Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.)

Weeds pose a major constraint in lentil cultivation, leading to decrease farmers' revenues by reducing the yield and increasing the management costs. The development of herbicide tolerant cultivars is essential to increase lentil yield. Even though herbicide tolerant lines have been identified in lentils, breeding efforts are still limited and lack proper validation. Marker assisted selection (MAS) can increase selection accuracy at early generations. Total 292 lentil accessions were evaluated under different dosages of two herbicides, metribuzin and imazethapyr, during two seasons at Marchouch, Morocco and Terbol, Lebanon. Highly significant differences among accessions were observed for days to flowering (DF) and maturity (DM), plant height (PH), biological yield (BY), seed yield (SY), number of pods per plant (NP), as well as the reduction indices (RI) for PH, BY, SY and NP. A total of 10,271 SNPs markers uniformly distributed along the lentil genome were assayed using Multispecies Pulse SNP chip developed at Agriculture Victoria, Melbourne. Meta-GWAS analysis was used to detect marker-trait associations, which detected 125 SNPs markers associated with different traits and clustered in 85 unique quantitative trait loci. These findings provide valuable insights for initiating MAS programs aiming to enhance herbicide tolerance in lentil crop.

Optimization of inoculum production of Stemphylium botryosum for large-scale resistance screening of lentils

BACKGROUND

Stemphylium blight incited by Stemphylium botryosum poses a significant threat to lentil crops worldwide, inducing severe defoliation and causing substantial yield losses in susceptible varieties under favorable conditions. While some moderate levels of resistance have been identified within lentil germplasm, a low number of resistant cultivars are available to farmers. Adding to the common constraints of resistance breeding, a notable challenge is generating a sufficient number of spores for large-scale screenings, which are essential for pinpointing additional sources of resistance for integration into breeding programs. Therefore, there is a pressing need to improve existing screening methods and tailor them for large-scale material selection. In pursuit of this objective, a protocol for the efficient production of fungal material has been adapted.

RESULTS

Optimization of fungal material production was successfully achieved by comparing the use of fungal mycelia and spores. Spore production was found to be optimal when produced on solid V8-PDA(hi) medium, while liquid Richard's medium was identified as superior for mycelium yield. Furthermore, a refined screening method was developed by evaluating the resistance of six lentil accessions to stemphylium blight. This assessment included the use of either fungal mycelia (at densities ranging from 1 to 5 g L- 1) or spores (with densities ranging from 5 × 104 to 2 × 105 conidia mL- 1) under three different relative humidity levels (from 50 to 100%). Both humidity levels and inoculum dose significantly influenced the final disease rating (DR) and the relative Area Under the Disease Progress Curve (rAUDPC). Differences among genotypes in final symptom severity (DR) became more pronounced after inoculation with inoculum densities of 5 g L- 1 of mycelium or of 105 and 2 × 105 conidia mL- 1 of spore under 100% relative humidity. Given the challenges associated with the large-scale production of S. botryosum spores, inoculations with 5 g L- 1 of mycelium is highly recommended as a practical alternative for conducting mass-scale screenings.

CONCLUSIONS

The findings from this study underscore the critical importance of maintaining high level of humidity during inoculation and disease progression development for accurately assessing resistance to stemphylium blight. The optimization of mycelial production for suspension inoculation emerges as a more reliable and efficient approach for conducting large-scale screening to assess germplasm resistance against stemphylium blight in lentil crops.

Genome-wide association study of common resistance to rust species in tetraploid wheat

Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.

Comparative Analysis of Secondary Metabolites Produced by Ascochyta fabae under In Vitro Conditions and Their Phytotoxicity on the Primary Host, Vicia faba, and Related Legume Crops

Ascochyta blight, caused by Ascochyta fabae, poses a significant threat to faba bean and other legumes worldwide. Necrotic lesions on stems, leaves, and pods characterize the disease. Given the economic impact of this pathogen and the potential involvement of secondary metabolites in symptom development, a study was conducted to investigate the fungus's ability to produce bioactive metabolites that might contribute to its pathogenicity. For this investigation, the fungus was cultured in three substrates (Czapek-Dox, PDB, and rice). The produced metabolites were analyzed by NMR and LC-HRMS methods, resulting in the dereplication of seven metabolites, which varied with the cultural substrates. Ascochlorin, ascofuranol, and (R)-mevalonolactone were isolated from the Czapek-Dox extract; ascosalipyrone, benzoic acid, and tyrosol from the PDB extract; and ascosalitoxin and ascosalipyrone from the rice extract. The phytotoxicity of the pure metabolites was assessed at different concentrations on their primary hosts and related legumes. The fungal exudates displayed varying degrees of phytotoxicity, with the Czapek-Dox medium's exudate exhibiting the highest activity across almost all legumes tested. The species belonging to the genus Vicia spp. were the most susceptible, with faba bean being susceptible to all metabolites, at least at the highest concentration tested, as expected. In particular, ascosalitoxin and benzoic acid were the most phytotoxic in the tested condition and, as a consequence, expected to play an important role on necrosis's appearance.

Identification of novel sources of partial and incomplete hypersensitive resistance to rust and associated genomic regions in common bean

Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.

Variability of Fatty Acid Composition and Lignan Content in Sesame Germplasm, and Effect of Roasting

Sesame (Sesamum indicum) seeds are highly valued for their culinary applications and for producing a premium-quality oil. This study investigated the polyphenol content and fatty acid composition of a set of sesame accessions and examined their association with seed colors. Among the different colors, black-seeded accessions exhibited the highest total lignan content, while white-seeded accessions had average lower levels. Brown-seeded accessions showed relatively lower concentrations of sesamol and intermediate levels of sesamolin and sesamin than other colors. The oil derived from these seeds contained unsaturated fatty acids (UFAs) and saturated fatty acids (SFAs), nutritionally crucial for human consumption. Brown varieties exhibited higher concentrations of these fatty acids. Roasting black and white sesame seeds at increasing temperatures (180 and 250 °C) significantly affected lignan and UFAs concentrations. Higher temperatures resulted in elevated levels of detrimental t-oleic and t-linoleic acids. Furthermore, sesamolin content notably decreased at 180 °C and became undetectable at 250 °C. The temperature also caused a marked increase in sesamol, regardless of seed color. PCA analysis highlighted clusters between white and black varieties according to roasting temperature, displaying the potential application of chemometrics to assess processing effects and ensure sesame quality and safety. This research provides valuable insights for exploiting sesame within agrosystems in Mediterranean climates.

Oligogenic Control of Quantitative Resistance Against Powdery Mildew Revealed in Portuguese Common Bean Germplasm

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes worldwide, and its production is severely affected by fungal diseases such as powdery mildew. Portugal has a diverse germplasm, with accessions of Andean, Mesoamerican, and admixed origin, making it a valuable resource for common bean genetic studies. In this work, we evaluated the response of a Portuguese collection of 146 common bean accessions to Erysiphe diffusa infection, observing a wide range of disease severity and different levels of compatible and incompatible reactions, revealing the presence of different resistance mechanisms. We identified 11 incompletely hypersensitive resistant and 80 partially resistant accessions. We performed a genome-wide association study to clarify its genetic control, resulting in the identification of eight disease severity-associated single-nucleotide polymorphisms, spread across chromosomes Pv03, Pv09, and Pv10. Two of the associations were unique to partial resistance and one to incomplete hypersensitive resistance. The proportion of variance explained by each association varied between 15 and 86%. The absence of a major locus, together with the relatively small number of loci controlling disease severity, suggested an oligogenic inheritance of both types of resistance. Seven candidate genes were proposed, including a disease resistance protein (toll interleukin 1 receptor-nucleotide binding site-leucine-rich repeat class), an NF-Y transcription factor complex component, and an ABC-2 type transporter family protein. This work contributes with new resistance sources and genomic targets valuable to develop selection molecular tools and support powdery mildew resistance precision breeding in common bean.

RGB image-based method for phenotyping rust disease progress in pea leaves using R

BACKGROUND

Rust is a damaging disease affecting vital crops, including pea, and identifying highly resistant genotypes remains a challenge. Accurate measurement of infection levels in large germplasm collections is crucial for finding new resistance sources. Current evaluation methods rely on visual estimation of disease severity and infection type under field or controlled conditions. While they identify some resistance sources, they are error-prone and time-consuming. An image analysis system proves useful, providing an easy-to-use and affordable way to quickly count and measure rust-induced pustules on pea samples. This study aimed to develop an automated image analysis pipeline for accurately calculating rust disease progression parameters under controlled conditions, ensuring reliable data collection.

RESULTS

A highly efficient and automatic image-based method for assessing rust disease in pea leaves was developed using R. The method's optimization and validation involved testing different segmentation indices and image resolutions on 600 pea leaflets with rust symptoms. The approach allows automatic estimation of parameters like pustule number, pustule size, leaf area, and percentage of pustule coverage. It reconstructs time series data for each leaf and integrates daily estimates into disease progression parameters, including latency period and area under the disease progression curve. Significant variation in disease responses was observed between genotypes using both visual ratings and image-based analysis. Among assessed segmentation indices, the Normalized Green Red Difference Index (NGRDI) proved fastest, analysing 600 leaflets at 60% resolution in 62 s with parallel processing. Lin's concordance correlation coefficient between image-based and visual pustule counting showed over 0.98 accuracy at full resolution. While lower resolution slightly reduced accuracy, differences were statistically insignificant for most disease progression parameters, significantly reducing processing time and storage space. NGRDI was optimal at all time points, providing highly accurate estimations with minimal accumulated error.

CONCLUSIONS

A new image-based method for monitoring pea rust disease in detached leaves, using RGB spectral indices segmentation and pixel value thresholding, improves resolution and precision. It rapidly analyses hundreds of images with accuracy comparable to visual methods and higher than other image-based approaches. This method evaluates rust progression in pea, eliminating rater-induced errors from traditional methods. Implementing this approach to evaluate large germplasm collections will improve our understanding of plant-pathogen interactions and aid future breeding for novel pea cultivars with increased rust resistance.

Uncovering Phytotoxic Compounds Produced by Colletotrichum spp. Involved in Legume Diseases Using an OSMAC-Metabolomics Approach

Different fungal species belonging to the Colletotrichum genus cause anthracnose disease in a range of major crops, resulting in huge economic losses worldwide. Typical symptoms include dark, sunken lesions on leaves, stems, or fruits. Colletotrichum spp. have synthesized, in vitro, a number of biologically active and structurally unusual metabolites that are involved in their host's infection process. In this study, we applied a one strain many compounds (OSMAC) approach, integrated with targeted and non-targeted metabolomics profiling, to shed light on the secondary phytotoxic metabolite panels produced by pathogenic isolates of Colletotrichum truncatum and Colletotrichum trifolii. The phytotoxicity of the fungal crude extracts was also assessed on their primary hosts and related legumes, and the results correlated with the metabolite profile that arose from the different cultural conditions. To the best of our knowledge, this is the first time that the OSMAC strategy integrated with metabolomics approaches has been applied to Colletotrichum species involved in legume diseases.

Lathyrus sativus resistance against the existing and emerging pathogens Erysiphe pisi and Erysiphe trifolii: A case of commonalities or total discrepancy?

Powdery mildew in Lathyrus sativus (grass pea), is commonly caused by Erysiphe pisi, the causal agent of pea powdery mildew. Erysiphe trifolii could also impose an additional threat to grass pea, as it does to pea. In order to understand the potential threat and the availability of resistance sources, the response to both pathogens was analyzed on a worldwide germplasm collection of 189 grass pea accessions. Infection type and disease severity (DS) of grass pea accessions, independently inoculated with E. pisi and E. trifolii, were evaluated under controlled conditions. Wide-range of responses was detected, with the previously uncharacterized partial resistance to E. trifolii in grass pea being less frequent and uncorrelated with partial resistance against E. pisi. To test for the lack of correlation at the genetic level, an exploratory association mapping study was undertook by statistically combining grass pea collection DS scores against both pathogens, with 5,651 previously screened genotype-by-sequencing-based single nucleotide polymorphisms (SNP). Mostly different genetic regions in grass pea were identified associated with the response to E. trifolii and E. pisi, anticipating an independent genetic basis that needs further validation in larger germplasm collections, with higher SNP densities. This study proposes common and unique partial resistance components against two different powdery mildews, implying the need for complementary approaches to introduce resistance to both pathogens into new grass pea varieties. The identified sources of resistance and predicted genomic targets will assist this multi powdery mildew-resistance breeding.

High Inter- and Intra- Diversity of Amino Acid Content and Protein Digestibility Disclosed in Five Cool Season Legume Species with a Growing Market Demand

Legumes have been sought as alternative protein sources to ensure food security and environmental sustainability. Characterizing their protein content and quality, including in underutilized grain legumes, e.g., grass pea, gives value to the legumes' underexplored variability. To fill the gap of knowledge in legumes' protein quality, for the first time, five extensive collections of cool season grain legumes were cropped under the same environmental conditions and further analyzed. Multivariate analysis showed the existent intra- and inter-species variability. The legume species with the highest protein content, grass pea, Lathyrus sativus (LS), was not the one with the overall highest individual amino acids content and in vitro protein digestibility. With these last characteristics lentil, Lens culinaris (LC), was highlighted. The highest average values of arginine (Arg), glutamic acid (Glu), and threonine (Thr) were found in LS and Vicia faba (VF). Cicer arietinum (CA) stood out as the species with the highest values of Thr and methionine (Met). Regarding the in vitro protein digestibility (IVPD), LC, followed by Pisum sativum (PS) and LS, were the legume species with the highest values. Ultimately, this study bought to the fore legume species that are not commonly used in western diets but have high adaptability to the European agricultural systems.

Status of Phytotoxins Isolated from Necrotrophic Fungi Causing Diseases on Grain Legumes

Fungal phytotoxins can be defined as secondary metabolites toxic to host plants and are believed to be involved in the symptoms developed of a number of plant diseases by targeting host cellular machineries or interfering with host immune responses. As any crop, legumes can be affected by a number of fungal diseases, causing severe yield losses worldwide. In this review, we report and discuss the isolation, chemical, and biological characterization of fungal phytotoxins produced by the most important necrotrophic fungi involved in legume diseases. Their possible role in plant-pathogen interaction and structure-toxicity relationship studies have also been reported and discussed. Moreover, multidisciplinary studies on other prominent biological activity conducted on reviewed phytotoxins are described. Finally, we explore the challenges in the identification of new fungal metabolites and their possible applications in future experiments.

Assessing the Stability of Herbicide-Tolerant Lentil Accessions (Lens culinaris Medik.) under Diverse Environments

Assessing the adaptability and stability of herbicide-tolerant lentil accessions to two broad-spectrum post-emergence herbicides in multi-environment trials has become a must in a breeding program to improve its selection. The adaptability and stability of 42 herbicide-tolerant lentil accessions were investigated using five stability parameters under eight different environments. Significant Genotype-Environment (GE) interaction was found for days to flowering (DFLR), days to maturity (DMAT), and seed yield per plant (SY). The analyzed stability parameters such as Cultivar superiority, Finlay-Wilkinson, Shukla, Static Stability, and Wricke's Ecovalence ranked the tested accessions differently, confirming the importance of using a combination of stability parameters when evaluating the performance of a group of accessions. GGE biplot of the SY trait accounted for 60.79% of sums of squares of the GE interaction and showed that cool and high rainfall environments are ideal for testing the agronomic performance of tolerant accessions. The GGE biplot of SY showed that IG4605(19), IG195(6), and IG156635(12) were specifically adapted to one mega environment, whereas IG70056(38) was identified as a superior line having a high and stable yield. These lines should be included in lentil crossing programs to develop herbicide-tolerant cultivars adapted to diverse environments.

Identification and Characterization of Resistance to Rust in Lentil and Its Wild Relatives

Lentil rust is a major disease worldwide caused by Uromyces viciae-fabae. In this study, we screened a large germplasm collection of cultivated lentils (Lens culinaris ssp. culinaris) and its wild relatives, both in adult plants in the field with a local rust isolate during 2 seasons and in seedlings under controlled conditions with four fungal isolates of worldwide origin. The main results from our study were the following: (1) a significant number of accessions with resistance based on hypersensitive reaction (reduced Infection Type (IT)) were identified in cultivated lentil and in L. ervoides, L. nigricans and L.c. orientalis. The IT scores showed a clear isolate-specific response suggesting race-specificity, so each fungal isolate might be considered a different race. Resistance was identified against all isolates what might be the basis to develop a standard differential set that should be a priority for rust definition and monitoring. (2) Interestingly, although at lower frequency than in L. ervoides and L. nigricans, the hypersensitive response was also observed within cultivated lentil, with accession 1561 (L.c. culinaris) displaying resistance to the four isolates making this accession a valuable ready-to-use resource for lentil resistance breeding. Resistance to all other rust isolates was also available within L.c. culinaris in an isolate-specific manner. Accession 1308 (L. ervoides) showed resistance against all isolates tested, as well as a reduced number of accessions belonging to other wild Lens species. (3) In addition, our screenings allowed the identification of several accessions with partial resistance (reduced Disease Severity (DS) despite high IT). Adult Plant Resistance resulting in reduced severity in adult plants in the field, despite high susceptibility in seedlings, was more frequently identified in L.c. culinaris, but also in L. nigricans and L.c. orientalis.

Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.

Climate change conditions the selection of rust-resistant candidate wild lentil populations for in situ conservation

Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, in situ conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus Uromyces viciae-fabae. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant vs. non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and in situ conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions.

In vitro characterization of iridoid and phenylethanoid glycosides from Cistanche phelypaea for nutraceutical and pharmacological applications

"Desert hyacinths" are a remarkable group of parasitic plants belonging to genus Cistanche, including more than 20 accepted species typically occurring in deserts or coastal dunes parasitizing roots of shrubs. Several Cistanche species have long been a source of traditional herbal medicine or food, being C. deserticola and C. tubulosa the most used in China. This manuscript reports the isolation and identification of some phenylethanoid and iridoid glycosides, obtained from the hydroalcoholic extract of C. phelypaea collected in Spain. The present study aims to characterize the antioxidant activity of C. phelypaea metabolites in the light of their application in nutraceutical and cosmeceutical industries and the effect of acetoside, the most abundant metabolite in C. phelypaea extract, on human keratinocyte and pluripotent stem cell proliferation and differentiation. Our study demonstrated that acetoside, besides its strong antioxidant potential, can preserve the proliferative potential of human basal keratinocytes and the stemness of mesenchymal progenitors necessary for tissue morphogenesis and renewal. Therefore, acetoside can be of practical relevance for the clinical application of human stem cell cultures in tissue engineering and regenerative medicine.

Advances in disease and pest resistance in faba bean

Faba bean (Vicia faba) is a grain legume crop widely cultivated in temperate areas for food and feed. Its productivity can be constrained by numerous diseases and pests that can be managed by a number of strategies, complemented with the deployment of resistant cultivars in an integrated manner. Few sources of resistance are available to some of them, although their phenotypic expression is usually insufficiently described, and their genetic basis is largely unknown. A few DNA markers have been developed for resistance to rust, ascochyta blight, and broomrape, but not yet for other diseases or pests. Still, germplasm screenings are allowing the identification of resistances that are being accumulated by classical breeding, succeeding in the development of cultivars with moderate levels of resistance. The adoption of novel phenotyping approaches and the unprecedented development of genomic resources along with speed breeding tools are speeding up resistance characterization and effective use in faba bean breeding.

Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes

Peyronellaea pinodes is a devastating pathogen of pea crop. Quantitative trait loci (QTL) associated with resistance have been identified, as well as genes differentially expressed between resistant and susceptible pea lines. The key question is which of these many genes located into these QTLs, or differentially expressed, are the key genes that distinguish resistant from susceptible plants and could be used as markers. To identify these key genes, in the present study we applied MACE (Massive Analysis of cDNA Ends) -Seq to a whole Recombinant Inbred Line population segregating for resistance to this disease and their parental lines and identified those genes which expression was more correlated with the level of resistance. We also compared gene expression profiles between the most resistant and the most susceptible families of the RIL population. A total of 6780 transcripts were differentially expressed between the parental lines after inoculation. Of them, 803 showed the same expression pattern in the bulks formed by the most resistant and most susceptible RIL families. These genes, showing a consistent expression pattern, could be used as expression markers to distinguish resistant from susceptible plants. The analysis of these genes also discovered the crucial mechanisms acting against P. pinodes.

Pea Breeding for Resistance to Rhizospheric Pathogens

Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.

Evaluation of Effective Class-Balancing Techniques for CNN-Based Assessment of Aphanomyces Root Rot Resistance in Pea (Pisum sativum L.)

Aphanomyces root rot (ARR) is a devastating disease that affects the production of pea. The plants are prone to infection at any growth stage, and there are no chemical or cultural controls. Thus, the development of resistant pea cultivars is important. Phenomics technologies to support the selection of resistant cultivars through phenotyping can be valuable. One such approach is to couple imaging technologies with deep learning algorithms that are considered efficient for the assessment of disease resistance across a large number of plant genotypes. In this study, the resistance to ARR was evaluated through a CNN-based assessment of pea root images. The proposed model, DeepARRNet, was designed to classify the pea root images into three classes based on ARR severity scores, namely, resistant, intermediate, and susceptible classes. The dataset consisted of 1581 pea root images with a skewed distribution. Hence, three effective data-balancing techniques were identified to solve the prevalent problem of unbalanced datasets. Random oversampling with image transformations, generative adversarial network (GAN)-based image synthesis, and loss function with class-weighted ratio were implemented during the training process. The result indicated that the classification F1-score was 0.92 ± 0.03 when GAN-synthesized images were added, 0.91 ± 0.04 for random resampling, and 0.88 ± 0.05 when class-weighted loss function was implemented, which was higher than when an unbalanced dataset without these techniques were used (0.83 ± 0.03). The systematic approaches evaluated in this study can be applied to other image-based phenotyping datasets, which can aid the development of deep-learning models with improved performance.

Identification and Characterization of Novel Sources of Resistance to Rust Caused by Uromyces pisi in Pisum spp

Pea rust is a major disease worldwide caused by Uromyces pisi in temperate climates. Only moderate levels of partial resistance against U. pisi have been identified so far in pea, urging for enlarging the levels of resistance available for breeding. Herein, we describe the responses to U. pisi of 320 Pisum spp. accessions, including cultivated pea and wild relatives, both under field and controlled conditions. Large variations for U. pisi infection response for most traits were observed between pea accessions under both field and controlled conditions, allowing the detection of genotypes with partial resistance. Simultaneous multi-trait indexes were applied to the datasets allowing the identification of partial resistance, particularly in accessions JI224, BGE004710, JI198, JI199, CGN10205, and CGN10206. Macroscopic observations were complemented with histological observations on the nine most resistant accessions and compared with three intermediates and three susceptible ones. This study confirmed that the reduced infection of resistant accessions was associated with smaller rust colonies due to a reduction in the number of haustoria and hyphal tips per colony. Additionally, a late acting hypersensitive response was identified for the first time in a pea accession (PI273209). These findings demonstrate that screening pea collections continues to be a necessary method in the search for complete resistance against U. pisi. In addition, the large phenotypic diversity contained in the studied collection will be useful for further association analysis and breeding perspectives.

Anthraquinones and their analogues as potential biocontrol agents of rust and powdery mildew diseases of field crops

BACKGROUND

Rusts and powdery mildews are severe fungal diseases of major crops worldwide, including cereals and legumes. They can be managed by chemical fungicide treatments, with negative consequences as environmental pollution and risk for human and animal health. Bioactive natural products could be the safest alternative for pest control. The family of anthraquinones, as well as analogue compounds containing an anthraquinone moiety or some modified anthraquinone rings, has been reported to exhibit certain antibiotic activity. Thus, the potential antifungal activity of some anthraquinones isolated from Ascochyta lentis, was assayed in this study for their effectiveness to reduce rust and powdery mildew diseases on pea and oat. Their effect on fungal development was macro- and microscopically assessed on inoculated leaves, and compared to the control achieved by the chemical fungicide (Tetraconazol 12.5% and Azoxystrobin 25%). In addition, the most promising compound was also tested at different concentrations in inoculated whole plants in order to evaluate its preventive and curative potential against fungal infection.

RESULTS

All metabolites studied strongly reduced the development of rust and powdery mildews in both pea and oat, being pachybasin and lentiquinone C the most effective ones in hampering fungal spore germination and appressoria formation. Some of them also affected post-penetration events reducing colony size and number of haustoria per colony. Results were confirmed for pachybasin in whole plants assays, showing an efficacy similar to the commercial fungicide to control fungal diseases, both in preventive and curative applications.

CONCLUSIONS

Some fungal anthraquinones and close metabolites, especially pachybasin, could be very promising molecules with effective potential as antifungal agents against both rust and powdery mildew of both pea and oat. Some structure activity-relationships feature have also been evaluated. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea

Rusts are among the most important foliar biotrophic fungal diseases in legumes. Lathyrus cicera crop can be severely damaged by Uromyces pisi, to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in L. cicera. To prioritise the causative variants controlling partial resistance to rust in L. cicera, a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs' U. pisi disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to U. pisi resistance in L. cicera was quantified for each RIL individual and used for eQTL mapping. One cis-eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance - a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.

Searching for Abiotic Tolerant and Biotic Stress Resistant Wild Lentils for Introgression Breeding Through Predictive Characterization

Crop wild relatives are species related to cultivated plants, whose populations have evolved in natural conditions and confer them valuable adaptive genetic diversity, that can be used in introgression breeding programs. Targeting four wild lentil taxa in Europe, we applied the predictive characterization approach through the filtering method to identify populations potentially tolerant to drought, salinity, and waterlogging. In parallel, the calibration method was applied to select wild populations potentially resistant to lentil rust and broomrape, using, respectively, 351 and 204 accessions evaluated for these diseases. An ecogeographic land characterization map was used to incorporate potential genetic diversity of adaptive value. We identified 13, 1, 21, and 30 populations potentially tolerant to drought, soil salinity, waterlogging, or resistance to rust, respectively. The models targeting broomrape resistance did not adjust well and thus, we were not able to select any population regarding this trait. The systematic use of predictive characterization techniques may boost the efficiency of introgression breeding programs by increasing the chances of collecting the most appropriate populations for the desired traits. However, these populations must still be experimentally tested to confirm the predictions.

Metabolomics profile responses to changing environments in a common bean (Phaseolus vulgaris L.) germplasm collection

Metabolomics is one of the most powerful -omics to assist plant breeding. Despite the recognized genetic diversity in Portuguese common bean germplasm, details on its metabolomics profiles are still missing. Aiming to promote their use and to understand the environment's effect in bean metabolomics profiles, 107 Portuguese common bean accessions, cropped under contrasting environments, were analyzed using spectrophotometric, untargeted and targeted mass spectrometry approaches. Although genotype was the most relevant factor on bean metabolomics profile, a clear genotype × environment interaction was also detected. Multivariate analysis highlighted, on the heat-stress environment, the existence of higher levels of salicylic acid, and lower levels of triterpene saponins. Three clusters were defined within each environment. White accessions presented the lowest content and the colored ones the highest levels of prenol lipids and flavonoids. Sources of interesting metabolomics profiles are now identified for bean breeding, focusing either on local or on broad adaptation.

Application of Crop Growth Models to Assist Breeding for Intercropping: Opportunities and Challenges

Intercropping of two or more species on the same piece of land can enhance biodiversity and resource use efficiency in agriculture. Traditionally, intercropping systems have been developed and improved by empirical methods within a specific local context. To support the development of promising intercropping systems, the individual species that are part of an intercrop can be subjected to breeding. Breeding for intercropping aims at resource foraging traits of the admixed species to maximize niche complementarity, niche facilitation, and intercrop performance. The breeding process can be facilitated by modeling tools that simulate the outcome of the combination of different species' (or genotypes') traits for growth and yield development, reducing the need of extensive field testing. Here, we revisit the challenges associated with breeding for intercropping, and give an outlook on applying crop growth models to assist breeding for intercropping. We conclude that crop growth models can assist breeding for intercropping, provided that (i) they incorporate the relevant plant features and mechanisms driving interspecific plant-plant interactions; (ii) they are based on model parameters that are closely linked to the traits that breeders would select for; and (iii) model calibration and validation is done with field data measured in intercrops. Minimalist crop growth models are more likely to incorporate the above elements than comprehensive but parameter-intensive crop growth models. Their lower complexity and reduced parameter requirement facilitate the exploration of mechanisms at play and fulfil the model requirements for calibration of the appropriate crop growth models.

Association Mapping of Lathyrus sativus Disease Response to Uromyces pisi Reveals Novel Loci Underlying Partial Resistance

Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding.

Portuguese Common Bean Natural Variation Helps to Clarify the Genetic Architecture of the Legume's Nutritional Composition and Protein Quality

Common bean is a nutritious food legume widely appreciated by consumers worldwide. It is a staple food in Latin America, and a component of the Mediterranean diet, being an affordable source of protein with high potential as a gourmet food. Breeding for nutritional quality, including both macro and micronutrients, and meeting organoleptic consumers' preferences is a difficult task which is facilitated by uncovering the genetic basis of related traits. This study explored the diversity of 106 Portuguese common bean accessions, under two contrasting environments, to gain insight into the genetic basis of nutritional composition (ash, carbohydrates, fat, fiber, moisture, protein, and resistant starch contents) and protein quality (amino acid contents and trypsin inhibitor activity) traits through a genome-wide association study. Single-nucleotide polymorphism-trait associations were tested using linear mixed models accounting for the accessions' genetic relatedness. Mapping resolution to the gene level was achieved in 56% of the cases, with 102 candidate genes proposed for 136 genomic regions associated with trait variation. Only one marker-trait association was stable across environments, highlighting the associations' environment-specific nature and the importance of genotype × environment interaction for crops' local adaptation and quality. This study provides novel information to better understand the molecular mechanisms regulating the nutritional quality in common bean and promising molecular tools to aid future breeding efforts to answer consumers' concerns.

Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective

Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.

Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi

Grass pea (Lathyrus sativus L.) is an annual legume species, phylogenetically close to pea (Pisum sativum L.), that may be infected by Fusarium oxysporum f. sp. pisi (Fop), the causal agent of fusarium wilt in peas with vast worldwide yield losses. A range of responses varying from high resistance to susceptibility to this pathogen has been reported in grass pea germplasm. Nevertheless, the genetic basis of that diversity of responses is still unknown, hampering its breeding exploitation. To identify genomic regions controlling grass pea resistance to fusarium wilt, a genome-wide association study approach was applied on a grass pea worldwide collection of accessions inoculated with Fop race 2. Disease responses were scored in this collection that was also subjected to high-throughput based single nucleotide polymorphisms (SNP) screening through genotyping-by-sequencing. A total of 5,651 high-quality SNPs were considered for association mapping analysis, performed using mixed linear models accounting for population structure. Because of the absence of a fully assembled grass pea reference genome, SNP markers' genomic positions were retrieved from the pea's reference genome v1a. In total, 17 genomic regions were associated with three fusarium wilt response traits in grass pea, anticipating an oligogenic control. Seven of these regions were located on pea chromosomes 1, 6, and 7. The candidate genes underlying these regions were putatively involved in secondary and amino acid metabolism, RNA (regulation of transcription), transport, and development. This study revealed important fusarium wilt resistance favorable grass pea SNP alleles, allowing the development of molecular tools for precision disease resistance breeding.

The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high-density linkage maps in comparative mapping and synteny analysis

Powdery mildews are major diseases for a range of crops. The loss of function of specific Mildew Locus O (MLO) genes has long been associated with pre-haustorial plant resistance to powdery mildew and has proven to be durable in several species. Erysiphe pisi is the major causal agent of powdery mildew in pea (Pisum sativum L.) and in the closely related Lathyrus sativus L. and Lathyrus cicera L. PsMLO1 has been extensively studied in pea. However, no MLO gene family members have been isolated and characterized in Lathyrus species so far. In this study, MLO1 genes were isolated and characterized in L. sativus and L. cicera genotypes with varied levels of partial resistance against powdery mildew. Phylogenetic analyses confirmed that Lathyrus MLO1 belongs to Clade V, like all dicot MLO proteins associated with powdery mildew susceptibility. A L. sativus recombinant inbred line population (RIL) was genotyped by sequencing to develop a high-density L. sativus genetic linkage map. DNA sequence polymorphisms between the analyzed genotypes allowed the location of MLO1 in the newly developed L. sativus RIL genetic linkage map. Subsequent comparative mapping between L. sativus and L. cicera genetic maps and P. sativum, Lens culinaris Medik., and Medicago truncatula Gaertn. reference genomes revealed important aspects of the conservation of the MLO1 locus position and of the overall chromosomal rearrangements occurring during legume evolution, with relevance to legume disease resistance breeding programs.

Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit

Common bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to "stress", "signaling", "cell wall", "hormone metabolism", and "secondary metabolism" functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.

Characterization of the Resistance to Powdery Mildew and Leaf Rust Carried by the Bread Wheat Cultivar Victo

Leaf rust and powdery mildew are two important foliar diseases in wheat. A recombinant inbred line (RIL) population, obtained by crossing two bread wheat cultivars (‘Victo’ and ‘Spada’), was evaluated for resistance to the two pathogens at seedling stage. Upon developing a genetic map of 8726 SNP loci, linkage analysis identified three resistance Quantitative Trait Loci (QTLs), with ‘Victo’ contributing the resistant alleles to all loci. One major QTL (QPm.gb-7A) was detected in response to Blumeria graminis on chromosome 7A, which explained 90% of phenotypic variation (PV). The co-positional relationship with known powdery mildew (Pm) resistance loci suggested that a new source of resistance was identified in T. aestivum. Two QTLs were detected in response to Puccinia triticina: a major gene on chromosome 5D (QLr.gb-5D), explaining a total PV of about 59%, and a minor QTL on chromosome 2B (QLr.gb-2B). A positional relationship was observed between the QLr.gb-5D with the known Lr1 gene, but polymorphisms were found between the cloned Lr1 and the corresponding ‘Victo’ allele, suggesting that QLr.gb-5D could represent a new functional Lr1 allele. Lastly, upon anchoring the QTL on the T. aestivum reference genome, candidate genes were hypothesized on the basis of gene annotation and in silico gene expression analysis.

Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.)

Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.

Partial Resistance Against Erysiphe pisi and E. trifolii Under Different Genetic Control in Lathyrus cicera: Outcomes from a Linkage Mapping Approach

Powdery mildew infections are among the most severe foliar biotrophic fungal diseases in grain legumes. Several accessions of Lathyrus cicera (chickling pea) show levels of partial resistance to Erysiphe pisi, the causal agent of pea powdery mildew, and to E. trifolii, a powdery mildew pathogen recently confirmed to infect pea and Lathyrus spp. Nevertheless, the underlying L. cicera resistance mechanisms against powdery mildews are poorly understood. To unveil the genetic control of resistance against powdery mildews in L. cicera, a recombinant inbred line population segregating for response to both species was used in resistance linkage analysis. An improved L. cicera genetic linkage map was used in this analysis. The new higher-density linkage map contains 1,468 polymorphic loci mapped on seven major and two minor linkage groups, covering a total of 712.4 cM. The percentage of the leaf area affected by either E. pisi or E. trifolii was recorded in independent screenings of the recombinant inbred line population, identifying a continuous range of resistance-susceptibility responses. Distinct quantitative trait loci (QTLs) for partial resistance against each pathogen were identified, suggesting different genetic bases are involved in the response to E. pisi and E. trifolii in L. cicera. Moreover, through comparative mapping of L. cicera QTL regions with the pea reference genome, candidate genes and pathways involved in resistance against powdery mildews were identified. This study extended the previously available genetic and genomic tools in Lathyrus species, providing clues about diverse powdery mildew resistance mechanisms useful for future resistance breeding of L. cicera and related species.

Legume Crops and Biotrophic Pathogen Interactions: A Continuous Cross-Talk of a Multilayered Array of Defense Mechanisms

Legume species are recognized for their nutritional benefits and contribution to the sustainability of agricultural systems. However, their production is threatened by biotic constraints with devastating impacts on crop yield. A deep understanding of the molecular and genetic architecture of resistance sources culminating in immunity is critical to assist new biotechnological approaches for plant protection. In this review, the current knowledge regarding the major plant immune system components of grain and forage legumes challenged with obligate airborne biotrophic fungi will be comprehensively evaluated and discussed while identifying future directions of research. To achieve this, we will address the multi-layered defense strategies deployed by legume crops at the biochemical, molecular, and physiological levels, leading to rapid pathogen recognition and carrying the necessary information to sub-cellular components, on-setting a dynamic and organized defense. Emphasis will be given to recent approaches such as the identification of critical components of host decentralized immune response negatively regulated by pathogens while targeting the loss-of-function of susceptibility genes. We conclude that advances in gene expression analysis in both host and pathogen, protocols for effectoromics pipelines, and high-throughput disease phenomics platforms are rapidly leading to a deeper understanding of the intricate host-pathogen interaction, crucial for efficient disease resistance breeding initiatives.

Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high-density integrated DArTseq SNP-based genetic map

BACKGROUND

Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251).

RESULTS

We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co-located with the QTLs identified.

CONCLUSIONS

Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi-component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker-assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry.

Quantitative Analysis of Target Peptides Related to Resistance Against Ascochyta Blight (Peyronellaea pinodes) in Pea

Peyronellaea pinodes causes Ascochyta blight, one of the major diseases in pea worldwide. Cultivated pea plants have a low resistance to this disease. Although quantitative trait loci (QTLs) involved in the resistance to Ascochyta blight have been identified, the specific genes associated with these QTLs remain unknown, which makes marker-assisted selection difficult. Complex traits alter proteins and their abundance. Quantitative estimation of proteins in pea might therefore be useful in selecting potential markers for breeding. In this work, we developed a strategy using a combination of shotgun proteomics (viz., high performance liquid chromatography-mass spectrometry data-dependent acquisition) and data-independent acquisition (DIA) analysis, to identify putative protein markers associated with resistance to Ascochyta blight and explored its use for breeding selection. For this purpose, an initial list of target peptides based on proteins closely related to resistance to P. pinodes was compiled by using two genotypes with contrasting responses to the disease. Then, targeted data analysis (viz., shotgun proteomics-DIA) was used for constitutive quantification of the target peptides in a representative number of the recombinant inbred line population segregated for resistance as derived from a cross between the two genotypes. Finally, a peptide panel of potential markers for resistance to P. pinodes was built. The results thus obtained are discussed and compared with those of previous gene expression studies using the same parental pea genotypes responding to the pathogen. Also, a molecular defense mechanism against Ascochyta blight in pea is proposed. To the authors' knowledge, this is the first time a targeted proteomics approach based on data analysis has been used to identify peptides associated with resistance to this disease.

Natural Variation in Portuguese Common Bean Germplasm Reveals New Sources of Resistance Against Fusarium oxysporum f. sp. phaseoli and Resistance-Associated Candidate Genes

Common bean (Phaseolus vulgaris) is one of the most consumed legume crops in the world, and Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. phaseoli, is one of the major diseases affecting its production. Portugal holds a very promising common bean germplasm with an admixed genetic background that may reveal novel genetic resistance combinations between the original Andean and Mesoamerican gene pools. To identify new sources of Fusarium wilt resistance and detect resistance-associated single-nucleotide polymorphisms (SNPs), we explored, for the first time, a diverse collection of the underused Portuguese common bean germplasm by using genome-wide association analyses. The collection was evaluated for Fusarium wilt resistance under growth chamber conditions, with the highly virulent F. oxysporum f. sp. phaseoli strain FOP-SP1 race 6. Fourteen of the 162 Portuguese accessions evaluated were highly resistant and 71 intermediate. The same collection was genotyped with DNA sequencing arrays, and SNP-resistance associations were tested via a mixed linear model accounting for the genetic relatedness between accessions. The results from the association mapping revealed nine SNPs associated with resistance on chromosomes Pv04, Pv05, Pv07, and Pv08, indicating that Fusarium wilt resistance is under oligogenic control. Putative candidate genes related to phytoalexin biosynthesis, hypersensitive response, and plant primary metabolism were identified. The results reported here highlight the importance of exploring underused germplasm for new sources of resistance and provide new genomic targets for the development of functional markers to support selection in future disease resistance breeding programs.

Identification of quantitative trait loci (QTL) controlling resistance to pea weevil (Bruchus pisorum) in a high-density integrated DArTseq SNP-based genetic map of pea

Pea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified in Pisum germplasm. To decipher the genetic control underlying the resistance previously identify in P. sativum ssp. syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL's DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM-1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTL BpSI.III that was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.

Impact of fungal and plant metabolites application on early development stages of pea powdery mildew

BACKGROUND

Pea powdery mildew incited by Erysiphe pisi represents a major constraint for pea crops worldwide. Crop protection is largely based on chemical control, although recently a renewed interest in the discovery of natural products as alternatives to synthetic fungicides application has emerged. Thus, 12 bioactive plant and fungal metabolites belonging to different class of natural compounds were evaluated, together with a commercial fungicide, at different concentrations on detached pea leaves for their potential to inhibit spore germination and subsequent stages of fungal growth. The most effective metabolites were tested at different concentrations in planta under controlled conditions to evaluate the level of control achieved by treatments before, concurrently and after pathogen inoculation. Pathogen development was macroscopically scored on whole plants as percentage of disease severity and area under the disease progress curve.

RESULTS

Cavoxin, inuloxin C and sphaeropsidin A strongly inhibited E. pisi germination and haustoria formation and reduced colony size. This effect was dose dependent. These results were further confirmed in whole plants by spraying the metabolites on plant leaves for preventive or curative control, which reduced fungal developmental of E. pisi at levels comparable with those obtained by application of the fungicide.

CONCLUSIONS

Cavoxin, inuloxin C and sphaeropsidin A have potential as alternatives to synthetic fungicides for the control of crop pathogens of economic importance such as powdery mildew. © 2019 Society of Chemical Industry.

Flower and Pod Source Influence on Pea Weevil (Bruchus pisorum) Oviposition Capacity and Preference

Bruchus pisorum is an insect pest causing major damage to pea seeds worldwide. Control is difficult and limited resistance is available. In this work we studied the effects of pollen and pod source on insect fecundity and oviposition by comparing resistant and susceptible Pisum spp. accessions and non-host (Lathyrus sativus and Vicia faba) species. A first no-choice assay revealed that the source of flower offered to adults for feeding might retard oviposition (the case of V. faba), reduce fertility (Pisum sativum ssp. syriacum, P. fulvum, and V. faba) or increase adult mortality (V. faba and P. sativum ssp. syriacum). A second no-choice assay with all adults fed with pollen of the same pea cultivar showed significant effect of the source of pods offered. Oviposition was reduced on pods of some resistant Pisum accessions, but particularly low on pods of the non-hosts, being retarded if ever happening and coupled with high mortality of adults. This was confirmed in a third experiment consisting on dual-choice assays showing reduced egg laying in V. faba, L. sativus, P. fulvum, and P. sativum ssp. syriacum compared to the commercial variety pea used as a control (Messire).

Antifeedant activity of long-chain alcohols, and fungal and plant metabolites against pea aphid (Acyrthosiphon pisum) as potential biocontrol strategy

Aphids are noxious insect pests of major crops including cereals and legumes. Particularly, pea aphid (Acyrthosiphon pisum) causes significant yield and quality loses in pea. Crop protection is largely based on noxious chemical pesticides which have prompted a renewed interest in the discovery of natural products as alternatives to synthetic insecticides. In this study different classes of natural compounds were tested in dual choice bioassays to evaluate their feeding deterrence and mortality effect on pea aphid. High feeding deterrence was produced by some of the compounds, particularly1-hexadecanol, gliotoxin, cyclopaldic acid and seiridin. On the contrary, aphid mortality was low although significant for 1-heptadecanol, cytochalasin A, 1-nonadecanol and gliotoxin. Phytotoxicity assessment showed low or imperceptible plant damaged for cytochalasin A, seiridin and 1-nonadecanol. The results obtained showed the potential of seiridin to be used as an alternative to synthetic insecticides.

Allelopathy for Parasitic Plant Management

A number of parasitic plants have adapted to agricultural environments becoming weedy and posing a serious threat to important crops. Available control measures rely heavily on use of synthetic herbicides. The side effects on environmental pollution and food health of chemical control prompted studies to find alternative strategies based on the use of natural products. This article reviews plant and fungal metabolites with potential for the development of specific and efficient methods for the control of parasitic plants.

Complexation of sesquiterpene lactones with cyclodextrins: synthesis and effects on their activities on parasitic weeds

Allelochemicals are safer, more selective and more active alternatives than synthetic agrochemicals for weed control. However, the low solubility of these compounds in aqueous media limits their use as agrochemicals. Herein, we propose the application of α-, β- and γ-cyclodextrins to improve the physicochemical properties and biological activities of three sesquiterpene lactones: dehydrocostuslactone, costunolide and (-)-α-santonin. Complexation was achieved by kneading and coprecipitation methods. Aqueous solubility was increased in the range 100-4600% and the solubility-phase diagrams suggested that complex formation had been successful. The results of the PM3 semiempirical calculations were consistent with the experimental results. The activities on etiolated wheat coleoptiles, Standard Target Species and parasitic weeds were improved. Cyclodextrins preserved or enhanced the activity of the three sesquiterpene lactones. Free cyclodextrins did not show significant activity and therefore the enhancement in activity was due to complexation. These results are promising for applications in agrochemical design.

Physical and Chemical Barriers in Root Tissues Contribute to Quantitative Resistance to Fusarium oxysporum f. sp. pisi in Pea

Fusarium wilt caused by Fusarium oxysporum f. sp. pisi (Fop) is one of the most destructive diseases of pea worldwide. Control of this disease is difficult and it is mainly based on the use of resistant cultivars. While monogenic resistance has been successfully used in the field, it is at risk of breakdown by the constant evolution of the pathogen. New sources of quantitative resistance have been recently identified from a wild relative Pisum spp. collection. Here, we characterize histologically the resistance mechanisms occurring in these sources of quantitative resistance. Detailed comparison, of the reaction at cellular level, of eight pea accessions with differential responses to Fop race 2, showed that resistant accessions established several barriers at the epidermis, exodermis, cortex, endodermis and vascular stele efficiently impeding fungal progression. The main components of these different barriers were carbohydrates and phenolic compounds including lignin. We found that these barriers were mainly based on three defense mechanisms including cell wall strengthening, formation of papilla-like structures at penetration sites and accumulation of different substances within and between cells. These defense reactions varied in intensity and localization between resistant accessions. Our results also clarify some steps of the infection process of F. oxysporum in plant and support the important role of cell wall-degrading enzymes in F. oxysporum pathogenicity.