Phenotyping revealed tolerance traits and genotypes for acidity and aluminum toxicity in European Vicia faba L.

Soil acidity is a global issue; soils with pH <4.5 are widespread in Europe. This acidity adversely affects nutrient availability to plants; pH levels <5.0 lead to aluminum (Al3+) toxicity, a significant problem that hinders root growth and nutrient uptake in faba bean (Vicia faba L.) and its symbiotic relationship with Rhizobium. However, little is known about the specific traits and tolerant genotypes among the European faba beans. This study aimed to identify response traits associated with tolerance to root zone acidity and Al3+ toxicity and potentially tolerant genotypes for future breeding efforts. Germplasm survey was conducted using 165 genotypes in a greenhouse aquaponics system. Data on the root and shoot systems were collected. Subsequently, 12 genotypes were selected for further phenotyping in peat medium, where data on physiological and morphological parameters were recorded along with biochemical responses in four selected genotypes. In the germplasm survey, about 30% of genotypes showed tolerance to acidity and approximately 10% exhibited tolerance to Al3+, while 7% showed tolerance to both. The phenotyping experiment indicated diverse morphological and physiological responses among treatments and genotypes. Acid and Al3+ increased proline concentration. Interaction between genotype and environment was observed for ascorbate peroxidase activity, malondialdehyde, and proline concentrations. Genomic markers associated with acidity and acid+Al3+-toxicity tolerances were identified using GWAS analysis. Four faba bean genotypes with varying levels of tolerance to acidity and Al3+ toxicity were identified.

Green synthesis of a dual-functional sulfur nanofertilizer to promote growth and enhance salt stress resilience in faba bean.

BACKGROUND: Salinity is a major abiotic stress, and the use of saline water in the agricultural sector will incur greater demand under the current and future climate changing scenarios. The objective of this study was to develop a dual-functional nanofertilizer capable of releasing a micronutrient that nourishes plant growth while enhancing salt stress resilience in faba bean (Vicia faba L.). RESULTS: Moringa oleifera leaf extract was used to synthesize sulfur nanoparticles (SNPs), which were applied as a foliar spray at different concentrations (0, 25, 50, and 100 mg/l) to mitigate the negative effects of salt stress (150 mM NaCl) on faba bean plants. The SNPs were characterized and found to be spherical in shape with an average size of 10.98 ± 2.91 nm. The results showed that salt stress had detrimental effects on the growth and photosynthetic performance (Fv/Fm) of faba bean compared with control, while foliar spraying with SNPs improved these parameters under salinity stress. SNPs application also increased the levels of osmolytes (soluble sugars, amino acids, proline, and glycine betaine) and nonenzymatic antioxidants, while reducing the levels of oxidative stress biomarkers (MDA and H2O2). Moreover, SNPs treatment under salinity stress stimulated the activity of antioxidant enzymes (ascorbate peroxidase (APX), and peroxidase (POD), polyphenol oxidase (PPO)) and upregulated the expression of stress-responsive genes: chlorophyll a-b binding protein of LHCII type 1-like (Lhcb1), ribulose bisphosphate carboxylase large chain-like (RbcL), cell wall invertase I (CWINV1), ornithine aminotransferase (OAT), and ethylene-responsive transcription factor 1 (ERF1), with the greatest upregulation observed at 50 mg/l SNPs. CONCLUSION: Overall, foliar application of sulfur nanofertilizers in agriculture could improve productivity while minimizing the deleterious effects of salt stress on plants. Therefore, this study provides a strong foundation for future research focused on evaluating the replacement of conventional sulfur-containing fertilizers with their nanoforms to reduce the harmful effects of salinity stress and enhance the productivity of faba beans.

Offsetting pb induced oxidative stress in Vicia faba plants by foliar spray of chitosan through adjustment of morpho-biochemical and molecular indices.

In the course of their life, plants face a multitude of environmental anomaly that affects their growth and production. In recent decades, lead (Pb) gained an increasing attention as it is among the most significant contaminants in the environment. Therefore, in this study the effects of Pb concentrations (0, 50 and 100 ppm) on Vicia faba plants and attempts to alleviate this stress using chitosan (Chs; 0 and 0.1%) were performed. The results validated that with increasing Pb concentrations, a decline in growth, pigments and protein contents was observed. In the same time, a significant upsurge in the stress markers, both malondialdehyde (MDA) and H2O2, was observed under Pb stress. Nonetheless, foliar spraying with Chs improves the faba bean growth, pigment fractions, protein, carbohydrates, reduces MDA and H2O2 contents and decreases Pb concentrations under Pb stress. Pb mitigation effects by Chs are probably related with the activity of antioxidant enzymes, phenylalanine ammonia lyase (PAL) and proline. The application of Chs enhanced the activities of peroxidase, catalase and PAL by 25.77, 17.71 and 20.07%, respectively at 100 ppm Pb compared to their control. Plant genomic material exhibits significant molecular polymorphism, with an average polymorphism of 91.66% across all primers. To assess the genetic distance created among treatments, the dendrogram was constructed and the results of the similarity index ranged from 0.75 to 0.95, indicating genetic divergence. Our research offers a thorough comprehension of the role of Chs in lessening the oxidative stress, which will encourage the use of Chs in agricultural plant protection.

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.

Transcriptional and physiological analyses uncover the mineralization and uptake mechanisms of phytic acid in symbiotically grown Vicia faba plants.

Legume-rhizobia symbiosis requires high phosphorus (P) in the form of ATP to convert atmospheric nitrogen (N) into ammonia. The fixed ammonia is converted to NH4+ by H+-ATPase via protonation. To the best of our knowledge, most of these research works resort to using only inorganic P (Pi) to the neglect of the organic P (Po) counterpart. As it stands, the potential regulating roles of plasma membrane (PM) H+-ATPases during legume-rhizobia symbiosis in response to phytic acid supply and how it alters and modulates the regulation of PM H+-ATPases remain obscure. To contribute to the above hypothesis, we investigate the mechanisms that coordinately facilitate the growth, uptake, and transcript expression of PM H+-ATPase gene isoforms in response to different P sources when hydroponically grown Vicia faba plants were exposed to three P treatments, viz., low- and high-Pi (2.0 and 200 µM KH2PO4; LPi and HPi), and phytic acid (200 µM; Po) and inoculated with Rhizobium leguminosarum bv. viciae 384 for 30 days. The results consistently reveal that the supply of Po improved not only the growth and biomass, but also enhanced photosynthetic parameters, P uptake and phosphatase activities in symbiotically grown Vicia faba relative to Pi. The supply of Po induced higher transcriptional expression of all PM H+-ATPase gene isoforms, with possible interactions between phosphatases and H+-ATPase genes in Vicia faba plants when exclusively reliant on N derived from nodule symbiosis. Overall, preliminary results suggest that Po could be used as an alternative nutrition in symbiotic crops to improve plant growth.

High-quality faba bean reference transcripts generated using PacBio and Illumina RNA-seq data.

The genome of faba bean was first published in 2023. To promote future molecular breeding studies, we improved the quality of the faba genome based on high-density genetic maps and the Illumina and Pacbio RNA-seq datasets. Two high-density genetic maps were used to conduct the scaffold ordering and orientation of faba bean, culminating in an increased length (i.e., 14.28 Mbp) of chromosomes and a decrease in the number of scaffolds by 45. In gene model mining and optimisation, the PacBio and Illumina RNA-seq datasets from 37 samples allowed for the identification and correction 121,606 transcripts, and the data facilitated a prediction of 15,640 alternative splicing events, 2,148 lncRNAs, and 1,752 fusion transcripts, thus allowing for a clearer understanding of the gene structures underlying the faba genome. Moreover, a total of 38,850 new genes including 56,188 transcripts were identified compared with the reference genome. Finally, the genetic data of the reference genome was integrated and a comprehensive and complete faba bean transcriptome sequence of 103,267 transcripts derived from 54,753 uni-genes was formed.

Assessing agronomic performance, chocolate spot resistance, and heat tolerance for diverse Vicia faba genotypes under varying environmental conditions.

Chocolate spot and heat stress devastatingly impact the production of faba bean, particularly under prevailing climatic changes and rising drastic environmental conditions. Hence, the adaptability of faba bean performance is a decisive objective of plant breeders to ensure its sustainable production. The present study aimed to evaluate the agronomic performance and stability of diverse eleven faba bean genotypes for yield characters, chocolate spot, and heat stress in eight different growing environments. The faba bean genotypes were evaluated at two sowing dates in two different locations during two growing seasons. The evaluated eleven faba bean genotypes were sown timely in autumn (25 October) and late sowing in early winter (25 November) in Bilbeis and Elkhatara during 2020 and 2021 growing seasons. The results exhibited substantial differences among the evaluated sowing dates, locations, and faba bean genotypes for all studied characters. The genotypes Sakha-3, Nubaria-3, Nubaria-5, Misr-3, and Wadi-1 were able to produce acceptable yield and quality characters under timely sowing in autumn and late sowing in early winter in all tested environments. Moreover, the genotypes Nubaria-3, Nubaria-4, Nubaria-5, Sakha-4, Giza-3, and Triple White exhibited better resistance to chocolate spot. The assessed faba bean genotypes were evaluated under late sowing to expose the plants to high temperature stress at flowering and throughout the anthesis and seed-filling stages. The genotypes Nubaria-5, Nubaria-3, Nubaria-4, Sakha-3, Sakha-4, Wadi-1, and Misr-3 possessed tolerance to heat stress more than the other genotypes. Different statistical methods were applied to study the stability of assessed genotypes such as joint regression, Additive Main Effect and Multiplicative Interaction (AMMI) analysis, AMMI stability value, Wricke's and Ecovalence values. The estimated stability parameters were consistent in depicting the stability of the assessed faba bean genotypes. The findings revealed that Sakha-1, Misr-3, Nubaria-4, and Nubaria-5 demonstrated stable and desirable performance across all tested environments. The heatmap was employed to classify the assessed faba bean genotypes into different groups based on agronomic performance, chocolate spot resistance and heat stress tolerance. Nubaria-3, Nubaria-4, Nubaria-5, and Misr-3 had the best performance for agronomic performance, chocolate spot resistance, and heat stress tolerance. The obtained results provide evidence of employing promising faba bean genotypes for improving the stability of agronomic performance, chocolate spot resistance, and heat stress tolerance in breeding programs principally under unprecedented climate fluctuations.

Genetic potential and inheritance pattern of agronomic traits in faba bean under free and infested Orobanche soil conditions.

BACKGROUND: Orobanche is an obligate parasite on faba bean in the Mediterranean region, causes considerable yield losses. Breeding tolerant faba bean genotypes to Orobanche is pivotal to sustain production and ensuring global food security, particularly considering the challenges posed by population growth. In the present study, seven faba bean lines and four testers were used in a line×tester mating design during 2020-2021 and 2021-2022 growing seasons. The eleven parents and their 28 F1 crosses were evaluated under Orobanche free and naturally infested soils. RESULTS: The results demonstrated considerable variations among the evaluated genotypes, wide diversity among the parental materials, and heterotic effects for all studied agronomic traits under Orobanche-free and infested soils. Orbanche infestation displayed a significant adverse impact on all the studied agronomic traits. The genotypes Line1, Line2, Line3, and Line5 displayed superior performance under Orobanche-infested conditions and recorded the highest values of all studied agronomic traits. Additionally, Line1, Line2, Line3, Line5, and Line7 exhibited desirable significant GCA for most evaluated traits under the two infestation conditions. The obtained crosses displayed significant negative or positive heterosis for studied agronomic characters such as plant height, number of branches per plant, number of pods per plant, number of seeds per plant, and seed weight per plant were observed. Furthermore, specific cross combinations such as Line2×Sakha3, Line3×Nubaria5, Line7 × Nubaria5, Line6×Nubaria1, Line5×Sakha3, Line1×Sakha3, and Line1 × Nubaria5 exhibited superior performance in seed yield and contributing traits under Orobanche-infested conditions. Moreover, these specific crosses showed superior efficacy in reducing dry weight of Orobanche spikes. The results obtained from GGE biplot analysis closely aligned with those from the line×tester procedure, affirming the significance of GGE biplot as a valuable statistical tool for assessing genotype combining ability in line× tester data. Both additive and non-additive gene actions were reported to be predominantly involved in the inheritance of the studied agronomic traits in faba bean. CONCLUSIONS: The detected genetic diversity within the evaluated faba bean genotypes and their developed crosses exhibits substantial potential for improving faba bean productivity under Orobanche-infested conditions. The parental genotypes, Line1, Line2, Line3, Line5, and Line7, were identified as effective and promising combiners. Moreover, the developed crosses Line2×Sakha3, Line3×Nubaria5, Line7×Nubaria5, Line6×Nubaria1, Line5×Sakha3, Line1×Sakha3, and Line1×Nubaria5 could be considered valuable candidates for developing high-yielding and tolerant faba bean genotypes to Orobanche.

Oxidative replication stress induced by long-term exposure to hydroxyurea in root meristem cells of Vicia faba.

KEY MESSAGE: Low concentrations of hydroxyurea, an inhibitor of DNA replication, induced oxidative and replicative stress in root apical meristem (RAM) cells of Vicia faba. Plant cells are constantly exposed to low-level endogenous stress factors that can affect DNA replication and lead to DNA damage. Long-term treatments of Vicia faba root apical meristems (RAMs) with HU leads to the appearance of atypical cells with intranuclear asynchrony. This rare form of abnormality was manifested by a gradual condensation of chromatin, from interphase to mitosis (so-called IM cells). Moreover, HU-treated root cells revealed abnormal chromosome structure, persisting DNA replication, and elevated levels of intracellular hydrogen peroxide (H2O2) and superoxide anion (O2∙-). Immunocytochemical studies have shown an increased number of fluorescent foci of H3 histones acetylated at lysine 56 (H3K56Ac; canonically connected with the DNA replication process). We show that continuous 3-day exposure to low concentrations (0.75 mM) of hydroxyurea (HU; an inhibitor of DNA replication) induces cellular response to reactive oxygen species and to DNA replication stress conditions.

The genome formula of a multipartite virus is regulated both at the individual segment and the segment group levels.

Differential accumulation of the distinct genome segments is a common feature of viruses with segmented genomes. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". There is speculation and some experimental support for a functional role of the genome formula by modulating gene expression through copy number variations. However, the mechanisms of genome formula regulation have not yet been identified. In this study, we investigated whether the genome formula of the octopartite nanovirus faba bean necrotic stunt virus (FBNSV) is regulated by processes acting at the individual segment vs. viral population levels. We used a leaf infiltration system to show that the two most accumulated genome segments of the FBNSV possess a greater intrinsic accumulation capacity in Vicia faba tissues than the other segments. Nevertheless, processes acting at the individual segment level are insufficient to generate the genome formula, suggesting the involvement of additional mechanisms acting at the supra-segment level. Indeed, the absence of segments with important functions during systemic infection strongly modifies the relative frequency of the others, indicating that the genome formula is a property of the segment group. Together, these results demonstrate that the FBNSV genome formula is shaped by a complex process acting at both the individual segment and the segment group levels.

Genotoxic effects and mitosis aberrations of chromium (VI) on root cells of Vicia faba and its molecular docking analysis.

Like other heavy metals, Cr (VI) is a powerful carcinogen and mutagen agent. Its toxic effects on plants are well considered. In order to elucidate its adverse effects, the present work aims to study the mitosis aberrations of Cr (VI) on the Vicia faba root-cells and its molecular docking analysis to understand the genotoxicity mechanisms. In-vivo, Vicia faba plants were exposed to 50 and 100 µM Cr (VI) for 48 h. In-silico, molecular docking and molecular dynamics simulation were used to study the interactions between dichromate and tubulin tyrosine ligase T2R-TTL (PDBID: 5XIW) with reference to Colchicine (microtubule inhibitor). According to our results, Cr (VI) affects growth and cell division and also induces many mitosis aberrations such as chromosome sticking, anaphase/telophase bridges, lagging chromosomes and fragmentation during all phases of mitosis. On the one hand, Cr (VI) reduces mitotic index and promotes micronuclei induction. The in-silico results showed that dichromate establishes very strong bonds at the binding site of the tubulin tyrosine ligase T2R-TTL, with a binding affinity of -5.17 Kcal/Mol and an inhibition constant of 163.59 µM. These interactions are similar to those of colchicine with this protein, so dichromate could be a very potent inhibitor of this protein's activity. TTL plays a fundamental role in the tyrosination/detyrosination of tubulin, which is crucial to the regulation of the microtubule cytoskeleton. Its inhibition leads to the appearance of many morphogenic abnormalities such as mitosis aberrations. In conclusion, our data confirm the highest genotoxicity effects of Cr (VI) on Vicia faba root-cells.

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.

Hybrid RNA sequencing of broad bean wilt virus 2 from faba beans.

IMPORTANCE: Globally, viral diseases impair the growth and vigor of cultivated crops such as grains, leading to a significant reduction in quality, marketability, and competitiveness. As an island nation, Australia has a distinct advantage in using its border to prevent the introduction of damaging viruses, which threaten the continental agricultural sector. However, breeding programs in Australia rely on imported seeds as new sources of genetic diversity. As such, it is critical to remain vigilant in identifying new and emerging viral pathogens, by ensuring the availability of accurate genomic diagnostic tools at the grain biosecurity border. High-throughput sequencing offers game-changing opportunities in biosecurity routine testing. Genomic results are more accurate and informative compared to traditional molecular methods or biological indexing. The present work contributes to strengthening accurate phytosanitary screening, to safeguard the Australian grains industry, and expedite germplasm release to the end users.

Epigenetic modifications evidenced by isolation of proteins on nascent DNA and immunofluorescence in hydroxyurea-treated root meristem cells of Vicia faba.

MAIN CONCLUSION: By implementation of the iPOND technique for plant material, changes in posttranslational modifications of histones were identified in hydroxyurea-treated root meristem cells of Vicia. Replication stress (RS) disrupts or inhibits replication forks and by altering epigenetic information of the newly formed chromatin can affect gene regulation and/or spatial organisation of DNA. Experiments on Vicia faba root meristem cells exposed to short-term treatment with 3 mM hydroxyurea (HU, an inhibitor of DNA replication) were aimed to understand epigenetic changes related to RS. To achieve this, the following histone modifications were studied using isolation of proteins on nascent DNA (iPOND) technique (for the first time on plant material) combined with immunofluorescence labeling: (i) acetylation of histone H3 at lysine 56 (H3K56Ac), (ii) acetylation of histone H4 at Lys 5 (H4K5Ac), and (iii) phosphorylation of histone H3 at threonine 45 (H3T45Ph). Certainly, the implementation of the iPOND method for plants may prove to be a key step for a more in-depth understanding of the cell's response to RS at the chromatin level.

Reference genome facilitates trait development for faba beans.

Reference genomes facilitate trait improvement by aiding in the elucidation of causal genetic elements. Thanks to the recent release of a reference sequence for the faba bean, breeders and geneticists are poised to accelerate precision breeding and genetic improvement of this important crop.

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.

Visual tracking of viral infection dynamics reveals the synergistic interactions between cucumber mosaic virus and broad bean wilt virus 2.

Cucumber mosaic virus (CMV) is one of the most prevalent plant viruses in the world, and causes severe damage to various crops. CMV has been studied as a model RNA virus to better understand viral replication, gene functions, evolution, virion structure, and pathogenicity. However, CMV infection and movement dynamics remain unexplored due to the lack of a stable recombinant virus tagged with a reporter gene. In this study, we generated a CMV infectious cDNA construct tagged with a variant of the flavin-binding LOV photoreceptor (iLOV). The iLOV gene was stably maintained in the CMV genome after more than four weeks of three serial passages between plants. Using the iLOV-tagged recombinant CMV, we visualized CMV infection and movement dynamics in living plants in a time course manner. We also examined whether CMV infection dynamics is influenced by co-infection with broad bean wilt virus 2 (BBWV2). Our results revealed that no spatial interference occurred between CMV and BBWV2. Specifically, BBWV2 facilitated the cell-to-cell movement of CMV in the upper young leaves. In addition, the BBWV2 accumulation level increased after co-infection with CMV.

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.

The giant diploid faba genome unlocks variation in a global protein crop.

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

Structure-guided mutagenesis of the capsid protein indicates that a nanovirus requires assembled viral particles for systemic infection.

Nanoviruses are plant multipartite viruses with a genome composed of six to eight circular single-stranded DNA segments. The distinct genome segments are encapsidated individually in icosahedral particles that measure ≈18 nm in diameter. Recent studies on the model species Faba bean necrotic stunt virus (FBNSV) revealed that complete sets of genomic segments rarely occur in infected plant cells and that the function encoded by a given viral segment can complement the others across neighbouring cells, presumably by translocation of the gene products through unknown molecular processes. This allows the viral genome to replicate, assemble into viral particles and infect anew, even with the distinct genome segments scattered in different cells. Here, we question the form under which the FBNSV genetic material propagates long distance within the vasculature of host plants and, in particular, whether viral particle assembly is required. Using structure-guided mutagenesis based on a 3.2 Å resolution cryogenic-electron-microscopy reconstruction of the FBNSV particles, we demonstrate that specific site-directed mutations preventing capsid formation systematically suppress FBNSV long-distance movement, and thus systemic infection of host plants, despite positive detection of the mutated coat protein when the corresponding segment is agroinfiltrated into plant leaves. These results strongly suggest that the viral genome does not propagate within the plant vascular system under the form of uncoated DNA molecules or DNA:coat-protein complexes, but rather moves long distance as assembled viral particles.