely to be related to the presence of null alleles. These markers will be useful in genetic population studies and the preservation of A. glutinosa diversity.

Winter hexaploid wheat (Triticum aestivum L.) was crossed with Aegilops variabilis to transfer resistance to powdery mildew into wheat. Following two backcrosses to wheat and from 5 to 9 generations of selfing, several disomic addition and substitution lines of hexaploid wheat resistant to the mildew pathogen were isolated. A pair of short satellited chromosomes was always observed in the resistant lines. Further evidence utilizing as markers for homoeologous group 1 HMW glutenin subunits and DNA hybridization with probe pGBX 3076 showed that an alien substitution involved this homoeologous group.

A full-length cDNA encoding common bean (Phaseolus vulgaris L.) sucrose synthase (designated as Pv_BAT93 Sus), which catalyses the synthesis and cleavage of sucrose, was isolated from seeds at 15 days after pollination (DAP) by rapid amplification of cDNA ends (RACE). The full-length cDNA of Pv_BAT93 Sus had a 2,418 bp open reading frame (ORF) encoding a protein of 806 amino acid residues. Sequence comparison analysis showed that Pv_BAT93 Sus was very similar to several members of the sucrose synthase family of other plant species. Tissue expression pattern analysis showed that Pv_BAT93 Sus was expressed in leaves, flowers, stems, roots, cotyledons, and particularly during seed development. Expression studies using in situ hybridization revealed altered spatial and temporal patterns of Sus expression in the EMS mutant relative to wild-type and confirmed Sus expression in common bean developing seeds. The expression and accumulation of Sus mRNA was clearly shown in several tissues, such as the suspensor and embryo, but also in the transfer cells and endothelium. The results highlight the diverse roles that Sus might play during seed development in common bean.

The gluten proteins of cereals such as bread wheat (Triticum aestivum ssp. aestivum) and spelt (T. aestivum ssp. spelta) are responsible for celiac disease (CD). The α-gliadins constitute the most immunogenic class of gluten proteins as they include four main T-cell stimulatory epitopes that affect CD patients. Spelt has been less studied than bread wheat and could constitute a source of valuable diversity. The objective of this work was to study the genetic diversity of spelt α-gliadin transcripts and to compare it with those of bread wheat. Genotyping data from 85 spelt accessions obtained with 19 simple sequence repeat (SSR) markers were used to select 11 contrasted accessions, from which 446 full open reading frame α-gliadin genes were cloned and sequenced, which revealed a high allelic diversity. High variations among the accessions were highlighted, in terms of the proportion of α-gliadin sequences from each of the three genomes (A, B and D), and their composition in the four T-cell stimulatory epitopes. An accession from Tajikistan stood out, having a particularly high proportion of α-gliadins from the B genome and a low immunogenic content. Even if no clear separation between spelt and bread wheat sequences was shown, spelt α-gliadins displayed specific features concerning e.g. the frequencies of some amino acid substitutions. Given this observation and the variations in toxicity revealed in the spelt accessions in this study, the high genetic diversity held in spelt germplasm collections could be a valuable resource in the development of safer varieties for CD patients.

Background Scab, 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. Results A 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. Conclusions This 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 material The online version of this article (doi:10.1186/1471-2164-15-1043) contains supplementary material, which is available to authorized users.

Background The industrial chicory, Cichorium intybus, is a member of the Asteraceae family that accumulates fructan of the inulin type in its root. Inulin is a low calories sweetener, a texture agent and a health promoting ingredient due to its prebiotic properties. Average inulin chain length is a critical parameter that is genotype and temperature dependent. In the context of the study of carbohydrate metabolism and to get insight into the transcriptome of chicory root and to visualize temporal changes of gene expression during the growing season, we obtained and characterized 10 cDNA libraries from chicory roots regularly sampled in field during a growing season. A leaf and a nodule libraries were also obtained for comparison. Results Approximately 1,000 Expressed Sequence Tags (EST) were obtained from each of twelve cDNA libraries resulting in a 12,226 EST dataset. Clustering of these ESTs returned 1,922 contigs and 4,869 singlets for a total of 6,791 putative unigenes. All ESTs were compared to public sequence databases and functionally classified. Data were specifically searched for sequences related to carbohydrate metabolism. Season wide evolution of functional classes was evaluated by comparing libraries at the level of functional categories and unigenes distribution. Conclusion This chicory EST dataset provides a season wide outlook of the genes expressed in the root and to a minor extent in leaves and nodules. The dataset contains more than 200 sequences related to carbohydrate metabolism and 3,500 new ESTs when compared to other recently released chicory EST datasets, probably because of the season wide coverage of the root samples. We believe that these sequences will contribute to accelerate research and breeding of the industrial chicory as well as of closely related species.