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.

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.

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.

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.

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.

Traditional Foods From Maize (Zea mays L.) in Europe

Maize (Zea mays L.) is one of the major crops of the world for feed, food, and industrial uses. It was originated in Central America and introduced into Europe and other continents after Columbus trips at the end of the 15th century. Due to the large adaptability of maize, farmers have originated a wide variability of genetic resources with wide diversity of adaptation, characteristics, and uses. Nowadays, in Europe, maize is mainly used for feed, but several food specialties were originated during these five centuries of maize history and became traditional food specialties. This review summarizes the state of the art of traditional foodstuffs made with maize in Southern, South-Western and South-Eastern Europe, from an historic evolution to the last research activities that focus on improving sustainability, quality and safety of food production.

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.

Shedding Light on the Volatile Composition of Broa, a Traditional Portuguese Maize Bread

In Portugal, maize has been used for centuries to produce an ethnic bread called broa, employing traditional maize varieties, which are preferred by the consumers in detriment of commercial hybrids. In order to evaluate the maize volatiles that can influence consumers’ acceptance of broas, twelve broas were prepared from twelve maize varieties (eleven traditional and one commercial hybrid), following a traditional recipe. All maize flours and broas were analyzed by HS-SPME-GC-MS (headspace solid-phase microextraction) and broas were appraised by a consumer sensory panel. In addition, the major soluble phenolics and total carotenoids contents were quantitated in order to evaluate their influence as precursors or inhibitors of volatile compounds. Results showed that the major volatiles detected in maize flours and broas were aldehydes and alcohols, derived from lipid oxidation, and some ketones derived from carotenoids’ oxidation. Both lipid and carotenoids’ oxidation reactions appeared to be inhibited by soluble phenolics. In contrast, phenolic compounds appeared to increase browning reactions during bread making and, consequently, the production of pyranones. Traditional samples, especially those with higher contents in pyranones and lower contents in aldehydes, were preferred by the consumer sensory panel. These findings suggest that, without awareness, consumers prefer broas prepared from traditional maize flours with higher contents in health-promoting phenolic compounds, reinforcing the importance of preserving these valuable genetic resources.

Projection to latent correlative structures, a dimension reduction strategy for spectral-based classification

Latent variables are used in chemometrics to reduce the dimension of the data. It is a crucial step with spectroscopic data where the number of explanatory variables can be very high. Principal component analysis (PCA) and partial least squares (PLS) are the most common. However, the resulting latent variables are mathematical constructs that do not always have a physicochemical interpretation. A new data reduction strategy, named projection to latent correlative structures (PLCS), is introduced in this manuscript. This approach requires a set of model spectra that will be used as references. Each latent variable is the relative similarity of a given spectrum to a pair of reference spectra. The latent structure is obtained using every possible combination of reference pairing. The approach has been validated using more than 500 FTIR-ATR spectra from cool-season culinary grain legumes assembled from germplasm banks and breeders' working collections. PLCS has been combined with soft discriminant analysis to detect outliers that could be particularly suitable for a deeper analysis.

Different representation of the data by selecting the latent variables.

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.

Broa, an Ethnic Maize Bread, as a Source of Phenolic Compounds

Maize is an important source of phenolic compounds, specially hydroxycinnamic acids, which are widely known for their antioxidant activity and associated health benefits. However, these effects depend on their bioaccessibility, which is influenced by the different techniques used for food processing. Several traditional products can be obtained from maize and, in Portugal, it is used for the production of an ethnic bread called broa. In order to evaluate the effect of processing on maize phenolic composition, one commercial hybrid and five open-pollinated maize flours and broas were studied. The total phenolic content and antioxidant activity were evaluated by the Folin-Ciocalteu and ORAC assays, respectively. The major phenolics, namely ferulic and p-coumaric acids (in their soluble-free, soluble-conjugated and insoluble forms), insoluble ferulic acid dimers and soluble hydroxycinnamic acid amides were quantitated. Results show that the total phenolic content, antioxidant activity and hydroxycinnamic acids resisted traditional processing conditions used in the production of broas. The content in soluble-free phenolics increased after processing, meaning that their bioaccessibility improved. Portuguese traditional broas, produced with open-pollinated maize varieties, can be considered an interesting dietary source of antioxidant compounds due to the higher content in hydroxycinnamic acids and derivatives.

Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety

Olea europaea 'Galega vulgar' variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. 'Galega vulgar' is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of 'Galega vulgar', 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the 'Galega vulgar' intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the 'Galega vulgar', with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of 'Galega vulgar'. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of 'Galega vulgar').

Common bean SNP alleles and candidate genes affecting photosynthesis under contrasting water regimes

Water deficit is a major worldwide constraint to common bean (Phaseolus vulgaris L.) production, being photosynthesis one of the most affected physiological processes. To gain insights into the genetic basis of the photosynthetic response of common bean under water-limited conditions, a collection of 158 Portuguese accessions was grown under both well-watered and water-deficit regimes. Leaf gas-exchange parameters were measured and photosynthetic pigments quantified. The same collection was genotyped using SNP arrays, and SNP-trait associations tested considering a linear mixed model accounting for the genetic relatedness among accessions. A total of 133 SNP-trait associations were identified for net CO2 assimilation rate, transpiration rate, stomatal conductance, and chlorophylls a and b, carotenes, and xanthophyll contents. Ninety of these associations were detected under water-deficit and 43 under well-watered conditions, with only two associations common to both treatments. Identified candidate genes revealed that stomatal regulation, protein translocation across membranes, redox mechanisms, hormone, and osmotic stress signaling were the most relevant processes involved in common bean response to water-limited conditions. These candidates are now preferential targets for common bean water-deficit-tolerance breeding. Additionally, new sources of water-deficit tolerance of Andean, Mesoamerican, and admixed origin were detected as accessions valuable for breeding, and not yet explored.

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.

Hydroxycinnamic Acids and Their Derivatives in Broa, a Traditional Ethnic Maize Bread

Maize is one of the most interesting dietary sources of hydroxycinnamic acids, widely known for their beneficial health effects, namely antioxidant properties. This work aims to identify hydroxycinnamic acids and their derivatives in broa, a Portuguese traditional ethnic maize bread, and corresponding maize flours. Soluble and insoluble phenolic fractions of diverse maize flours and corresponding broas were prepared and analysed by HPLC-DAD-MS/MS (high-performance liquid chromatography coupled with diode array detector and tandem mass spectrometry). Besides free hydroxycinnamic acids, mainly ferulic and p-coumaric acids, several structural isomers and stereoisomers of insoluble ferulic acid dehydrodimers (n = 18) and trimers (n = 11), were also identified. Hydroxycinnamic acid amides consisting of coumaroyl and feruloyl conjugates (n = 22) were present in both soluble and insoluble fractions of maize flours and breads, in different isomeric forms. A new compound was putatively identified as bis-N,N′-diferuloyl putrescine. Additionally, more complex and insoluble hydroxycinnamic acid amides, derived from ferulic acid dehydrodimers (n = 47) and trimers (n = 18), were also putatively identified for the first time, suggesting that hydroxycinnamic acid amides are also linked to maize cell walls. Since hydroxycinnamic derivatives were not only identified in maize flours, but also in broas, they can contribute to the antioxidant properties and beneficial health effects of maize-based foods.

Volatilome-Genome-Wide Association Study on Wholemeal Maize Flour

Odor and aroma, resulting from the perception of volatiles by the olfactory receptors, are important in consumer food acceptance. To develop more efficient molecular breeding tools to improve the odor/aroma on maize (Zea mays L.), a staple food crop, increasing the knowledge on the genetic basis of maize volatilome is needed. In this work, we conducted a genome-wide association study on a unique germplasm collection to identify genomic regions controlling maize wholemeal flour's volatilome. We identified 64 regions on the maize genome and candidate genes controlling the levels of 15 volatiles, mainly aldehydes. As an example, the Zm00001d033623 gene was within a region associated with 2-octenal (E) and 2-nonenal (E), two byproducts of linoleic acid oxidation. This gene codes for linoleate 9S-lipoxygenase, an enzyme responsible for oxidizing linoleic acid. This knowledge can now support the development of molecular tools to increase the selection efficacy/efficiency of these volatiles within maize breeding programs.

Alleles to Enhance Antioxidant Content in Maize-A Genome-Wide Association Approach

The interest in antioxidant compound breeding in maize (Zea mays L.), a major food crop, has increased in recent years. However, breeding of antioxidant compounds in maize can be hampered, given the complex genetic nature of these compounds. In this work, we followed a genome-wide association approach, using a unique germplasm collection (containing Portuguese germplasm), to study the genetic basis of several antioxidants in maize. Sixty-seven genomic regions associated with seven antioxidant compounds and two color-related traits were identified. Several significant associations were located within or near genes involved in the carotenoid (Zm00001d036345) and tocopherol biosynthetic pathways (Zm00001d017746). Some indications of a negative selection against α-tocopherol levels were detected in the Portuguese maize germplasm. The strongest single nucleotide polymorphism (SNP)-trait associations and the SNP alleles with larger effect sizes were pinpointed and set as priority for future validation studies; these associations detected now constitute a benchmark for developing molecular selection tools for antioxidant compound selection in maize.

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.

Variation in Pea (Pisum sativum L.) Seed Quality Traits Defined by Physicochemical Functional Properties

Pea is one of the most produced and consumed pulse crops around the world. The study of genetic variability within pea germplasm is an important tool to identify outstanding accessions with optimal functional and nutritional qualities. In the present study, a collection of 105 pea accessions was analysed for physicochemical properties, pasting viscosity, and basic composition parameters. While pasting viscosities were negatively correlated to hydration capacity, cooking time, and basic composition, a positive correlation was found between the hydration capacity and the basic composition parameters. Basic composition (protein, fibre, fat, and resistant starch) parameters were further evaluated regarding seed trait morphology, namely, seed shape, colour, and surface. Allelic characterisation at the r and rb genetic loci was performed in a subgroup of 32 accessions (3 phenotyped as smooth and 29 as rough seeded), revealing that none of the initially classified rough-seeded accessions were rb mutants, 19 were r mutants, and 13 were neither r nor rb. Despite their initial phenotypic classification, the 13 accessions genetically classified as smooth behaved differently (p < 0.05) to the 19 r mutants in terms of physicochemical properties, pasting viscosity, and basic composition parameters. Using multivariate analysis of the most discriminatory parameters for the food-related traits studied, the best-performing accessions at functional and nutritional levels were identified for future plant breeding to improve field pea production and consumption.

Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour

BACKGROUND

Maize is a crop in high demand for food purposes and consumers worldwide are increasingly concerned with food quality. However, breeding for improved quality is a complex task and therefore developing tools to select for better quality products is of great importance. Kernel composition, flour pasting behavior, and flour particle size have been previously identified as crucial for maize-based food quality. In this work we carried out a genome-wide association study to identify genomic regions controlling compositional and pasting properties of maize wholemeal flour.

RESULTS

A collection of 132 diverse inbred lines, with a considerable representation of the food used Portuguese unique germplasm, was trialed during two seasons, and harvested samples characterized for main compositional traits, flour pasting parameters and mean particle size. The collection was genotyped with the MaizeSNP50 array. SNP-trait associations were tested using a mixed linear model accounting for genetic relatedness. Fifty-seven genomic regions were identified, associated with the 11 different quality-related traits evaluated. Regions controlling multiple traits were detected and potential candidate genes identified. As an example, for two viscosity parameters that reflect the capacity of the starch to absorb water and swell, the strongest common associated region was located near the dull endosperm 1 gene that encodes a starch synthase and is determinant on the starch endosperm structure in maize.

CONCLUSIONS

This study allowed for identifying relevant regions on the maize genome affecting maize kernel composition and flour pasting behavior, candidate genes for the majority of the quality-associated genomic regions, or the most promising target regions to develop molecular tools to increase efficacy and efficiency of quality traits selection (such as "breadability") within maize breeding programs.

Warm Season Grain Legume Landraces From the South of Europe for Germplasm Conservation and Genetic Improvement

Currently, there is a high concern from consumers regarding food quality, with emphasis on the origin of food sources. We here review the current situation of beans (Phaseolus spp.) and cowpea (Vigna unguiculata (L.) Walp.) landraces in the South of Europe focusing on morpho-agronomic and genetic diversity and physiological adaptation to the different agrosystems, including the symbiotic association with rhizobia. Despite the reduction in the production and consumption of grain legumes in Southern Europe, the variability of common bean, runner bean and cowpea landraces in this region is adequately preserved ex situ in germplasm banks and in breeder collections in Portugal, Spain, Italy and Greece; however, on-farm (in situ) conservation in isolated areas mainly in gardens and small fields for farmers own consumption and local markets is not guaranteed. This variability can be used for the genetic improvement of varieties, which will result in environmental-friendly improved legumes for a sustainable production in the South of Europe as well as in other regions of the World.

Elucidating potential utilization of Portuguese common bean varieties in rice based processed foods

The present study was aimed at studying the physico-chemical and functional properties of 31 Portuguese common bean varieties. In addition, the whole bean flours (WBF) and starch isolates (SI) of three representative bean varieties and their rice: bean blends (70:30; 50:50) were assessed for amylose content, thermal and pasting properties in view of supplementation in rice based processed foods. Bean varieties showed significant differences in protein content (20.78-27.10%), fat content (1.16-2.18%), hydration capacity (95.90-149.30%), unhydrated seeds (4.00-40.00%), γ tocopherol (3.20-98.05 mg/100 g fat), δ tocopherol (0.06-4.72 mg/100 g fat) and pasting behavior. Amylose content of WBF (11.4-20.2%) was significantly lower than rice flour (23.51%) whereas SI of beans (40.00-47.26%) had significantly higher amylose content than SI of rice (28.13%). DSC results showed that WBF (11.4-20.2 °C) had significantly broader and lower gelatinization temperature range (∆Tr) than corresponding SI (20.9-23.1 °C). WBF had significantly lower pasting viscosity due to low starch content and compositional matrix effect as compared to SI. Setback viscosities of WBF and rice: bean blends was lower than rice flour. Low setback viscosities of rice:bean blends may be used to prevent syneresis and stabilizing the quality of frozen foods in rice based processed foods.

First genetic linkage map of Lathyrus cicera based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance

The Lathyrus cicera transcriptome was analysed in response to rust (Uromyces pisi) infection to develop novel molecular breeding tools with potential for genetic mapping of resistance in this robust orphan legume species. One RNA-seq library each was generated from control and rust-inoculated leaves from two L. cicera genotypes with contrasting quantitative resistance, de novo assembled into contigs and sequence polymorphisms were identified. In toto, 19,224 SNPs differentiate the susceptible from the partially resistant genotype's transcriptome. In addition, we developed and tested 341 expressed E-SSR markers from the contigs, of which 60.7% varied between the two L. cicera genotypes. A first L. cicera linkage map was created using part of the developed markers in a RIL population from the cross of the two genotypes. This map contains 307 markers, covered 724.2 cM and is organised in 7 major and 2 minor linkage groups, with an average mapping interval of 2.4 cM. The genic markers also enabled us to compare their position in L. cicera map with the physical position of the same markers mapped on Medicago truncatula genome, highlighting a high macrosyntenic conservation between both species. This study provides a large new set of genic polymorphic molecular markers with potential for mapping rust resistances. It represents the first step towards genomics-assisted precision breeding in L. cicera.

Relevance, structure and analysis of ferulic acid in maize cell walls

Phenolic compounds in foods have been widely studied due to their health benefits. In cereals, phenolic compounds are extensively linked to cell wall polysaccharides, mainly arabinoxylans, which cross-link with each other and with other cell wall components. In maize, ferulic acid is the phenolic acid present in the highest concentration, forming ferulic acid dehydrodimers, trimers and tetramers. The cross-linking of polysaccharides is important for the cell wall structure and growth, and may protect against pathogen invasion. In addition to the importance for maize physiology, ferulic acid has been recognized as an important chemical structure with a wide range of health benefits when consumed in a diet rich in fibre. This review paper presents the different ways ferulic acid can be present in maize, the importance of ferulic acid derivatives and the methodologies that can be used for their analysis.

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic–climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long‐term participatory breeding/on‐farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on‐farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common‐garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low‐cost methodologies, proved to be an alternative strategy for genetic resources’ on‐farm conservation.

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny

MAIZE EAR FASCIATION

Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces.

MATERIAL AND METHODS

Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed.

RESULTS AND DISCUSSION

Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection.

CONCLUSIONS

Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning.

Allelic diversity in the transcriptomes of contrasting rust-infected genotypes of Lathyrus sativus, a lasting resource for smart breeding

BACKGROUND

Grass pea (Lathyrus sativus L.) is a valuable resource for potentially durable partial resistance to rust. To gain insight into the resistance mechanism and identify potential resistance genes, we generated the first comprehensive transcriptome assemblies from control and Uromyces pisi inoculated leafs of a susceptible and a partially rust-resistant grass pea genotype by RNA-seq.

RESULTS

134,914 contigs, shared by both libraries, were used to analyse their differential expression in response to rust infection. Functional annotation grouped 60.4% of the contigs present in plant databases (37.8% of total) to 33 main functional categories, being "protein", "RNA", "signalling", "transport" and "stress" the most represented. Transcription profiles revealed considerable differences in regulation of major phytohormone signalling pathways: whereas Salicylic and Abscisic Acid pathways were up-regulated in the resistant genotype, Jasmonate and Ethylene pathways were down-regulated in the susceptible one. As potential Resistance-genes we identified a mildew resistance locus O (MLO)-like gene, and MLO-related transcripts. Also, several pathogenesis-related genes were up-regulated in the resistant and exclusively down regulated in the susceptible genotype. Pathogen effectors identified in both inoculated libraries, as e.g. the rust Rtp1 transcript, may be responsible for the down-regulation of defence-related transcripts. The two genotypes contained 4,892 polymorphic contigs with SNPs unevenly distributed between different functional categories. Protein degradation (29.7%) and signalling receptor kinases (8.2%) were the most diverged, illustrating evolutionary adaptation of grass pea to the host/pathogens arms race.

CONCLUSIONS

The vast array of novel, resistance-related genomic information we present here provides a highly valuable resource for future smart breeding approaches in this hitherto under-researched, valuable legume crop.

Performance index: An expeditious tool to screen for improved drought resistance in the Lathyrus genus

Some species of the Lathyrus genus are among the most promising crops for marginal lands, with high resilience to drought, flood, and fungal diseases, combined with high yields and seed nutritional value. However, lack of knowledge on the mechanisms underlying its outstanding performance and methodologies to identify elite genotypes has hampered its proper use in breeding. Chlorophyll a fast fluorescence transient (JIP test), was used to evaluate water deficit (WD) resistance in Lathyrus genus. Our results reveal unaltered photochemical values for all studied genotypes showing resistance to mild WD. Under severe WD, two Lathyrus sativus genotypes showed remarkable resilience maintaining the photochemical efficiency, contrary to other genotypes studied. Performance index (PIABS) is the best parameter to screen genotypes with improved performance and grain production under WD. Moreover, we found that JIP indices are good indicators of genotypic grain production under WD. Quantum yield of electron transport (ϕEo) and efficiency with which trapped excitons can move electrons further than QA (ψ0) revealed as important traits related to improved photosynthetic performance and should be exploited in future Lathyrus germplasm improvements. The JIP test herein described showed to be an expeditious tool to screen and to identify elite genotypes with improved drought resistance.

Unveiling common responses of Medicago truncatula to appropriate and inappropriate rust species

Little is known about the nature of effective defense mechanisms in legumes to pathogens of remotely related plant species. Some rust species are among pathogens with broad host range causing dramatic losses in various crop plants. To understand and compare the different host and nonhost resistance (NHR) responses of legume species against rusts, we characterized the reaction of the model legume Medicago truncatula to one appropriate (Uromyces striatus) and two inappropriate (U. viciae-fabae and U. lupinicolus) rusts. We found that similar pre and post-haustorial mechanisms of resistance appear to be operative in M. truncatula against appropriate and inappropriate rust fungus. The appropriate U. striatus germinated better on M. truncatula accessions then the inappropriate U. viciae-fabae and U. lupinicolus, but once germinated, germ tubes of the three rusts had a similar level of success in finding stomata and forming an appressoria over a stoma. However, responses to different inappropriate rust species also showed some specificity, suggesting a combination of non-specific and specific responses underlying this legume NHR to rust fungi. Further genetic and expression analysis studies will contribute to the development of the necessary molecular tools to use the present information on host and NHR mechanisms to breed for broad-spectrum resistance to rust in legume species.