Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World

Identification of novel sources of partial and incomplete hypersensitive resistance to rust and associated genomic regions in common bean

Common bean (Phaseolus vulgaris) is one of the legume crops most consumed worldwide and bean rust is one of the most severe foliar biotrophic fungal diseases impacting its production. In this work, we searched for new sources of rust resistance (Uromyces appendiculatus) in a representative collection of the Portuguese germplasm, known to have accessions with an admixed genetic background between Mesoamerican and Andean gene pools. We identified six accessions with incomplete hypersensitive resistance and 20 partially resistant accessions of Andean, Mesoamerican, and admixed origin. We detected 11 disease severity-associated single-nucleotide polymorphisms (SNPs) using a genome-wide association approach. Six of the associations were related to partial (incomplete non-hypersensitive) resistance and five to incomplete hypersensitive resistance, and the proportion of variance explained by each association varied from 4.7 to 25.2%. Bean rust severity values ranged from 0.2 to 49.1% and all the infection types were identified, reflecting the diversity of resistance mechanisms deployed by the Portuguese germplasm.The associations with U. appendiculatus partial resistance were located in chromosome Pv08, and with incomplete hypersensitive resistance in chromosomes Pv06, Pv07, and Pv08, suggesting an oligogenic inheritance of both types of resistance. A resolution to the gene level was achieved for eight of the associations. The candidate genes proposed included several resistance-associated enzymes, namely β-amylase 7, acyl-CoA thioesterase, protein kinase, and aspartyl protease. Both SNPs and candidate genes here identified constitute promising genomics targets to develop functional molecular tools to support bean rust resistance precision breeding.

Oligogenic Control of Quantitative Resistance Against Powdery Mildew Revealed in Portuguese Common Bean Germplasm

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes worldwide, and its production is severely affected by fungal diseases such as powdery mildew. Portugal has a diverse germplasm, with accessions of Andean, Mesoamerican, and admixed origin, making it a valuable resource for common bean genetic studies. In this work, we evaluated the response of a Portuguese collection of 146 common bean accessions to Erysiphe diffusa infection, observing a wide range of disease severity and different levels of compatible and incompatible reactions, revealing the presence of different resistance mechanisms. We identified 11 incompletely hypersensitive resistant and 80 partially resistant accessions. We performed a genome-wide association study to clarify its genetic control, resulting in the identification of eight disease severity-associated single-nucleotide polymorphisms, spread across chromosomes Pv03, Pv09, and Pv10. Two of the associations were unique to partial resistance and one to incomplete hypersensitive resistance. The proportion of variance explained by each association varied between 15 and 86%. The absence of a major locus, together with the relatively small number of loci controlling disease severity, suggested an oligogenic inheritance of both types of resistance. Seven candidate genes were proposed, including a disease resistance protein (toll interleukin 1 receptor-nucleotide binding site-leucine-rich repeat class), an NF-Y transcription factor complex component, and an ABC-2 type transporter family protein. This work contributes with new resistance sources and genomic targets valuable to develop selection molecular tools and support powdery mildew resistance precision breeding in common bean.

Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy

Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.

Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers

BACKGROUND

Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems.

MATERIALS AND METHODS

In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification.

RESULTS

The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin.

CONCLUSIONS

A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.

Portuguese Common Bean Natural Variation Helps to Clarify the Genetic Architecture of the Legume's Nutritional Composition and Protein Quality

Common bean is a nutritious food legume widely appreciated by consumers worldwide. It is a staple food in Latin America, and a component of the Mediterranean diet, being an affordable source of protein with high potential as a gourmet food. Breeding for nutritional quality, including both macro and micronutrients, and meeting organoleptic consumers' preferences is a difficult task which is facilitated by uncovering the genetic basis of related traits. This study explored the diversity of 106 Portuguese common bean accessions, under two contrasting environments, to gain insight into the genetic basis of nutritional composition (ash, carbohydrates, fat, fiber, moisture, protein, and resistant starch contents) and protein quality (amino acid contents and trypsin inhibitor activity) traits through a genome-wide association study. Single-nucleotide polymorphism-trait associations were tested using linear mixed models accounting for the accessions' genetic relatedness. Mapping resolution to the gene level was achieved in 56% of the cases, with 102 candidate genes proposed for 136 genomic regions associated with trait variation. Only one marker-trait association was stable across environments, highlighting the associations' environment-specific nature and the importance of genotype × environment interaction for crops' local adaptation and quality. This study provides novel information to better understand the molecular mechanisms regulating the nutritional quality in common bean and promising molecular tools to aid future breeding efforts to answer consumers' concerns.

Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed.

Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer's selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker-trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

Genome-Wide Association Studies of Mineral Content in Common Bean

Micronutrient malnutrition is one of the main public health problems in many parts of the world. This problem raises the attention of all valuable sources of micronutrients for the human diet, such as common bean (Phaseolus vulgaris L.). In this research, a panel of 174 accessions representing Croatian common bean landraces was phenotyped for seed content of eight nutrients (N, P, K, Ca, Mg, Fe, Zn, and Mn), and genotyped using 6,311 high-quality DArTseq-derived SNP markers. A genome-wide association study (GWAS) was then performed to identify new genetic sources for improving seed mineral content. Twenty-two quantitative trait nucleotides (QTN) associated with seed nitrogen content were discovered on chromosomes Pv01, Pv02, Pv03, Pv05, Pv07, Pv08, and Pv10. Five QTNs were associated with seed phosphorus content, four on chromosome Pv07, and one on Pv08. A single significant QTN was found for seed calcium content on chromosome Pv09 and for seed magnesium content on Pv08. Finally, two QTNs associated with seed zinc content were identified on Pv06 while no QTNs were found to be associated with seed potassium, iron, or manganese content. Our results demonstrate the utility of GWAS for understanding the genetic architecture of seed nutritional traits in common bean and have utility for future enrichment of seed with macro- and micronutrients through genomics-assisted breeding.

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

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

Pulse Consumption among Portuguese Adults: Potential Drivers and Barriers towards a Sustainable Diet

The transition from diets rich in animal products to plant-based protein foods—like pulses—is crucial, for both environmental sustainability and human health. The aim of this study was to characterize the current consumption and to describe the drivers of and barriers to pulse intake in Portugal. Using a quantitative approach, a semi-structured questionnaire was distributed online, and 1174 valid responses were obtained. The most consumed pulses were beans and peas, consumed at least once a week by 48.3% and 44.4% of the sample, respectively. When participants were asked about the possibility of replacement, even partially, of animal products for pulses, 15.0% stated they would not substitute even in a food scarcity scenario. In the qualitative study, ten individuals involved at different steps of pulses’ supply and value chain were interviewed in order to study individual behaviors and experiences linked knowledge and consumption of pulses. It was noticed that the lack of recognition of their nutritional value, the high cooking time and the effect of the anti-nutritional factors were commonly pointed out as barriers. The identification and understanding of perceived barriers for that low consumption will leverage the development of new strategies to promote this promising alternative.

Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection

The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the "Living Plants Germplasm Bank" at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the "Sicilian Plant Germplasm Repository" of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.

Natural Variation in Portuguese Common Bean Germplasm Reveals New Sources of Resistance Against Fusarium oxysporum f. sp. phaseoli and Resistance-Associated Candidate Genes

Common bean (Phaseolus vulgaris) is one of the most consumed legume crops in the world, and Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. phaseoli, is one of the major diseases affecting its production. Portugal holds a very promising common bean germplasm with an admixed genetic background that may reveal novel genetic resistance combinations between the original Andean and Mesoamerican gene pools. To identify new sources of Fusarium wilt resistance and detect resistance-associated single-nucleotide polymorphisms (SNPs), we explored, for the first time, a diverse collection of the underused Portuguese common bean germplasm by using genome-wide association analyses. The collection was evaluated for Fusarium wilt resistance under growth chamber conditions, with the highly virulent F. oxysporum f. sp. phaseoli strain FOP-SP1 race 6. Fourteen of the 162 Portuguese accessions evaluated were highly resistant and 71 intermediate. The same collection was genotyped with DNA sequencing arrays, and SNP-resistance associations were tested via a mixed linear model accounting for the genetic relatedness between accessions. The results from the association mapping revealed nine SNPs associated with resistance on chromosomes Pv04, Pv05, Pv07, and Pv08, indicating that Fusarium wilt resistance is under oligogenic control. Putative candidate genes related to phytoalexin biosynthesis, hypersensitive response, and plant primary metabolism were identified. The results reported here highlight the importance of exploring underused germplasm for new sources of resistance and provide new genomic targets for the development of functional markers to support selection in future disease resistance breeding programs.

In-Depth Characterisation of Common Bean Diversity Discloses Its Breeding Potential for Sustainable Agriculture

Legumes’ cultivation contributes services to agro-ecosystems and society, in line with the principles of sustainability. Among pulses, the common bean is one of the most important sources of plant proteins and other important nutrients for humans. Extensive phenotypic and genetic characterisations of unexplored bean germplasm are still needed to unlock its breeding potential. To the purpose, a panel of 192 diverse genotypes, mainly developed starting from European landrace accessions, was characterised for relevant morpho-phenological traits; a partially replicated experimental design was used. For each quantitative trait, Best Linear Unbiased Predictors and broad-sense heritability were estimated. The screened panel revealed a high level of diversity for most of the measured traits, especially for days to flowering and hundred-seed weight. The same material was also characterised by means of double-digest Restriction-site Associated DNA; a high number of SNP markers were successfully produced. The genotyping allowed understanding the fine genetic structure of the panel. Genetic information was also used to study morpho-phenological traits considering different genetic groups existing within the panel. At the same time, genotypes characterised by favourable traits were identified. The availability of such collection with its extensive characterisation, make this material an excellent resource for common bean improvement.

Characterization of Soaking Process' Impact in Common Beans Phenolic Composition: Contribute from the Unexplored Portuguese Germplasm

Despite the common beans' nutritional and phytochemical value, in Portugal its consumption decreased more than 50% in the last decade. The present study aimed to characterize phenolic composition of the Portuguese traditional varieties and corresponding soaked seed fractions (including soaking water). With such purpose, the phenolic composition (total content of soluble phenolics, flavonoids, and proanthocyanidins) and in vitro antioxidant activity were evaluated in the raw whole flour of 31 Portuguese common bean varieties. The phenolic composition of the soaked fractions was respectively compared to the raw flour. Phenolic compounds' identification and relative quantification were achieved by UPLC-TripleTOF-MS for one representative variety and their fractions. The highest phenolic content was found in colored varieties and the brown market class highlighted as the richest one. The loss of phenolic compounds to the soaking water was highly dependent on variety. The predominant phenolic compounds' classes were flavan-3-ols (soaking water and coats), flavonols (coats), and phenolic acids (cotyledons). This characterization study showed the diversity on the phenolic composition of Portuguese varieties and the need to adjust the soaking and peeling processes to the variety (considering the possible loss of potential health promoter compounds, e.g., phenolic compounds).

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

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

Maintaining Genome Integrity during Seed Development in Phaseolus vulgaris L.: Evidence from a Transcriptomic Profiling Study

The maintenance of genome integrity is crucial in seeds, due to the constant challenge of several endogenous and exogenous factors. The knowledge concerning DNA damage response and chromatin remodeling during seed development is still scarce, especially in Phaseolus vulgaris L. A transcriptomic profiling of the expression of genes related to DNA damage response/chromatin remodeling mechanisms was performed in P. vulgaris seeds at four distinct developmental stages, spanning from late embryogenesis to seed desiccation. Of the 14,001 expressed genes identified using massive analysis of cDNA ends, 301 belong to the DNA MapMan category. In late embryogenesis, a high expression of genes related to DNA damage sensing and repair suggests there is a tight control of DNA integrity. At the end of filling and the onset of seed dehydration, the upregulation of genes implicated in sensing of DNA double-strand breaks suggests that genome integrity is challenged. The expression of chromatin remodelers seems to imply a concomitant action of chromatin remodeling with DNA repair machinery, maintaining genome stability. The expression of genes related to nucleotide excision repair and chromatin structure is evidenced during the desiccation stage. An overview of the genes involved in DNA damage response and chromatin remodeling during P. vulgaris seed development is presented, providing insights into the mechanisms used by developing seeds to cope with DNA damage.