A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

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.

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.

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.

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.

Construction of a high-density genetic map for faba bean (Vicia faba L.) and quantitative trait loci mapping of seed-related traits

Faba bean (Vicia faba L.) is a valuable legume crop and data on its seed-related traits is required for yield and quality improvements. However, basic research on faba bean is lagging compared to that of other major crops. In this study, an F₂ faba bean population, including 121 plants derived from the cross WY7×TCX7, was genotyped using the Faba_bean_130 K targeted next-generation sequencing genotyping platform. The data were used to construct the first ultra-dense faba bean genetic map consisting of 12,023 single nucleotide polymorphisms markers covering 1,182.65 cM with an average distance of 0.098 cM. The map consisted of 6 linkage groups, which is consistent with the 6 faba bean chromosome pairs. A total of 65 quantitative trait loci (QTL) for seed-related traits were identified (3 for 100-seed weight, 28 for seed shape, 12 for seed coat color, and 22 for nutritional quality). Furthermore, 333 candidate genes that are likely to participate in the regulation of seed-related traits were also identified. Our research findings can provide a basis for future faba bean marker-assisted breeding and be helpful to further modify and improve the reference genome.

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.

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.

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.

Genetic and Metabolite Variability among Commercial Varieties and Advanced Lines of Vicia faba L

Vicia faba L. (faba bean) is one of the most promising pulse crops due to its nutritional value and high nitrogen fixation capacity. The aim of the present study was to compare the genetic diversity and the seed metabolite profiles of five genetic materials of faba bean. Specifically, three newly developed advanced lines (KK18, KK14 and KK10) and two commercial cultivars (POLIKARPI and TANAGRA), were evaluated for this purpose. Genetic diversity among populations was assessed by SCoT molecular markers. Through UPGMA dendrogram, genetic distances between populations were estimated. Untargeted metabolomics analysis of the seeds was performed employing GC/EI/MS. The cultivar POLYKARPI exhibited the highest polymorphism. All varieties showed a higher within-cultivars and advanced lines variability than between. POLYKARPI and KK14 had the lowest genetic distances, while KK18 and TANAGRA presented the highest ones. The advanced line KK18 displayed the best nutritional profile, the highest concentration of desirable metabolites (lactic acid and trehalose), the lowest concentration of anti-nutritional factors (oxalic acid) and the lowest concentration of saturated fatty acids (palmitic and stearic acid). According to the results of the present study, KK18 line is a very promising material for further exploration and utilization in breeding programs.

NM, Jebakani K. S, Selvaraj S, Pramitha J. L, Selvaraj R, Petchiammal K. I, Kather Sheriff S, Thinakaran J, Rathinamoorthy S, Kumar P. R. Genetic manipulation of anti-nutritional factors in major crops for a sustainable diet in future

The consumption of healthy food, in order to strengthen the immune system, is now a major focus of people worldwide and is essential to tackle the emerging pandemic concerns. Moreover, research in this area paves the way for diversification of human diets by incorporating underutilized crops which are highly nutritious and climate-resilient in nature. However, although the consumption of healthy foods increases nutritional uptake, the bioavailability of nutrients and their absorption from foods also play an essential role in curbing malnutrition in developing countries. This has led to a focus on anti-nutrients that interfere with the digestion and absorption of nutrients and proteins from foods. Anti-nutritional factors in crops, such as phytic acid, gossypol, goitrogens, glucosinolates, lectins, oxalic acid, saponins, raffinose, tannins, enzyme inhibitors, alkaloids, β-N-oxalyl amino alanine (BOAA), and hydrogen cyanide (HCN), are synthesized in crop metabolic pathways and are interconnected with other essential growth regulation factors. Hence, breeding with the aim of completely eliminating anti-nutrition factors tends to compromise desirable features such as yield and seed size. However, advanced techniques, such as integrated multi-omics, RNAi, gene editing, and genomics-assisted breeding, aim to breed crops in which negative traits are minimized and to provide new strategies to handle these traits in crop improvement programs. There is also a need to emphasize individual crop-based approaches in upcoming research programs to achieve smart foods with minimum constraints in future. This review focuses on progress in molecular breeding and prospects for additional approaches to improve nutrient bioavailability in major crops.

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.

RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China

Background

Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.

Methods

Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.

Results

A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.

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.

A QTL approach in faba bean highlights the conservation of genetic control of frost tolerance among legume species

Frost is a major abiotic stress of winter type faba beans (Vica faba L.) and has adverse effects on crop yield. Climate change, far from reducing the incidence of frost events, is making these phenomena more and more common, severe, and prolonged. Despite the important interaction that the environment has in the tolerance of faba bean to frost, this trait seems to have good levels of heritability. Several QTLs for frost tolerance have already been reported, however, a more robust identification is needed to more precisely identify the genomic regions involved in faba bean tolerance to sub-zero temperatures. Several pea (Pisum sativum L.) and barrel medic (Medicago truncatula L.) frost tolerance QTLs appear to be conserved between these two species, furthering the hypothesis that the genetic control of frost tolerance in legume species might be more generally conserved. In this work, the QTL mapping in two faba bean recombinant inbred line (RIL) populations connected by a common winter-type parent has led to the identification of five genomic regions involved in the control of frost tolerance on linkage groups I, III, IV, and V. Among them, a major and robust QTL of great interest for marker-assisted selection was identified on the lower part of the long-arm of LGI. The synteny between the faba bean frost tolerance QTLs and those previously identified in other legume species such as barrel medic, pea or soybean highlighted at least partial conservation of the genetic control of frost tolerance among different faba bean genetic pools and legume species. Four novel RILs showing high and stable levels of tolerance and the ability to recover from freezing temperatures by accumulating frost tolerance QTLs are now available for breeding programs.

Genome-wide association mapping for root traits associated with frost tolerance in faba beans using KASP-SNP markers

Frost is an abiotic stress factor that threatens plant development and crop productivity not only in cold regions but also in temperate zones. Roots play an important role in plant growth during frost stress. Therefore, variation in root characteristics could be studied to improve frost tolerance in winter faba bean. The present study aimed to identify the genomic regions that control frost tolerance in a winter faba bean population by focusing on root-related traits. A set of 185 genotypes were tested for frost tolerance under artificial frost growth conditions at −16°C, −18°C, and −19°C in a growth chamber. Frost stress reduced the root-related parameters in all genotypes, with a wide variation among genotypes. A genome-wide association study identified nine novel single-nucleotide polymorphisms that are associated with the root-related traits. The most frost-tolerant genotypes were identified; two genotypes, S_028 and S_220, exhibited remarkable performance under frost stress. Moreover, they harbored all four of the alleles favorable for frost tolerance. Remarkably, two markers showed genetic pleiotropic effects with positive allele effects on root fresh matter and root dry matter. Thus, both genotypes can be implemented in a breeding program to provide the alleles for healthier roots under frost conditions to develop more frost-tolerant varieties, and the two markers can be used to screen large collections to select for frost tolerance. These results may provide novel insights for improving frost tolerance in faba beans and in other legume crops.

Transcriptome analysis and characterization of genes associated to leaf tannin content in foxtail millet [Setaria italica (L.) P. Beauv.]

Background

Chinese chestnut is an economically important tree species whose yield and quality are seriously affected by red spider attack. Tannins is one of the most important class secondary metabolites in plants, and is closely associated with plant defense mechanisms against insect and herbivory. In our previous studies, it was revealed that several low-tannin foxtail millet varieties growing under the Chinese chestnut trees could attract red spiders to feed on their leaves and protect the chestnut trees from the infestation of red spiders, meanwhile, the growth and yield of foxtail millet plants themselves were not greatly affected.

Results

To identify genes related to leaf tannin content and selection of foxtail millet germplasm resources with low tannin content for interplanting with Chinese chestnut and preventing the red spider attack, the leaves of 4 varieties with different levels of tannin content were harvested for comparative transcriptome analysis. In total, 335 differentially expressed genes (DEGs) were identified. For acquisition of gene functions and biological pathways they involved in, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed, and several DEGs were found to possibly participate in the tannins biosynthesis pathway and transport processes of precursors. In addition, according to the PlantTFDB database, some transcription factors were predicted among the DEGs, suggesting their role in regulation of tannins biosynthesis pathway.

Conclusion

Our results provide valuable gene resources for understanding the biosynthesis and regulation mechanisms of tannins in foxtail millet, and pave the way for speeding up the breeding of low-tannin varieties through marker-assisted selection, which could be utilized for interplanting with Chinese chestnut trees to confer protection against red spider attack.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08746-8.

Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in faba bean (Vicia faba L.)

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTL) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross Mélodie/2 × ILB 938/2 were genotyped and evaluated for CS reactions under replicated controlled climate conditions. The RIL population showed significant variation in response to CS resistance. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 28.4% and 12.5%, respectively, of the total phenotypic variance. The results of this study not only provide insight into disease-resistance QTL, but also can be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01307-7.

Genetic Dissection of Heat Stress Tolerance in Faba Bean (Vicia faba L.) Using GWAS

Heat waves are expected to become more frequent and intense, which will impact faba bean cultivation globally. Conventional breeding methods are effective but take considerable time to achieve breeding goals, and, therefore, the identification of molecular markers associated with key genes controlling heat tolerance can facilitate and accelerate efficient variety development. We phenotyped 134 accessions in six open field experiments during summer seasons at Terbol, Lebanon, at Hudeiba, Sudan, and at Central Ferry, WA, USA from 2015 to 2018. These accessions were genotyped using genotyping by sequencing (GBS), and 10,794 high quality single nucleotide polymorphisms (SNPs) were discovered. These accessions were clustered in one diverse large group, although several discrete groups may exist surrounding it. Fifteen lines belonging to different botanical groups were identified as tolerant to heat. SNPs associated with heat tolerance using single-trait (ST) and multi-trait (MT) genome-wide association studies (GWASs) showed 9 and 11 significant associations, respectively. Through the annotation of the discovered significant SNPs, we found that SNPs from transcription factor helix-loop-helix bHLH143-like S-adenosylmethionine carrier, putative pentatricopeptide repeat-containing protein At5g08310, protein NLP8-like, and photosystem II reaction center PSB28 proteins are associated with heat tolerance.

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F₁ population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F₁ individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection

Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.

Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content

Quinoa (Chenopodium quinoa Willd.) is a crop that has great potential for increased cultivation in diverse climate regions. The seed protein quality obtained from this crop is high concerning the requirements to meet human nutritional needs, but the seed protein content is relatively low if compared to crops such as grain legumes. Increased seed protein content is desirable for increasing the economic viability of this crop in order for it to be used as a protein crop. In this study, we characterized three genotypes of quinoa with different levels of seed protein content. By performing RNA sequencing of developing seeds, we determined the genotype differences in gene expression and identified genetic polymorphisms that could be associated with increased protein content. Storage nutrient analyses of seeds of three quinoa genotypes (Titicaca, Pasankalla, and Regalona) from different ecoregions grown under controlled climate conditions showed that Pasankalla had the highest protein content (20%) and the lowest starch content (46%). Our seed transcriptome analyses revealed highly differentially expressed transcripts (DETs) in Pasankalla as compared to the other genotypes. These DETs encoded functions in sugar transport, starch and protein synthesis, genes regulating embryo size, and seed transcription factors. We selected 60 genes that encode functions in the central carbon metabolism and transcription factors as potential targets for the development of high-precision markers. Genetic polymorphisms, such as single nucleotide polymorphisms (SNPs) and base insertions and deletions (InDels), were found in 19 of the 60 selected genes, which can be further evaluated for the development of genetic markers for high seed protein content in quinoa. Increased cultivation of quinoa can contribute to a more diversified agriculture and support the plant protein diet shift. The identification of quinoa genotypes with contrasting seed quality can help establish a model system that can be used for the identification of precise breeding targets to improve the seed quality of quinoa. The data presented in this study based on nutrient and transcriptome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa and suggest high-precision candidate markers for such traits.

A high-resolution consensus linkage map for barley based on GBS-derived genotypes

As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregating progenies. We adopted a uniform set of SNP-calling and filtering conditions to identify 50 875 distinct SNPs segregating in at least one population. These SNPs were grouped into 18 580 non-redundant SNPs (bins). The resulting consensus linkage map spanned 1050.1 cM, providing an average density of 17.7 bins and 48.4 SNPs per cM. The consensus map is characterized by the absence of large intervals devoid of marker coverage (significant gaps), the largest interval between bins was only 3.7 cM and the mean distance between adjacent bins was 0.06 cM. This high-resolution linkage map will contribute to several applications in genomic research, such as providing useful information on the recombination landscape for QTLs/genes identified via GWAS or ensuring a uniform distribution of SNPs when developing low-cost genotyping tools offering a limited number of markers.

QTL dissection and mining of candidate genes for Ascochyta fabae and Orobanche crenata resistance in faba bean (Vicia faba L.)

BACKGROUND

Ascochyta blight caused by Ascochyta fabae Speg. and broomrape (Orobanche crenata) are among the economically most significant pathogens of faba bean. Several QTLs conferring resistance against the two pathogens have been identified and validated in different genetic backgrounds. The aim of this study was to saturate the most stable QTLs for ascochyta and broomrape resistance in two Recombinant Inbred Line (RIL) populations, 29H x Vf136 and Vf6 x Vf136, to identify candidate genes conferring resistance against these two pathogens.

RESULTS

We exploited the synteny between faba bean and the model species Medicago truncatula by selecting a set of 219 genes encoding putative WRKY transcription factors and defense related proteins falling within the target QTL intervals, for genotyping and marker saturation in the two RIL populations. Seventy and 50 of the candidate genes could be mapped in 29H x Vf136 and Vf6 x Vf136, respectively. Besides the strong reduction of the QTL intervals, the mapping process allowed replacing previous dominant and pedigree-specific RAPD flanking markers with robust and transferrable SNP markers, revealing promising candidates for resistance against the two pathogens.

CONCLUSIONS

Although further efforts in association mapping and expression studies will be required to corroborate the candidate genes for resistance, the fine-mapping approach proposed here increases the genetic resolution of relevant QTL regions and paves the way for an efficient deployment of useful alleles for faba bean ascochyta and broomrape resistance through marker-assisted breeding.

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.

Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing

KEY MESSAGE

Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.

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

Faba bean (Vicia faba L.), a member of the Fabaceae family, is one of the important food legumes cultivated in cool temperate regions. It holds great importance for human consumption and livestock feed because of its high protein content, dietary fibre, and nutritional value. Major faba bean breeding challenges include its mixed breeding system, unknown wild progenitor, and genome size of ~13 Gb, which is the largest among diploid field crops. The key breeding objectives in faba bean include improved resistance to biotic and abiotic stress and enhanced seed quality traits. Regarding quality traits, major progress on reduction of vicine-convicine and seed coat tannins, the main anti-nutritional factors limiting faba bean seed usage, have been recently achieved through gene discovery. Genomic resources are relatively less advanced compared with other grain legume species, but significant improvements are underway due to a recent increase in research activities. A number of bi-parental populations have been constructed and mapped for targeted traits in the last decade. Faba bean now benefits from saturated synteny-based genetic maps, along with next-generation sequencing and high-throughput genotyping technologies that are paving the way for marker-assisted selection. Developing a reference genome, and ultimately a pan-genome, will provide a foundational resource for molecular breeding. In this review, we cover the recent development and deployment of genomic tools for faba bean breeding.

Paternal outcrossing success differs among faba bean genotypes and impacts breeding of synthetic cultivars

Faba bean genotypes showed significant and marked genetic differences in their success as pollen donors to cross-fertilized seeds. The findings may improve exploitation of heterosis in synthetic cultivars. In partially allogamous crops such as faba bean (Vicia faba L.), increasing the share of heterosis in a synthetic cultivar can improve yield and yield stability. The share of heterosis in such synthetic cultivars is increased by higher degrees of cross-fertilization. This trait is defined as percentage of cross-fertilized seeds among all seeds and is a crucial parameter in breeders' yield predictions. Current approaches use degree of cross-fertilization to predict inbreeding and share of heterosis, they even consider genotype-specific degrees; yet, all genotypes are assumed to contribute equally to the cross-fertilized seeds. Here, we expect faba bean genotypes to differ in their success rates as pollen donors, i.e. in paternal outcrossing success. To quantify the variation of both, the degree of cross-fertilization and the paternal outcrossing success, we assessed these parameters in inbred lines and F1 hybrids, grown in four polycrosses composed of eight genotypes each. We identified the paternal genotype of 500 to 800 seeds per genotype and polycross using SNP markers. In both traits, we found marked and significant variation among inbred lines and among F1 hybrids, as well as between inbred lines and F1. Based on our findings, we discuss how differential paternal outcrossing success influences the amount of inbreeding in synthetic cultivars. Our findings offer the potential for a better management and exploitation of heterotic yield increase in faba bean.

Linkage mapping and QTL analysis of flowering time in faba bean

Flowering time marks the transition from vegetative to reproductive growth and is key for optimal yield in any crop. The molecular mechanisms controlling this trait have been extensively studied in model plants such as Arabidopsis thaliana and rice. While knowledge on the molecular regulation of this trait is rapidly increasing in sequenced galegoid legume crops, understanding in faba bean remains limited. Here we exploited translational genomics from model legume crops to identify and fine map QTLs linked to flowering time in faba bean. Among the 31 candidate genes relevant for flowering control in A. thaliana and Cicer arietinum assayed, 25 could be mapped in a segregating faba bean RIL population. While most of the genes showed conserved synteny among related legume species, none of them co-localized with the 9 significant QTL regions identified. The FT gene, previously implicated in the control of flowering time in numerous members of the temperate legume clade, mapped close to the most relevant stable and conserved QTL in chromosome V. Interestingly, QTL analysis suggests an important role of epigenetic modifications in faba bean flowering control. The new QTLs and candidate genes assayed here provide a robust framework for further genetic studies and will contribute to the elucidation of the molecular mechanisms controlling this trait.

Linkage mapping and QTL analysis of flowering time in faba bean

Flowering time marks the transition from vegetative to reproductive growth and is key for optimal yield in any crop. The molecular mechanisms controlling this trait have been extensively studied in model plants such as Arabidopsis thaliana and rice. While knowledge on the molecular regulation of this trait is rapidly increasing in sequenced galegoid legume crops, understanding in faba bean remains limited. Here we exploited translational genomics from model legume crops to identify and fine map QTLs linked to flowering time in faba bean. Among the 31 candidate genes relevant for flowering control in A. thaliana and Cicer arietinum assayed, 25 could be mapped in a segregating faba bean RIL population. While most of the genes showed conserved synteny among related legume species, none of them co-localized with the 9 significant QTL regions identified. The FT gene, previously implicated in the control of flowering time in numerous members of the temperate legume clade, mapped close to the most relevant stable and conserved QTL in chromosome V. Interestingly, QTL analysis suggests an important role of epigenetic modifications in faba bean flowering control. The new QTLs and candidate genes assayed here provide a robust framework for further genetic studies and will contribute to the elucidation of the molecular mechanisms controlling this trait.

VC1 catalyses a key step in the biosynthesis of vicine in faba bean

Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds¹. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals². Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.

VC1 catalyses a key step in the biosynthesis of vicine in faba bean

Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds¹. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals². Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.

VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

First approach to pod dehiscence in faba bean: genetic and histological analyses

Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.

The influence of soil drought stress on the leaf transcriptome of faba bean (Vicia faba L.) in the Qinghai-Tibet Plateau

Water deficit has a significant impact on growth, development and yield of fava bean (Vicia fava L.) in arid and semi-arid climates. The aim of this study was to identify differentially expressed genes in the Qinghai 13 genotype under soil drought through leaf transcriptome analysis. A total of 256.95 M clean reads were obtained and assembled into 176334 unigenes, with an average length of 766 bp. A total of 9126 (4439 upregulated and 4687 downregulated) differentially expressed genes (DEGs) were identified in faba bean leaves under soil drought. In total, 324 putative transcription factors were identified and classified as belonging to different transcription factor families. According to GO and KEGG analysis, the soil drought stress-inducible DEGs encoded proteins mainly involved in regulating photosynthesis, osmotic adjustment, detoxification, autophagy and other functions. In addition, a large portion of DEGs appeared to be novel because they could not be annotated in any functional databases, therefore, suggesting a specific response to soil drought in faba bean. Finally, RNA-seq analysis was validated by quantitative reverse-transcription PCR analysis. This work provides comprehensive and valuable information for understanding the molecular mechanisms which faba bean uses to respond to soil drought.

The bHLH transcription factor VfTT8 underlies zt2, the locus determining zero tannin content in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is an important protein-rich fodder crop, which is widely cultivated in temperate areas. However, antinutritional compounds such as condensed tannins, limit the use of this protein source in monogastric feed formulations. Previous studies demonstrated that two recessive and complementary genes, zt1 and zt2, control absence of tannin and white flower colour in faba bean. An ortholog of the Medicago WD40 transcription factor TTG1 was reported to encode the zt1 phenotype, but the responsible gene for zt2 is still unknown. Here we used a candidate gene approach combined with linkage mapping, comparative genomics and gene expression to fine map the zt2 genomic region and to identify the regulatory gene controlling both traits. Seventy-two genes, including 23 MYB and bHLH regulatory genes predicted to be associated with anthocyanin expression together with WRKY proteins, were screened and genotyped in three mapping populations. The linkage groups constructed identified the regulatory gene, TRANSPARENT TESTA8 (TT8), encoding a basic helix-loop-helix (bHLH) transcription factor, as the candidate for zt2. This finding was supported by qPCR analysis and further validated in different genetic backgrounds. Accordingly, VfTT8 was downregulated in white flowered types while showing high levels of expression in wild genotypes. Our results provide new insights on the regulatory mechanisms of tannin biosynthesis in faba bean and will facilitate the development of an ultimate zt2 diagnostic marker for the fast generation of new value-added cultivars free of tannins and with improved nutritional value.

Identification and Quantification of Major Faba Bean Seed Proteins

Faba bean (Vicia faba L.) holds great importance for human and animal nutrition for its high protein content. However, better understanding of its seed protein composition is required in order to develop cultivars that meet market demands for plant proteins with specific quality attributes. In this study, we screened 35 diverse Vicia faba genotypes by employing the one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1D SDS-PAGE) method, and 35 major protein bands obtained from three genotypes with contrasting seed protein profiles were further analyzed by mass spectrometry (MS). Twenty-five of these protein bands (MW range: ∼ 9-107 kDa) had significant (p ≤ 0.05) matches to polypeptides in protein databases. MS analysis showed that most of the analyzed protein bands contained more than one protein type and, in total, over 100 proteins were identified. These included major seed storage proteins such as legumin, vicilin, and convicilin, as well as other protein classes like lipoxygenase, heat shock proteins, sucrose-binding proteins, albumin, and defensin. Furthermore, seed protein extracts were separated by size-exclusion high-performance liquid chromatography (SE-HPLC), and percentages of the major protein classes were determined. On average, legumin and vicilin/convicilin accounted for 50 and 27% of the total protein extract, respectively. However, the proportions of these proteins varied considerably among genotypes, with the ratio of legumin:vicilin/convicilin ranging from 1:1 to 1:3. In addition, there was a significant (p < 0.01) negative correlation between the contents of these major fractions (r = -0.83). This study significantly extends the number of identified Vicia faba seed proteins and reveals new qualitative and quantitative variation in seed protein composition, filling a significant gap in the literature. Moreover, the germplasm and screening methods presented here are expected to contribute in selecting varieties with improved protein content and quality.

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.

Do Faba Bean Genotypes Carrying Different Zero-Tannin Genes (zt1 and zt2) Differ in Phenolic Profiles?

Faba bean is a cool season grain legume that produces seeds with a high protein content. Seed coat tannins limit its use in food and feed. A low-tannin phenotype is controlled by either of two unlinked recessive genes zt1 and zt2. Liquid chromatography-mass spectrometry was used to characterize phenolic profiles of seed coat and flower tissue of three faba bean genotypes: CDC Snowdrop (zt1 gene), Disco/2 (zt2 gene), and ILB 938/2 (tannin-containing). For both tissues, clear differences in phenolic profiles of ILB 938/2 were observed in comparison to both low-tannin lines. Although seed coat phenolic profiles of zt1 and zt2 genotypes were similar, distinct differences were evident in flower tissue, suggesting that the gene action results in some different end products of the phenolic biosynthetic pathway. These distinctive compounds could be used as biochemical markers to distinguish between low-tannin phenotypes.

Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map

Faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based SNPs, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 gene-based SNP markers polymorphic in three recombinant line populations was selected to enable the construction of a high-density consensus genetic map encompassing 1,728 markers well distributed in six linkage groups and spanning 1,547.71 cM with an average inter-marker distance of 0.89 cM. Orthology-based comparison of the faba bean consensus map with legume genome assemblies highlighted synteny patterns that partly reflected the phylogenetic relationships among species. Solid blocks of macrosynteny were observed between faba bean and the most closely-related sequenced legume species such as pea, barrel medic or chickpea. Numerous blocks could also be identified in more divergent species such as common bean or cowpea. The genetic tools developed in this work can be used in association mapping, genetic diversity, linkage disequilibrium or comparative genomics and provide a backbone for map-based cloning. This will make the identification of candidate genes of interest more efficient and will accelerate marker-assisted selection (MAS) and genomic-assisted breeding (GAB) in faba bean.

Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study

Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

BACKGROUND

Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies.

RESULTS

Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F₁ population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16-60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9-1, Q18-66 and Q18-73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis.

CONCLUSIONS

This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

Legume genomics and transcriptomics: From classic breeding to modern technologies

Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs.

Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.

Characterization and diagnostic marker for TTG1 regulating tannin and anthocyanin biosynthesis in faba bean

Condensed tannins, found in coloured-flowering varieties of faba bean (Vicia faba L) are, after vicine and convicine, one of the major anti-nutritional factors for monogastric animals. The development of tannin-free cultivars is a key goal in breeding to broaden the use of this legume in the animal feed industry. Two recessive genes, zt-1 and zt-2, control the zero-tannin content and promote white-flowered plants. Previous studies exploiting synteny with the model Medicago truncatula reported a mutation in TTG1, a gene encoding a WD40 transcription factor located in chromosome II, as the responsible for the zt-1 phenotypes. Here a comprehensive analysis of VfTTG1 (including phylogenetic relationships, gene structure and gene expression) has been conducted to confirm the identity of the gene and to reveal structural changes that may result in different functional alleles. The results confirmed the identity of the candidate and revealed the existence of two different alleles responsible for the phenotype: ttg1-a, probably due to a mutation in the promoter region, and ttg1-b caused by a deletion at the 5′end of VfTTG1. Based on the sequencing results, an allele-specific diagnostic marker was designed that differentiate zt-1 from wild and zt-2 genotypes and facilitates its deployment in faba bean breeding programs.

Improving pulse crops as a source of protein, starch and micronutrients

Pulse crops have been known for a long time to have beneficial nutritional profiles for human diets but have been neglected in terms of cultivation, consumption and scientific research in many parts of the world. Broad dietary shifts will be required if anthropogenic climate change is to be mitigated in the future, and pulse crops should be an important component of this change by providing an environmentally sustainable source of protein, resistant starch and micronutrients. Further enhancement of the nutritional composition of pulse crops could benefit human health, helping to alleviate micronutrient deficiencies and reduce risk of chronic diseases such as type 2 diabetes. This paper reviews current knowledge regarding the nutritional content of pea (Pisum sativum L.) and faba bean (Vicia faba L.), two major UK pulse crops, and discusses the potential for their genetic improvement.

Charting oat (Avena sativa) embryo and endosperm transcription factor expression reveals differential expression of potential importance for seed development

Uniquely, oat, among cereals, accumulates an appreciable amount of oil in the endosperm together with starch. Oat is also recognized for its soluble fibers in the form of β-glucans. Despite high and increasing interest in oat yield and quality, the genetic and molecular understanding of oat grain development is still very limited. Transcription factors (TFs) are important regulatory components for plant development, product quality and yield. This study aimed to develop a workflow to determine seed tissue specificity of transcripts encoding transcription factors to reveal differential expression of potential importance for storage compound deposition and quality characters in oat. We created a workflow through the de novo assembly of sequenced seed endosperm and embryo, and publicly available oat seed RNAseq dataset, later followed by TF identification. RNAseq data were assembled into 33,878 transcripts with approximately 90% completeness. A total of 3875 putative TF encoding transcripts were identified from the oat hybrid assemblies. Members of the B3, bHLH, bZIP, C3H, ERF, NAC, MYB and WRKY families were the most abundant TF transcripts. A total of 514 transcripts which were differentially expressed between embryo and endosperm were identified with a threshold of 16-fold expression difference. Among those, 36 TF transcript homologs, belonging to 7 TF families, could be identified through similarity search in wheat embryo and endosperm EST libraries of NCBI Unigene database, and almost all the closest homologs were specifically expressed in seed when explored in WheatExp database. We verified our findings by cloning, sequencing and finally confirming differential expression of two TF encoding transcripts in oat seed embryo and endosperm. The developed workflow for identifying tissue-specific transcription factors allows further functional characterization of specific genes to increase our understanding of grain filling and quality.

Seed Storage Proteins of Faba Bean ( Vicia faba L): Current Status and Prospects for Genetic Improvement

Faba bean ( Vicia faba L.) is one of the foremost candidate crops for simultaneously increasing both sustainability and global supply of plant protein. On a dry matter basis, its seeds contain about 29% protein of which more than 80% consists of globulin storage proteins (vicilin and legumin). However, to achieve optimum utilization of this crop for human and animal nutrition, both protein content and quality have to be improved. Though initial investigations on the heritability of these traits indicated the possibility for genetic improvement, little has been achieved so far, partly due to the lack of genetic information coupled with the complex relationship between protein content and grain yield. This review reports on the current knowledge on Vicia faba seed storage proteins, their structure, composition, and genetic control, and highlights key areas for further improvement of the content and composition of Vicia faba seed storage proteins on the basis of recent advances in Vicia faba genome knowledge and genetic tools.

Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing

Drought and salinity are the major factors that limit the faba bean (Vicia faba L.) production worldwide. The aim of this study is to identify the water stress differentially expressed genes (DEGs) through the root transcriptome analyses of the drought-tolerant Hassawi 2 genotype at vegetative and flowering stages. A total of 624.8 M high-quality Illumina reads were generated and assembled into 198,155 all-unigenes with a mean length of 738 bp and an N50 length of 1347 bp. Among all-unigenes, 78,262 were assigned to non-redundant (Nr), 66,254 to nucleotide (Nt), 54,034 to KEGG, and 43,913 to gene ontology (GO) annotations. A total of 36,834 and 35,510 unigenes were differentially expressed at the vegetative and flowering stages of Hassawi 2 under drought stress, respectively. The majority of unigenes were down-regulated at both developmental stages. However, the number of genes up-regulated (15,366) at the flowering stage exceeded the number of those up-regulated (14,097) at the vegetative stage, and the number of genes down-regulated (20,144) at the flowering stage was smaller than the number of those down-regulated (22,737) at the vegetative stage. The drought stress-responsive differentially expressed unigenes coded for various regulatory proteins, including protein kinases and phosphatases, transcription factors and plant hormones and functional proteins including enzymes for osmoprotectant, detoxification and transporters were differentially expressed, most of which were largely up-regulated. Moreover, a substantial proportion of the DEGs identified in this study were novel, most exhibited a significant change in their expression levels under water stress, making them an unexploited resource that might control specific responses to drought stress in the faba bean. Finally, qRT-PCR results were found almost consistent with the results of next-generation sequencing. Our data will help in understanding the drought tolerance mechanisms in plants and will provide resources for functional genomics.

High-density multi-population consensus genetic linkage map for peach

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.