Recent advances in faba bean genetic and genomic tools for crop improvement

Targeted genotyping (90K-SPET) facilitates genome-wide association studies and the prediction of yield-related traits in faba bean (Vicia faba L.)

BACKGROUND

Establishing faba bean (Vicia faba L.) as a major protein crop in Europe requires developing high-yielding varieties. However, the genetic regulation of yield-related traits is currently under-explored. These traits can be improved by exploiting the extensive but largely uncharacterized faba bean germplasm. Our study aimed to identify associations between 38,014 single nucleotide polymorphisms (SNPs) and flowering time (FT), plant height (PH), pod length (PL), seeds per pod (SP), and single seed weight (SSW) in 245 faba bean accessions (CGN panel) via a Genome-Wide Association Study (GWAS). The accessions were grown in 2021 and 2022 in the Netherlands. Additionally, we developed genomic selection (GS) models to predict the genetic merit within large germplasm collections for the mentioned traits, as well as yield (YLD).

RESULTS

The CGN panel was an optimal panel for performing high-resolution GWAS, showing large phenotypic variation, high narrow-sense heritability for all traits, and minimal genetic relatedness among accessions. Population structure analysis revealed the presence of four genetic groups. GWAS uncovered 33 SNP-trait associations in 2021 and 17 in 2022. We identified one stable QTL for FT and four for SSW over the two years, representing key molecular markers for testing in breeding applications. Short linkage disequilibrium decay (~ 268 Kbp) facilitated the identification of several important candidate genes with interesting homologs in other crops. Ten SNPs in 2021 and five in 2022 were predicted to be intra-genic missense variants, potentially altering protein function. Moreover, modeling the SNP effect simultaneously via Bayesian GS showed promising predictive ability (PA) and prediction accuracy (ACC), supporting their potential application in germplasm-improvement programs. Predictive ability ranged from 0.58 to 0.81 in 2021, and 0.47 to 0.85 in 2022 for different traits. Additionally, across-year predictions showed stable PA.

CONCLUSION

GWAS revealed promising QTLs for use in molecular breeding and highlighted new candidate genes. Interestingly, the prediction of intra-genic SNPs categorized 15 SNPs as putatively affecting protein function. Moreover, we demonstrated for the first time in faba bean that GS has the potential to unlock untapped diversity in genebank collections and accelerate trait integration into faba bean breeding programs.

A high-density linkage map and fine QTL mapping of architecture, phenology, and yield-related traits in faba bean (Vicia faba L.)

Faba bean is a key protein feed and food worldwide that still requires accurate genomic tools to facilitate molecular marker-assisted breeding. Efficient quantitative trait locus (QTL) mapping in faba bean is restricted by the low or medium density of most of the available genetic maps. In this study, a recombinant inbred line faba bean population including 124 lines from the cross Vf6 x Vf27, highly segregating for autofertility, flowering time, plant architecture, dehiscence, and yield-related traits, was genotyped using the 'Vfaba_v2' SNP array. Genotypic data were used to generate a high-density genetic map that, after quality control and filtering, included 2,296 SNP markers. The final map consisted of 1,674 bin markers distributed across the six faba bean chromosomes, covering 2,963.87 cM with an average marker distance of 1.77 cM. A comparison of the physical and genetic maps revealed a good correspondence between chromosomes and linkage groups. QTL analysis of 66 segregating traits, previously phenotyped in different environments and years, identified 99 significant QTLs corresponding to 35 of the traits. Most QTLs were stable over the years and QTLs for highly correlated traits were mapped to the same or adjacent genomic regions. Colocalization of QTLs occurred in 13 major regions, joining three or more overlapping QTLs. Some of the pleiotropic QTL regions, especially in chromosome VI, shared the same significant marker for different traits related to pollen quantity and size, number of ovules per ovary, seeds per pod, and pod set. Finally, several putative candidate genes for yield-related traits, recently identified using a genome-wide association study, fall inside the colocalizing groups described in this study, indicating that, apart from refining the position of the QTLs and the detection of candidates, the dense new map provides a valuable tool for validation of causative loci derived from association studies and will help advance breeding programs in this crop.

A special short-wing petal faba genome and genetic dissection of floral and yield-related traits accelerate breeding and improvement of faba bean

BACKGROUND

A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of the seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate.

RESULTS

To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome-wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combining quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences, and protein structure variation.

CONCLUSIONS

Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.

Lower vicine content reduces the reproductive yield performance in faba bean (Vicia faba L.)

Faba bean is a nutritionally and medicinally rich popular legume crop. However, vicine-convicine remain as potential threats for "favism" in human beings. In this study, 189 diverse faba bean accessions have been evaluated for yield component traits and vicine content in seeds followed by a correlation study. Combined genetic variability analysis shows that traits like days to pod initiation (DPI), pod length (PL), test weight (TW) and grain yield have minimally been influenced by the environment. PCA revealed that TW, PL and PW were the primary indicators for deciding yield performance. LC-MS/MS confirms that vicine concentration varied in between 3.489 and 10.025 g/kg and a significant positive correlation (0.40***) was observed between vicine conc. and grain yield of faba bean. Thus, present study demonstrated that the faba bean genotypes containing lower vicine were mostly poor yielding, which might be regulated by vicine in faba bean. Therefore, complete elimination of vicine or development of near-zero vicine faba bean could drastically reduce the yield potential of the crop, hence one has to be very cautious and follow efficient selection strategies while optimizing lower concentration of vicine for development of low vicine varieties. This study shows that faba bean genotypes containing 4.0-5.5 g/kg vicine were fairly productive and also have considerably lower vicine.

The Jan Sjödin faba bean mutant collection: morphological and molecular characterization

BACKGROUND

Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934-2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays.

RESULTS

We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype.

CONCLUSIONS

The mutants' phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies.

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

Transcriptome Analysis of Stigmas of Vicia faba L. Flowers

Pollination in angiosperms depends on complex communication between pollen grains and stigmas, classified as wet or dry, depending on the presence or absence of secretions at the stigma surface, respectively. In species with wet stigma, the cuticle is disrupted and the presence of exudates is indicative of their receptivity. Most stigma studies are focused on a few species and families, many of them with self-incompatibility systems. However, there is scarce knowledge about the stigma composition in Fabaceae, the third angiosperm family, whose stigmas have been classified as semidry. Here we report the first transcriptome profiling and DEGs of Vicia faba L. styles and stigmas from autofertile (flowers able to self-fertilize in the absence of manipulation, whose exudate is released spontaneously) and autosterile (flowers that need to be manipulated to break the cuticle and release the exudates to be receptive) inbred lines. From the 76,269 contigs obtained from the de novo assembly, only 45.1% of the sequences were annotated with at least one GO term. A total of 115,920, 75,489, and 70,801 annotations were assigned to Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) categories, respectively, and 5918 differentially expressed genes (DEGs) were identified between the autofertile and the autosterile lines. Among the most enriched metabolic pathways in the DEGs subset were those related with amino acid biosynthesis, terpenoid metabolism, or signal transduction. Some DEGs have been related with previous QTLs identified for autofertility traits, and their putative functions are discussed. The results derived from this work provide an important transcriptomic reference for style-stigma processes to aid our understanding of the molecular mechanisms involved in faba bean fertilization.

Identification of Faba bean genetic loci associated with quantitative resistance to the fungus Botrytis fabae, causal agent of chocolate spot

Introduction

Chocolate spot, caused by the ascomycete fungus Botrytis fabae, is a devastating foliar disease and a major constraint on the quality and yield of faba beans (Vicia faba). The use of fungicides is the primary strategy for controlling the disease. However, high levels of partial genetic resistance have been identified and can be exploited to mitigate the disease.

Methods

The partially resistant V. faba cultivar Maris Bead and susceptible Egyptian accession ig70726 were crossed, and a genetic mapping population of 184 individuals was genotyped in the F2 generation and screened for resistance to B. fabae infection in the F3, F5, and F6 generations in a series of field experiments. A high-density linkage map of V. faba containing 3897 DArT markers spanning 1713.7 cM was constructed.

Results

Multiple candidate quantitative trait loci (QTLs) in 11 separate regions of the V. faba genome were identified; some on chromosomes 2, 3, and 6 overlapped with loci previously linked to resistance to Ascochyta leaf and pod blight caused by the necrotrophic fungus Ascochyta fabae. A transcriptomics experiment was conducted at 18 h post-inoculation in seedlings of both parents of the mapping population, identifying several differentially expressed transcripts potentially involved in early stage defence against B. fabae, including cell-wall associated protein kinases, NLR genes, and genes involved in metabolism and response to reactive oxygen species.

Discussion

This study identified several novel candidate QTLs in the V. faba genome that contribute to partial resistance to chocolate spot, but differences between growing seasons highlighted the importance of multi-year phenotyping experiments when searching for candidate QTLs for partial resistance.

Genome-wide association study for yield-related traits in faba bean (Vicia faba L.)

Yield is the most complex trait to improve crop production, and identifying the genetic determinants for high yield is a major issue in breeding new varieties. In faba bean (Vicia faba L.), quantitative trait loci (QTLs) have previously been detected in studies of biparental mapping populations, but the genes controlling the main trait components remain largely unknown. In this study, we investigated for the first time the genetic control of six faba bean yield-related traits: shattering (SH), pods per plant (PP), seeds per pod (SP), seeds per plant (SPL), 100-seed weight (HSW), and plot yield (PY), using a genome-wide association study (GWAS) on a worldwide collection of 352 homozygous faba bean accessions with the aim of identifying markers associated with them. Phenotyping was carried out in field trials at three locations (Spain, United Kingdom, and Serbia) over 2 years. The faba bean panel was genotyped with the Affymetrix faba bean SNP-chip yielding 22,867 SNP markers. The GWAS analysis identified 112 marker-trait associations (MTAs) in 97 candidate genes, distributed over the six faba bean chromosomes. Eight MTAs were detected in at least two environments, and five were associated with multiple traits. The next step will be to validate these candidates in different genetic backgrounds to provide resources for marker-assisted breeding of faba bean yield.

Novel SNP markers for flowering and seed quality traits in faba bean (Vicia faba L.): characterization and GWAS of a diversity panel

Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.

Thaumatin-like protein family genes VfTLP4-3 and VfTLP5 are critical for faba bean's response to drought stress at the seedling stage

Thaumatin-like proteins (TLPs) are a diverse family of pathogenesis-related proteins (PR-5) found in various plant species. Faba bean is an economically important crop known for its nutritional value and resilience to harsh environmental conditions, including drought. In this study, we conducted a comprehensive analysis of the gene structure, phylogenetics, and expression patterns of TLP genes in faba bean, with a specific focus on their response to drought stress. A total of 10 TLP genes were identified and characterized from the faba bean transcriptome, which could be classified into four distinct groups based on their evolutionary relationships. Conserved cysteine residues and REDDD motifs, which are characteristic features of TLPs, were found in most of the identified VfTLP members, and these proteins were likely to reside in the cytoplasm. Two genes, VfTLP4-3 and VfTLP5, exhibited significant upregulation under drought conditions. Additionally, ectopically expressing VfTLP4-3 and VfTLP5 in tobacco leaves resulted in enhanced drought tolerance and increased peroxidase (POD) activity. Moreover, the protein VfTLP4-3 was hypothesized to interact with glycoside hydrolase family 18 (GH18), endochitinase, dehydrin, Barwin, and aldolase, all of which are implicated in chitin metabolism. Conversely, VfTLP5 was anticipated to associate with peptidyl-prolyl cis-trans isomerase-like 3, a molecule linked to the synthesis of proline. These findings suggest that these genes may play crucial roles in mediating the drought response in faba bean through the regulation of these metabolic pathways, and serve as a foundation for future genetic improvement strategies targeting enhanced drought resilience in this economically important crop.

The challenge of breeding for reduced off-flavor in faba bean ingredients

The growing interest in plant protein sources, such as pulses, is driven by the necessity for sustainable food production and climate change mitigation strategies. Faba bean (Vicia faba L.) is a promising protein crop for temperate climates, owing to its remarkable yield potential (up to 8 tonnes ha-1 in favourable growing conditions) and high protein content (~29% dry matter basis). Nevertheless, the adoption of faba bean protein in plant-based products that aim to resemble animal-derived counterparts is hindered by its distinctive taste and aroma, regarded as "off-flavors". In this review, we propose to introduce off-flavor as a trait in breeding programs by identifying molecules involved in sensory perception and defining key breeding targets. We discuss the role of lipid oxidation in producing volatile and non-volatile compounds responsible for the beany aroma and bitter taste, respectively. We further investigate the contribution of saponin, tannin, and other polyphenols to bitterness and astringency. To develop faba bean varieties with diminished off-flavors, we suggest targeting genes to reduce lipid oxidation, such as lipoxygenases (lox) and fatty acid desaturases (fad), and genes involved in phenylpropanoid and saponin biosynthesis, such as zero-tannin (zt), chalcone isomerase (chi), chalcone synthase (chs), β-amyrin (bas1). Additionally, we address potential challenges, including the need for high-throughput phenotyping and possible limitations that could arise during the genetic improvement process. The breeding approach can facilitate the use of faba bean protein in plant-based food such as meat and dairy analogues more extensively, fostering a transition toward more sustainable and climate-resilient diets.

Generation Mean Analysis, Heterosis, and Genetic Diversity in Five Egyptian Faba Beans and Their Hybrids

The faba bean (Vicia faba L.) is a major legume crop; thus, it is important to apply various biometrical techniques to develop the most efficient breeding procedures to face biotic and abiotic stressors. During the four consecutive winter seasons of 2017–2021, five populations of five faba bean hybrids were studied at Sakha agricultural research station in Egypt. Five basic generations, including two parents (P1 and P2) and the first, second, and third generations, were studied. This analysis found significant variations between generations in all attributes studied in all crosses (P1, P2, F1, F2, and F3). Sakha 4 was the earliest parent (138 days) based on the maturity date, whereas Giza 40 had the most significant number of pods and seeds per plant (25.68–78.94), and Giza 716 had the tallest plant height (124.00 cm). Giza 843 and Sakha 4 had the highest seed yield per plant values (62.84 g and 61.77 g). The data demonstrated highly substantial heterosis in the favorable direction over mid and better parents for all features, except for the number of branches in Cross 3 (Giza 40 × Giza 843) over mid and better parents and a maturity date in Cross 1 over mid parents. Contrarily, opposite-direction dominance and dominance × dominance effects increased narrow-sense heredity. Broad-sense heritability values for all examined characteristics were high in all crosses, ranging from 90.24% to 97.67%. In both Crosses 5 (Giza 716 × Qahera 4) and 3, genetic advance through selection ranged from 1.73% at the maturity date to 95.12% for seed yield per plant. Cross 3 (Giza 40 × Giza 843) had the greatest number of branches, pods, and seeds per plant. In conclusion, this study advances our understanding of employing faba beans in breeding programs.

Homolog of Pea SGR Controls Stay-Green in Faba Bean (Vicia faba L.)

Faba bean is an important legume crop consumed as a vegetable or snack food, and its green cotyledons could present an attractive color for consumers. A mutation in SGR causes stay-green in plants. In this study, vfsgr was identified from a green-cotyledon-mutant faba bean, SNB7, by homologous blast between the SGR of pea and the transcriptome of faba bean. Sequence analysis revealed that a SNP at position 513 of the CDS of VfSGR caused a pre-stop codon, resulting in a shorter protein in the green-cotyledon faba bean SNB7. A dCaps marker was developed according to the SNP that caused the pre-stop, and this marker was completely associated with the color of the cotyledon of faba bean. SNB7 stayed green during dark treatment, while the expression level of VfSGR increased during dark-induced senescence in the yellow-cotyledon faba bean HST. Transient expression of VfSGR in Nicotiana. benthamiana leaves resulted in chlorophyll degradation. These results indicate that vfsgr is the gene responsible for the stay-green of faba bean, and the dCaps marker developed in this study provides a molecular tool for the breeding of green-cotyledon faba beans.

Genetic analysis of global faba bean diversity, agronomic traits and selection signatures

KEY MESSAGE

We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.

Identifying physiological and genetic determinants of faba bean transpiration response to evaporative demand

BACKGROUND AND AIMS

Limiting maximum transpiration rate (TR) under high vapour pressure deficit (VPD) works as a water conservation strategy. While some breeding programmes have incorporated this trait into some crops to boost yields in water-limited environments, its underlying physiological mechanisms and genetic regulation remain unknown for faba bean (Vicia faba). Thus, we aimed to identify genetic variation in the TR response to VPD in a population of faba bean recombinant inbred lines (RILs) derived from two parental lines with contrasting water use (Mélodie/2 and ILB 938/2).

METHODS

Plants were grown in well-watered soil in a climate-controlled glasshouse with diurnally fluctuating VPD and light conditions. Whole plant transpiration was measured in a gas exchange chamber that tightly regulated VPD around the shoot under constant light, while whole-plant hydraulic conductance and its components (root and stem hydraulic conductance) were calculated from dividing TR by water potential gradients measured with a pressure chamber.

KEY RESULTS

Although TR of Mélodie/2 increased linearly with VPD, ILB 938/2 limited its TR above 2.0 kPa. Nevertheless, Mélodie/2 had a higher leaf water potential than ILB 938/2 at both low (1.0 kPa) and high (3.2 kPa) VPD. Almost 90 % of the RILs limited their TR at high VPD with a break-point (BP) range of 1.5-3.0 kPa and about 10 % had a linear TR response to VPD. Thirteen genomic regions contributing to minimum and maximum transpiration, and whole-plant and root hydraulic conductance, were identified on chromosomes 1 and 3, while one locus associated with BP transpiration was identified on chromosome 5.

CONCLUSIONS

This study provides insight into the physiological and genetic control of transpiration in faba bean and opportunities for marker-assisted selection to improve its performance in water-limited environments.

Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is an important high protein legume adapted to diverse climatic conditions with multiple benefits for the overall sustainability of the cropping systems. Plant-based protein demand is being expanded and faba bean is a good candidate to cover this need. However, the crop is very sensitive to abiotic stresses, especially drought, which severely affects faba bean yield and development worldwide. Therefore, identifying genes associated with drought stress tolerance is a major challenge in faba bean breeding. Although the faba bean response to drought stress has been widely studied, the molecular approaches to improve drought tolerance in this crop are still limited. Here we built on recent genomic advances such as the development of the first high-density SNP genotyping array, to conduct a genome-wide association study (GWAS) using thousands of genetic polymorphisms throughout the entire faba bean genome. A worldwide collection of 100 faba bean accessions was grown under control and drought conditions and 10 morphological, phenological and physiological traits were evaluated to identify single nucleotide polymorphism (SNP) markers associated with drought tolerance. We identified 29 SNP markers significantly correlated with these traits under drought stress conditions. The flanking sequences were blasted to the Medicago truncatula reference genomes in order to annotate potential candidate genes underlying the causal variants. Three of the SNPs for chlorophyll content after the stress, correspond to uncharacterized proteins indicating the presence of novel genes associated with drought tolerance in faba bean. The significance of stress-inducible signal transducers provides valuable information on the possible mechanisms underlying the faba bean response to drought stress, thus providing a foundation for future marker-assisted breeding in the crop.

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.

Seed Development and Protein Accumulation Patterns in Faba Bean (Vicia faba, L.)

A major objective in faba bean breeding is to improve its protein quality by selecting cultivars with enhanced desirable physicochemical properties. However, the protein composition of the mature seed is determined by a series of biological processes occurring during seed growth. Thus, any attempt to explain the final seed composition must consider the dynamics of the seed proteome during seed development. Here, we investigated the proteomic profile of developing faba bean seeds across 12 growth stages from 20 days after pollination (DAP) to full maturity. We analyzed trypsin-digested total protein extracts from the seeds at different growth stages by liquid chromatography-tandem mass spectrometry (LC-MS/MS), identifying 1217 proteins. The functional clusters of these proteins showed that, in early growth stages, proteins related to cell growth, division, and metabolism were most abundant compared to seed storage proteins that began to accumulate from 45 DAP. Moreover, label-free quantification of the relative abundance of seed proteins, including important globulin proteins, revealed several distinct temporal accumulation trends among the protein classes. These results suggest that these proteins are regulated differently and require further understanding of the impact of the different environmental stresses occurring at different grain filling stages on the expression and accumulation of these seed storage proteins.

Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects

Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.

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.

Genetic Variability of Tunisian Faba Beans (Vicia faba L.) Based on Seeds’ Morphophysical Properties as Assessed by Statistical Analysis

Faba bean (Vicia faba L.) is a legume crop cultivated for its nutritious seeds that are an important worldwide source of human food and feed. Seeds characterization is a prerequisite step for faba bean quality improvement. The morphophysical characterization of the seeds of twenty-four local faba bean accessions following the UPOV descriptors and the AOAC International standards was carried out and assessed with an approach based on Euclidean statistical model. “205 Bulk” was the unique accession harboring white hilum color seed which is linked to low convicine grain content. Irregular seed shape was the most observed character among the studied accessions except “Badii” displaying an elliptical seed shape; therefore, seed shape did not allow discrimination within our Tunisian germplasm. Interestingly, the physical characters of the seeds showed significant diversity between the accessions for all the measured parameters. A highly significant variability was observed for axial, length, and width dimensions of seeds, with “Memdouh” being the longest and largest seed accession, whereas “01-02” was the shortest and narrowest. Classification of the studied faba bean germplasm accessions based on morphophysical characters using clustering by Euclidean distance revealed three different groups. Moreover, multivariate PCA analysis further classified the faba bean accessions into four main clusters. Correlation study performed by using Spearman’s test established positive correlations within physical parameters of seeds such as between mean length and mean width of seeds. Therefore, using morphophysical parameters screening, valuable phenotypes have been selected for deeper physiological characterization and further breeding programs.

Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean (Vicia Faba L.)

Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc -) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.