Genome-wide association and genomic prediction for iron and zinc concentration and iron bioavailability in a collection of yellow dry beans

Dry bean is a nutrient-dense food targeted in biofortification programs to increase seed iron and zinc levels. The underlying assumption of breeding for higher mineral content is that enhanced iron and zinc levels will deliver health benefits to the consumers of these biofortified foods. This study characterized a diversity panel of 275 genotypes comprising the Yellow Bean Collection (YBC) for seed Fe and Zn concentration, Fe bioavailability (FeBio), and seed yield across 2 years in two field locations. The genetic architecture of each trait was elucidated via genome-wide association studies (GWAS) and the efficacy of genomic prediction (GP) was assessed. Moreover, 82 yellow breeding lines were evaluated for seed Fe and Zn concentrations as well as seed yield, serving as a prediction set for GP models. Large phenotypic variability was identified in all traits evaluated, and variations of up to 2.8 and 13.7-fold were observed for Fe concentration and FeBio, respectively. Prediction accuracies in the YBC ranged from a low of 0.12 for Fe concentration, to a high of 0.72 for FeBio, and an accuracy improvement of 0.03 was observed when a QTN, identified through GWAS, was used as a fixed effect for FeBio. This study provides evidence of the lack of correlation between FeBio estimated in vitro and Fe concentration and highlights the potential of GP in accurately predicting FeBio in yellow beans, offering a cost-effective alternative to the traditional assessment of using Caco2 cell methodologies.

Assessing common bean genotypes for resistance to Diabrotica speciosa (Coleoptera: Chrysomelidae)

Diabrotica speciosa (Germar) (Coleoptera: Chrysomelidae) is a major pest of common bean (Phaseolus vulgaris L.; Fabales: Fabaceae), and adults can defoliate plants during the whole crop cycle. This study was conducted to evaluate the resistance to D. speciosa in 16 common bean genotypes (14 landraces and 2 cultivars), through three different experiments. In the laboratory, choice and no-choice feeding tests were performed to evaluate the percentage of leaf consumption. In the greenhouse, plant height, numbers of leaves, percentage of injured leaves, percentage of injury per leaf, weight of seeds, and D. speciosa survival were evaluated. Furthermore, trichome density, levels of peroxidase (POD), superoxide dismutase (SOD), and protein content in common bean leaves were assessed. In the laboratory, the genotypes Chumbinho Branco, Dobalde, Manteigado, IPR Tuiuiú, and 90D Mouro were the least consumed by D. speciosa. In the greenhouse, the genotypes Dobalde, Manteigado, and IPR Tuiuiú expressed tolerance to the pest, which was associated with a higher plant height and/or unchanged POD and SOD levels and protein content following insect feeding, and no reduction in seed production. The landrace 90D Mouro exhibited antixenosis and tolerance to D. speciosa, observed as a lower leaf injury, higher trichome density, lower protein contents, higher SOD level and no reduction in seed weight. Overall, we have shown that antixenosis and tolerance can help overcome damages resulting from D. speciosa feeding, with emphasis on four common bean genotypes that may be useful in plant breeding programs aimed at controlling D. speciosa in common bean crops.

Low doses of glyphosate do not damage the secondary metabolism of common bean

Glyphosate application, even in low doses, changes the metabolism of crops. This research aimed to evaluate the effects of glyphosate low doses and sowing season on metabolic changes of early-cycle common beans. Two experiments were conducted in the field, one in the winter season and one in the wet season. The experimental design was a randomized complete block design consisting of the application of glyphosate low doses [0.0, 1.8, 7.2, 12.0, 36.0, 54.0, and 108.0 g acid equivalent (a.e.) ha^-1] in the phenological stage V4 with four replications. In the winter season, glyphosate and shikimic acid were increased five days after the application of treatments. In contrast, the same compounds increased only at doses of 36 g a.e. ha^-1 and above in the wet season. The dose of 7.2 g a.e. ha^-1 increased phenylalanine ammonia-lyase and benzoic acid in the winter season. The doses of 54 and 108 g a.e. ha^-1 increased benzoic acid, caffeic acid, and salicylic acid. Our study indicated that glyphosate low doses increase the concentration of shikimic, benzoic, salicylic and caffeic acid, PAL and tyrosine. There was no reduction in aromatic amino acids and in secondary compounds from the shikimic acid pathway.

Intrinsic labelling of common beans with 2H2O to enable estimates of protein digestibility

BACKGROUND

The use of plant protein intrinsically labelled with stable isotopes provides an innovative solution to assess the efficiency of protein intake by humans. Here, the incorporation of 2H has been applied to intrinsically labelled plant protein in the common bean. This study aimed to evaluate which is the best phenological phase of seed maturation to incorporate the heavy hydrogen isotope 2H into seed amino acids. Common beans (Phaseolus vulgaris L.) were grown in pots, then, after 50 days sowing, 2H2O dissolved in irrigation water was applied, then again at an interval of either 3, 6, 9, and 12 days.

RESULTS

Applications of 2H2O at 6, 9, and 12 days after the first application, in the full-flowering stage, were the best treatments for enriching protein-bound amino acids in the bean seed with 2H.

CONCLUSION

All treatments resulted in enrichment above 500 ppm, so the treatments (quantity and timing of 2H2O addition) were deemed successful for enriching bean seeds. This makes the intrinsically labelled seeds suitable for preparing test meals to assess the digestion and essential amino acid absorption of common bean amino acids in human subjects.

Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans

Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.

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.

The effects of blanching on composition and modification of proteins in navy beans (Phaseolus vulgaris)

Blanching is an important process in the preparation of navy beans (Phaseolus vulgaris L.) for canning. We here explore the effect of blanching which can profoundly affect protein composition and introduce protein-primary-level modifications. Amino acid analysis showed significantly decreased protein abundance (58.5%) in blanched beans compared to raw beans. Proteomic analyses revealed a decrease in high molecular weight isoforms of the major storage globulin proteins phaseolin (mean fold-change -3.7) and legumin (mean fold-change -2.5) and concomitant increase in their low molecular weight isoforms (mean fold-change 6.4 and 8.3, respectively). Blanched beans also had decreased abundance of lipoxygenase (mean fold-change -13.1), an enzyme responsible for product spoilage during storage. Increased lysinoalanine (up to 47%) and highly modified protein fragments were found in the processing waters, indicating heat- induced modifications. Correlating these molecular level changes thus provides a basis for evaluating how processing parameters can be modified to increase protein food quality.

Characterization of extractable phenolic profile of common bean seeds (Phaseolus vulgaris L.) in a Spanish diversity panel

Phenolic compounds are important bioactive compounds in common bean (Phaseolus vulgaris L.). The aim of this work was the characterization of extractable phenolic profile (corresponding to 12 hydroxycinnamic acids and derivatives, 13 anthocyanins and 15 flavonols) in a bean diversity panel constituted by 220 lines, all grown under the same environmental conditions. Hydroxycinnamic derivatives were detected in all samples, while anthocyanins and flavonols were not detected in samples with completely white seed coats. In general, lines with black seeds showed higher contents of anthocyanins, followed by some red-seeded lines, while notable levels of flavonols were detected in market classes, including those with yellow, pink, and cream seed coats. However, a clear relationship between phenolic composition and seed phenotype could not be established, indicating the great influence of the genotype. This wide variability in the phenolic profiles analyzed is of particular interest for further breeding trials and the selection of varieties on the basis of this group of compounds.

Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification

A single loop-mediated isothermal amplification (LAMP) assay was developed for specific detection of both pathogens that cause bacterial blight in common bean, Xanthomonas phaseoli pv. phaseoli (Xpp) and Xanthomonas citri pv. fuscans (Xcf). The objective was to provide a simple, easy-to-use, specific, and sensitive method to investigate the presence of one or both pathogens in plant material and seeds for routine diagnosis. The detection limits for both pathogens were 10 CFU/ml for cell suspensions and 1 fg of DNA, whereas in conventional PCR, the primers detected up to 10⁵ CFU/ml and 1 ng of DNA. Specificity was confirmed by testing DNA from bean leaves, other Xanthomonas species, common fungal and bacterial bean pathogens, and bacteria from the leaf microbiota. The method was tested with bean leaves inoculated with Xpp, and the pathogen could be detected from 4 h up to 15 days postinoculation, even before disease symptoms were visible. When the method was applied to bacterium detection (Xpp or Xcf) in seed lots from infected plants, the bacterium detection rate was 100% (24 of 24). The pathogens were detected in seeds incubated for just 1 h in saline solution (0.85%), reducing the time needed for bacterium detection. The LAMP assay could be useful as a tool in bean bacterial blight management. Rapid and sensitive detection of bacteria in bean seed lots would reduce the risks of planting highly contaminated seeds in environments favorable to blight multiplication.

Cookies elaborated with oat and common bean flours improved serum markers in diabetic rats

BACKGROUND

Common beans have been associated with anti-diabetic effects, due to its high content of bioactive compounds. Nevertheless, its consumption has decreased worldwide. Therefore, there is an increasing interest in the development of novel functional foods elaborated with common beans. The aim of this study was to evaluate the anti-diabetic effect of oat-bean flour cookies, and to analyze its bioactive composition, using commercial oat-wheat cookies for comparative purposes.

RESULTS

Oat-bean cookies (1.2 g kg^-1 ) slightly decreased serum glucose levels (∼1.1-fold) and increased insulin levels (∼1.2-fold) in diabetic rats, reducing the hyperglycemic peak in healthy rats (∼1.1-fold). Oat-bean cookies (0.8 and 1.2 g kg^-1 ) exerted a greater hypolipidemic effect than commercial oat-wheat cookies (1.2 g kg^-1 ), as observed in decreased serum triglycerides and low-density lipoprotein cholesterol. Furthermore, the supplementation with 1.2 g kg^-1 oat-bean cookies decreased atherogenic index and serum C-reactive protein levels, suggesting their cardioprotective potential. The beneficial effect of oat-bean cookies was associated with their high content of dietary fiber and galacto oligosaccharides, as well as chlorogenic acid, rutin, protocatechuic acid, β-sitosterol and soyasaponins.

CONCLUSION

These results suggest that common beans can be used as functional ingredients for the elaboration of cookies with anti-diabetic effects. © 2017 Society of Chemical Industry.

In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

BACKGROUND

Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.

RESULTS

Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST  = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST  = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.

CONCLUSIONS

For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Microwave and micronization treatments affect dehulling characteristics and bioactive contents of dry beans (Phaseolus vulgaris L.)

BACKGROUND

Heat pretreatment is considered the first step in grain milling. This study therefore evaluated microwave and micronization heat treatments in improving the dehulling characteristics, phenolic composition and antioxidant and α-amylase activities of bean cultivars from three market classes.

RESULTS

Heat treatments improved dehulling characteristics (hull yield, rate coefficient and reduced abrasive hardness index) depending on bean cultivar, whereas treatment effects increased with dehulling time. Micronization increased minor phenolic components (tartaric esters, flavonols and anthocyanins) of all beans but had variable effects on total phenolic content depending on market class. Microwave treatment increased α-amylase inhibitor concentration, activity and potency, which were strongly correlated (r²  = 0.71, P < 0.0001) with the flavonol content of beans. Heat treatment had variable effects on the phenolic composition of bean hulls obtained by abrasive dehulling without significantly altering the antioxidant activity of black and pinto bean hulls. Principal component analysis on 22 constituents analyzed in this study demonstrated the differences in dehulling characteristics and phenolic components of beans and hulls as major factors in segregating the beneficial heat treatment effects.

CONCLUSION

Heat treatment may be useful in developing novel dietary fibers from beans with variable composition and bioactivity with a considerable range of applications as functional food ingredients.

Developing a common bean core collection suitable for association mapping studies

Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.

Minerals (Zn, Fe, Ca and Mg) and Antinutrient (Phytic Acid) Constituents in Common Bean

In this study, the variation of zinc (Zn), iron (Fe), calcium (Ca) and magnesium (Mg) and the interference of phytic acid (PA) on their availability was investigated in 29 US grown and CIAT breeding genotypes of common bean. Fe levels showed the highest variation (8.9-112.9 mg kg^-1) followed by Ca (58.67-122.98 mg kg^-1) and Zn (30.90-64.60 mg kg^-1) while variability of Mg concentration (6.47-11.05 mg kg^-1) is the least among the mineral components. PA showed a wide range of variability (12.52-316.42 m kg^-1) and inversely correlated with Fe, Ca and Mg concentrations. The results of the minerals and PA concentration can be interpreted in terms of expected bio-availability of minerals and the correlation study indicated that the presence of high concentration of PA inhibit the availability of most minerals under study in common beans. We suggest that the genotypes, MIB466, MIB465, MIB152 and JaloEEP 558 could be considered as sources of high Zn and Vista and NUA56-1770 for high seed Fe. We also identified G122 for high Ca and JaloEEP558 genotype for high Mg. We conclude that there is scope for the enhancement of mineral contents of common bean by selecting suitable genotype and bean products require processing for dephytinization for the improvement of mineral availability.