Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism

The Potential Genetic Effect for Yield and Foliar Disease Resistance in Faba Bean (Vicia faba L.) Assessed via Morphological and SCoT Markers

Faba bean is considered one of the most prominent grain legumes, with high protein content for human food consumption and livestock feed. The present study evaluated the nature of gene action and determined the genetic diversity among different populations of three crosses for resistance to foliar diseases at the molecular level. Analysis of variance exposed significant differences among the generations for all measured traits. Both dominance and additive gene effects were essential, but dominance genes, for the most part, exhibited greater effects than additive ones. This indicates an essential role for dominant genes alongside the additives one in inheriting such traits. The third cross (Marina × Giza 40) gave desired significant and positive (additive × additive) values for the number of pods/plant, seeds/plant, and seed yield/plant, in addition to desirable negative values for chocolate spot and rust characteristics. Furthermore, assessing the lines under study using seven SCoT primers disclosed three bands with recorded molecular weights of 260, 207, and 178 bp, generated by SCoT-1, SCoT-4, and SCoT-7 primers, respectively. These bands exist in the resistant parent (Marina), which could be attributed to the high-disease-resistance phenotypes, and they are absent in the sensitive parent (Giza 40) and other putative sensitive lines. Based on the molecular profiles and the genetic similarity between parents and the selected lines, the highest similarity value (0.91) was detected between Marina genotype and BC1, revealing a high foliar disease resistance. Meanwhile, Giza 40 (susceptible to foliar diseases) exhibited the maximum value (0.93) with F2. Additionally, cluster analysis based on genetic relationships was performed, and a high level of correlation between the results of PCR-based SCoT analysis and the foliar disease reactions was observed in the field. Consequently, this study concluded that SCoT markers created reliable banding profiles for evaluating genetic polymorphism among faba bean lines, which could be a foundation for developing an efficient breeding program.

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.

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.

Developing a new genic SSR primer database in faba bean (Vicia faba L.)

The goal of this research was to develop a new genetic database of simple sequence repetition (SSR) primers for faba and classify them according to their target genes and respective biological processes. Approximately 75,605 and 148,196 previously published genomic and transcriptomic faba sequences, respectively, have been used to detect possible SSRs. The numbers of identified SSRs from each dataset were 25,502 and 12,319, respectively. The distribution of different repeat classes indicated that trinucleotides represent the largest number of repeat counts, followed by dinucleotides. The extracted genic SSR sequences were used to design 1091 polymerase chain reaction (PCR) primers, of which only 238 (21.8%) primers target genomic sequences and the other 853 PCR primers targeted transcriptomic sequences. The annotation of gene-targeted SSRs showed that approximately 897 genes were targeted by our SSR primers. Approximately 1890 gene ontology (GO) identification codes have been obtained. The GO keywords were distributed among distinct molecular cell features. The highest redundancies involved 554 technical words, 196 domains, and 160 molecular feature phrases. These GO codes belonged to the general level of GO and included molecular function, cellular component, and biological process (544, 670, and 676 GOs, respectively). Twenty-seven SSR PCR primers were synthesized to 12 Egyptian faba bean genotypes. Approximately 11 SSR provided one to two PCR bands, whereas other SSRs provided only one sharp band with polymorphic band size. There were 13 polymorphic primers. The polymorphism information content was 0.3, which implied moderate informativeness.

Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene

At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.

AFLP-Based Analysis of Variation and Population Structure in Mutagenesis Induced Faba Bean

Genetic diversity enrichment is urgently necessary to develop climate-resilient faba bean cultivars. The present study aimed to measure the enrichment of genetic diversity and changes in the population structure of faba bean, following induced mutagenesis. 120 samples, including 116 M2 mutant plants, generated by exposing the ILB4347 accession to four mutagen treatments (25 and 50 Gray gamma radiation and 0.01%, and 0.05% diethyl sulfate) and four reference genotypes were characterized using 11 amplified fragment length polymorphism (AFLP) primer combinations. The AFLP markers generated 1687 polymorphic alleles, including 756 alleles (45%) that were detected infrequently (f ≤ 0.1). The total allele count of the mutant plants ranged from 117 to 545. We observed a wide range of banding patterns and counts among the mutant plants, showing the high genetic diversity induced by mutation. Mutations also changed the population structure, by altering 31.78% of the total membership coefficient (Q). Although mutations changed the population structure, Nei’s genetic distance showed that the mutant population remained closely related to its control parent. This is the first report examining genetic diversity and population changes in faba bean mutant populations and, thus, could facilitate the application of induced mutagenesis during faba bean breeding.

Advances in Faba Bean Genetics and Genomics

Vicia faba L, is a globally important grain legume whose main centers of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six) of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favored plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are discussed. The bottleneck in associating genes and their functions has therefore moved from locating gene candidates to validating their function and the last part of this review covers mutagenesis and genetic transformation, two complementary routes to validating gene function and unlocking novel trait variation for the improvement of this important grain legume.

Genetic Diversity and Population Structure in Vicia faba L. Landraces and Wild Related Species Assessed by Nuclear SSRs

Faba bean (Vicia faba L.) is a facultative cross-pollinating legume crop with a great importance for food and feed due to its high protein content as well as the important role in soil fertility and nitrogen fixation. In this work we evaluated genetic diversity and population structure of faba bean accessions from the Western Mediterranean basin and wild related species. For that purpose we screened 53 V. faba, 2 V. johannis and 7 V. narbonensis accessions from Portugal, Spain and Morocco with 28 faba bean Single Sequence Repeats (SSR). SSR genotyping showed that the number of alleles detected per locus for the polymorphic markers ranged between 2 and 10, with Polymorphic Information Content (PIC) values between 0.662 and 0.071, and heterozygosity (H_O) between 0–0.467. Heterozygosity and inbreeding coefficient levels indicate a higher level of inbreeding in wild related species than in cultivated Vicia. The analysis of molecular variance (AMOVA) showed a superior genetic diversity within accessions than between accessions even from distant regions. These results are in accordance to population structure analysis showing that individuals from the same accession can be genetically more similar to individuals from far away accessions, than from individuals from the same accession. In all three levels of analysis (whole panel of cultivated and wild accessions, cultivated faba bean accessions and Portuguese accessions) no population structure was observed based on geography or climatic factors. Differences between V. narbonensis and V. johannis are undetectable although these wild taxa are clearly distinct from V. faba accessions. Thus, a limited gene flow occurred between cultivated accessions and wild relatives. Contrastingly, the lack of population structure seems to indicate a high degree of gene flow between V. faba accessions, possibly explained by the partially allogamous habit in association with frequent seed exchange/introduction.

Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may control frost tolerance genes. The two genetic backgrounds were useful in detecting new variation for improving frost tolerance in winter faba bean. Of the five validated SNP markers, one (VF_Mt3g086600) was found to be associated with frost tolerance and FAC in both populations. This marker was also associated with winter hardiness and high yield in earlier studies. This marker is located in a gene of unknown function.

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

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5' end of the gene.

Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.)

A multi-parent advanced generation inter-cross (MAGIC) derived from 11 founder lines in faba bean was used in this study to identify quantitative trait loci (QTL) for frost tolerance traits using the association mapping method with 156 SNP markers. This MAGIC population consists of a set of 189 genotypes from the Göttingen Winter Bean Population. The association panel was tested in two different experiments, i.e. a frost and a hardening experiment. Six morphological traits, leaf fatty acid composition, relative water content in shoots were scored in this study. The genotypes presented a large genetic variation for all traits that were highly heritable after frost and after hardening. High phenotypic significant correlations were established between traits. The principal coordinates analysis resulted in no clear structure in the current population. Association mapping was performed using a general linear model and mixed linear model with kinship. A False discovery rate of 0.20 (and 0.05) was used to test the significance of marker-trait association. As a result, many putative QTLs for 13 morphological and physiological traits were detected using both models. The results reveal that QTL mapping by association analysis is a powerful method of detecting the alleles associated with frost tolerance in the winter faba bean which can be used in accelerating breeding programs.

Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives

The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.