Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene.

Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.

Multi-trait index: selection and recommendation of superior black bean genotypes as new improved varieties.

Common bean provides diet rich in vitamins, fiber, minerals, and protein, which could contribute into food security of needy populations in many countries. Developing genotypes that associate favorable agronomic and grain quality traits in the common bean crop could increase the chances of adopting new cultivars black bean. In this context, the present study aimed at selection of superior black bean lines using multi-variate indexes, Smith-Hazel-index, and genotype by yield*trait biplot analysis. These trials were conducted in Campos dos Goytacazes - RJ, in 2020 and 2021. The experimental design used was randomized blocks, with 28 treatments and three replications. The experimental unit consisted of four rows 4.0 m long, spaced at 0.50 m apart, with a sowing density of 15 seeds per meter. The two central rows were used for the evaluations. The selection of superior genotypes was conducted using the multiple trait stability index (MTSI), multi-trait genotype-ideotype distance index (MGIDI), multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP), Smith-Hazel index, and Genotype by Yield*Trait Biplot (GYT). The multivariate indexes efficiently selected the best black bean genotypes, presenting desirable selection gains for most traits. The use of multivariate indexes and GYT enable the selection of early genotypes with higher grain yields. These lines G9, G13, G17, G23, and G27 were selected based on their performance for multiple traits closest to the ideotype and could be recommended as new varieties.

Genome-Wide Identification and Characterization of U-Box Gene Family Members and Analysis of Their Expression Patterns in Phaseolus vulgaris L. under Cold Stress.

The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.

Evaluation of Polyphenols Synthesized in Mature Seeds of Common Bean (Phaseolus vulgaris L.) Advanced Mutant Lines.

This study aimed to investigate the availability of flavonoids, anthocyanins, and phenolic acids in mutant bean seeds, focusing on M7 mutant lines, and their corresponding initial and local cultivars. HPLC-DAD-MS/MS and HPLC-MS/MS were used to analyze twenty-eight genotypes of common bean. The obtained results suggest that the mutations resulted in four newly synthesized anthocyanins in the mutant bean seeds, namely, delphinidin 3-O-glucoside, cyanidin 3-O-glucoside, pelargonidin 3-O-glucoside, and petunidin 3-O-glucoside, in 20 accessions with colored seed shapes out of the total of 28. Importantly, the initial cultivar with white seeds, as well as the mutant white seeds, did not contain anthocyanins. The mutant lines were classified into groups based on their colors as novel qualitative characteristics. Five phenolic acids were further quantified: ferulic, p-coumaric, caffeic, sinapic, and traces of chlorogenic acids. Flavonoids were represented by epicatechin, quercetin, and luteolin, and their concentrations in the mutant genotypes were several-fold superior compared to those of the initial cultivar. All mutant lines exhibited higher concentrations of phenolic acids and flavonoids. These findings contribute to the understanding of the genetics and biochemistry of phenolic accumulation and anthocyanin production in common bean seeds, which is relevant to health benefits and might have implications for common bean breeding programs and food security efforts.

Silicon, by promoting a homeostatic balance of C:N:P and nutrient use efficiency, attenuates K deficiency, favoring sustainable bean cultivation.

BACKGROUND: In many regions of the world, K is being depleted from soils due to agricultural intensification a lack of accessibility, and the high cost of K. Thus, there is an urgent need for a sustainable strategy for crops in this environment. Si is an option for mitigating stress due to nutritional deficiency. However, the underlying effects of Si in mitigating K deficiency C:N:P homeostasis still remains unknown for bean plants. This is a species of great worldwide importance. Thus, this study aims to evaluate whether i) K deficiency modifies the homeostatic balance of C, N and P, and, if so, ii) Si supply can reduce damage caused to nutritional stoichiometry, nutrient use efficiency, and production of dry mass in bean plants. RESULTS: K deficiency caused a reduction in the stoichiometric ratios C:N, C:P, and P:Si in shoots and C:N, C:P, C:Si, N:Si, and P:Si in roots, resulting in a decrease in K content and use efficiency and reducing biomass production. The application of Si in K-deficient plants modified the ratios C:N, C:Si, N:P, N:Si, and P:Si in shoots and C:N, C:P, C:Si, N:Si, N:P, and P:Si in roots, increasing the K content and efficiency, reducing the loss of biomass. In bean plants with K sufficiency, Si also changed the stoichiometric ratios C:N, C:P, C:Si, N:P, N:Si, and P:Si in shoots and C:N, C:Si, N:Si, and P:Si in roots, increasing K content only in roots and the use efficiency of C and P in shoots and C, N, and P in roots, increasing the biomass production only in roots. CONCLUSION: K deficiency causes damage to the C:N:P homeostatic balance, reducing the efficiency of nutrient use and biomass production. However, Si is a viable alternative to attenuate these nutritional damages, favoring bean growth. The future perspective is that the use of Si in agriculture in underdeveloped economies with restrictions on the use of K will constitute a sustainable strategy to increase food security.

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 glycemic index common bean snack increased satiety without modifying energy intake in adults with normal weight: randomized crossover trials.

This study aimed to evaluate the short-term effect of a common bean baked snack (CBBS) and cooked bean consumption on energy intake, satiety, glycemic response, and palatability in subjects with normal weight (Study 1) and overweight (Study 2) and to determine the glycemic index of CBBS (Study 3). For studies 1 and 2, satiety and glycemic response were measured over 45 min after consuming CBBS, cooked beans or white bread preload, and energy intake at an ad libitum test meal was calculated. Energy intake remained similar after consuming the three preloads in both studies. Compared to white bread, CBBS consumption increased fullness by 52% in subjects with normal weight but not in those with overweight. The CBBS calculated glycemic index was considered low (42). Consumption of low glycemic index CBBS increased satiety in adults with a normal weight. Long-term trials assessing the effects on body weight management are necessary.

Selection Behavior and OBP-Transcription Response of Western Flower Thrips, Frankliniella occidentalis, to Six Plant VOCs from Kidney Beans.

Plant volatile organic compounds (VOCs) are an important link that mediates chemical communication between plants and plants, plants and insects, and plants and natural enemies of insect pests. In this study, we tested the response in the selective behavior of western flower thrips, Frankliniella occidentalis, to the VOCs of kidney bean, Phaseolus vulgaris L., to explore their "attraction" or "repellent" effects regarding their application in integrated pest management (i.e., IPM). The results indicated that 12.7 µL/mL (E, E, E, E)-squalene, 3.2 µL/mL dioctyl phthalate, and 82.2 µL/mL ethyl benzene had a significantly attractive effect on the selective behavior of F. occidentalis, while 10.7 µL/mL and 21.4 µL/mL 2,6-ditert-butyl-4-methyl phenol had a significantly repulsive effect on the selective behavior of F. occidentalis, showing that F. occidentalis responds differently to specific concentrations of VOCs from P. vulgaris plant emissions. Interestingly, the three compounds with the specific above concentrations, after being mixed in pairs, significantly attracted F. occidentalis compared to the control treatment; however, the mixture with the three above compounds had no significant different effect on F. occidentalis compared to the control treatment. It can be seen that the effect with the mixtures of three kinds of VOCs had the same function and may not get better. Simultaneously, the reasons for this result from the transcription levels of odorant-binding protein genes (OBPs) were determined. There were differences in the types and transcription levels of OBPs, which played a major role in the host selection behavior of F. occidentalis under the mixed treatment of different VOCs. It is presumed that there are specific VOCs from P. vulgaris plants that have a good repellent or attracting effect on the selective behavior of F. occidentalis, which can be used for the development of plant-derived insect attractants and repellents to serve as IPM in fields. But attention should be paid to the antagonism between plant-derived preparations and VOCs produced by plants themselves after application.

1-Methylcyclopropene Alleviates Postharvest Chilling Injury of Snap Beans by Enhancing Antioxidant Defense System.

Research background: Chilling injury is a major disorder affecting the quality of tropical and subtropical vegetables during low temperature storage. Snap bean (Phaseolus vulgaris L.) is sensitive to chilling injury. The main purpose of the present study is to investigate the alleviating effects of 1-methylcyclopropene (1-MCP) on chilling injury of snap bean. In addition, the related mechanisms were also detected from the perspective of the changes of antioxidant defense system. Experimental approach: Snap beans were exposed to different volume fractions of 1-MCP. After 24 h of treatment, snap beans were stored at 4 °C for up to 14 days. Chilling injury index, electrolyte leakage, titratable acidity and total soluble solids were determined. Contents of chlorophyll, ascorbic acid and malondialdehyde were assessed. The total antioxidant capacity, Fe(II) ion chelating capacity, scavenging capacities on free radicals and activities of antioxidant enzymes were detected. Total phenol content and activities of related metabolic enzymes were also determined. Results and conclusions: 1-MCP treatment reduced chilling injury index, electrolyte leakage rate and malondialdehyde content of snap beans. The amounts of total soluble solids, titratable acid, ascorbic acid and total chlorophyll in 1-MCP-treated snap beans were significantly higher than those of control. The snap beans treated with 1-MCP showed stronger total antioxidant capacity and metal chelating activity. The 1-MCP treatment enhanced scavenging effects of snap beans on superoxide, hydroxyl and 1,1-diphenyl-2-trinitrophenylhydrazine radicals. The activities of peroxidase, ascorbate peroxidase, superoxide dismutase and catalase in 1-MCP-treated group were higher than of control. The treatment also enhanced the accumulation of phenolic compounds in snap beans by regulating the activities of phenol-metabolizing enzymes such as shikimate dehydrogenase, phenylalanine ammonia lyase enzyme, cinnamic acid 4-hydroxylase and polyphenol oxidase. In conclusion, with the mechanism that involves the activation of enzymatic and non-enzymatic antioxidant systems, 1-MCP has the ability to avoid chilling injury of snap bean. Novelty and scientific contribution: This study gives insights into whether 1-MCP can regulate postharvest cold resistance in vegetables by enhancing the enzymatic antioxidant system and inducing the accumulation of non-enzymatic antioxidants. Considering the results, 1-MCP treatment could be an effective method to alleviate postharvest chilling injury of snap beans during low temperature storage.

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.

Effects of chemical inhibition of histone deacetylase proteins in the growth and virulence of Macrophomina phaseolina (Tassi) Goid.

Chromatin remodeling enzymes are important "writers", "readers" and "erasers" of the epigenetic code. These proteins are responsible for the placement, recognition, and removal of molecular marks in histone tails that trigger structural and functional changes in chromatin. This is also the case for histone deacetylases (HDACs), i.e., enzymes that remove acetyl groups from histone tails, signaling heterochromatin formation. Chromatin remodeling is necessary for cell differentiation processes in eukaryotes, and fungal pathogenesis in plants includes many adaptations to cause disease. Macrophomina phaseolina (Tassi) Goid. is a nonspecific, necrotrophic ascomycete phytopathogen that causes charcoal root disease. M. phaseolina is a frequent and highly destructive pathogen in crops such as common beans (Phaseolus vulgaris L.), particularly under both water and high temperature stresses. Here, we evaluated the effects of the classical HDAC inhibitor trichostatin A (TSA) on M. phaseolinain vitro growth and virulence. During inhibition assays, the growth of M. phaseolina in solid media, as well as the size of the microsclerotia, were reduced (p<0.05), and the colony morphology was remarkably affected. Under greenhouse experiments, treatment with TSA reduced (p<0.05) fungal virulence in common bean cv. BAT 477. Tests of LIPK, MAC1 and PMK1 gene expression during the interaction of fungi with BAT 477 revealed noticeable deregulation. Our results provide additional evidence about the role of HATs and HDACs in important biological processes of M. phaseolina.

Stomata on the abaxial and adaxial leaf surfaces contribute differently to leaf gas exchange and photosynthesis in wheat.

Although stomata are typically found in greater numbers on the abaxial surface, wheat flag leaves have greater densities on the adaxial surface. We determine the impact of this less common stomatal patterning on gaseous fluxes using a novel chamber that simultaneously measures both leaf surfaces. Using a combination of differential illuminations and CO2 concentrations at each leaf surface, we found that mesophyll cells associated with the adaxial leaf surface have a higher photosynthetic capacity than those associated with the abaxial leaf surface, which is supported by an increased stomatal conductance (driven by differences in stomatal density). When vertical gas flux at the abaxial leaf surface was blocked, no compensation by adaxial stomata was observed, suggesting each surface operates independently. Similar stomatal kinetics suggested some co-ordination between the two surfaces, but factors other than light intensity played a role in these responses. Higher photosynthetic capacity on the adaxial surface facilitates greater carbon assimilation, along with higher adaxial stomatal conductance, which would also support greater evaporative leaf cooling to maintain optimal leaf temperatures for photosynthesis. Furthermore, abaxial gas exchange contributed c. 50% to leaf photosynthesis and therefore represents an important contributor to overall leaf gas exchange.

Identification and Characterization of a Mutant PV-PUR Gene Responsible for the Purple Phenotype of Snap Bean (Phaseolus vulgaris L.).

Pod color is a major economic trait of snap beans (Phaseolus vulgaris L.), among which the pod with a purple stripe is more attractive to people. A stable purple mutant with purple stripes on the pods was obtained by artificial mutagenesis with the high generation snap bean inbred line 'A18-1'. In order to reveal the genetic factors and pathways responsible for the purple appearance in snap bean, we performed transcriptome and metabolome analyses using the green stem and yellow pod cultivar 'A18-1' and its purple mutant 'pv-pur' via 60Co-γ radiation. Transcriptome analysis showed that three genes in the anthocyanin biosynthetic pathway were differentially expressed, among which the expression level of F3'5'H (Phvul.006G018800) was increased in the mutant 'pv-pur', while expression of F3'H (Phvul.004G021200) and ANS (Phvul.002G152700) was downregulated. Anthocyanin-targeted metabonomics analysis showed significant differences in the contents of 10 metabolites between the wild type and mutant plants. Combined analysis of transcriptome and metabolomics showed that one differential metabolite, delphinidin, was related to the differential expression of Phvul.006G024700, Phvul.002G152700, and Phvul.006G018800. Based on the levels of six anthocyanins in wild type and mutant plants, we speculative that the purple appearance of the mutant 'pv-pur' is caused by the increased expression of F3'5'H (Phvul.006G018800), the key enzyme in the transformation from dihydroflavanol (DHK) to dihydromyricetone (DHM) in the anthocyanin biosynthetic pathway. The results lay a foundation for further studies on the molecular mechanism of anthocyanin synthesis in snap bean, and provide a framework for breeding different colors of snap bean.

Screening of Indanoyl-Type Compounds as Elicitors of Isoflavonoid Phytoalexins in Colombian Common Bean Cultivars.

Eleven indanoyl derivatives were synthesized and, along with methyl jasmonate, evaluated as isoflavonoid-phytoalexin elicitors in two cultivars of common bean (Phaseolus vulgaris L. cvs. ICA-Cerinza and Uribe Rosado, tolerant and susceptible to anthracnose, respectively). Indanoyl derivatives (an ester, two amides, and eight indanoyl-amino acid conjugates) were obtained from 1-oxo-indane-4-carboxylic acid. In general, the accumulation of isoflavonoid-type phytoalexins, such as isoflavones (genistein, daidzein, and 2'-hydroxygenistein), isoflavanones (dalbergioidin and kievitone), isoflavan (phaseollinisoflavan), coumestrol, and pterocarpans (phaseollidin and phaseollin), was dependent on the common bean cultivar, the post-induction time, and the elicitor structure. Isoflavones, dalbergioidin, and coumestrol reached their highest amounts during the first 48 to 72 h, whereas kievitone, phaseollinisoflavano, and the pterocarpans reached maximum levels between 72 and 96 h. The 1-oxo-indanoyl-L-isoleucine methyl ester elicited the highest levels of phytoalexins (similar to those elicited by the methyl jasmonate) and showed no significant phytotoxic effects on common bean seedlings. The indanoyl-type synthetic elicitor, 1-oxo-indanoyl-L-isoleucine methyl ester, may represent a promising agronomic alternative for disease control in common bean by enhancing the accumulation of antimicrobial isoflavonoid phytoalexins.

The Common Bean Small Heat Shock Protein Nodulin 22 from Phaseolus vulgaris L. Assembles into Functional High-Molecular-Weight Oligomers.

Small heat shock proteins (sHsps) are present in all domains of life. These proteins are responsible for binding unfolded proteins to prevent their aggregation. sHsps form dynamic oligomers of different sizes and constitute transient reservoirs for folding competent proteins that are subsequently refolded by ATP-dependent chaperone systems. In plants, the sHsp family is rather diverse and has been associated with the ability of plants to survive diverse environmental stresses. Nodulin 22 (PvNod22) is an sHsp of the common bean (Phaseolus vulgaris L.) located in the endoplasmic reticulum. This protein is expressed in response to stress (heat or oxidative) or in plant roots during mycorrhizal and rhizobial symbiosis. In this work, we study its oligomeric state using a combination of in silico and experimental approaches. We found that recombinant PvNod22 was able to protect a target protein from heat unfolding in vitro. We also demonstrated that PvNod22 assembles into high-molecular-weight oligomers with diameters of ~15 nm under stress-free conditions. These oligomers can cluster together to form high-weight polydisperse agglomerates with temperature-dependent interactions; in contrast, the oligomers are stable regarding temperature.

Monitoring Stimulated Darkening from UV-C Light on Different Bean Genotypes by NMR Spectroscopy.

The use of UV-C cool white light on bean (Phaseolus vulgaris L.) seeds significantly increases the biochemical seed coat post-harvest darkening process, whilst preserving seed germination. The aim of this work consists in monitoring the effect caused by the incidence of UV-C light on different bean genotypes using NMR spectroscopy. The genotype samples named IAC Alvorada; TAA Dama; BRS Estilo and BRS Pérola from the Agronomic Institute (IAC; Campinas; SP; Brazil) were evaluated. The following two methodologies were used: a prolonged darkening, in which the grain is placed in a room at a controlled temperature (298 K) and humidity for 90 days, simulating the supermarket shelf; an accelerated darkening, where the grains are exposed to UV-C light (254 nm) for 96 h. The experiments were performed using the following innovative time-domain (TD) NMR approaches: the RK-ROSE pulse sequence; one- and two-dimensional high resolution (HR) NMR experiments (1H; 1H-1H COSY and 1H-13C HSQC); chemometrics tools, such as PLS-DA and heat plots. The results suggest that the observed darkening occurs on the tegument after prolonged (90 days) and accelerated (96 h) conditions. In addition, the results indicate that phenylalanine is the relevant metabolite within this context, being able to participate in the chemical reactions accounted for by the darkening processes. Additionally, it is possible to confirm that a UV-C lamp accelerates oxidative enzymatic reactions and that the NMR methods used were a trustworthy approach to monitor and understand the darkening in bean seeds at metabolite level.

Glyphosate at low doses changes the physiology and increases the productivity of common bean as affected by sowing seasons.

Glyphosate applied at low doses can stimulate photosynthesis and yield. The objective of this study was to evaluate the application of low doses of glyphosate and sowing seasons in physiological characteristics and grain yield of common bean of early cycle. Two experiments were conducted in the field, the first in winter season and the second in wet season. The experimental design was a randomized complete block design, consisting of five and seven low doses of glyphosate and one period of application, with four replications. Glyphosate low dose of 108.0 g a.e. ha-1 impaired net CO2 assimilation rate, stomatal conductance, transpiration rate, instantaneous carboxylation efficiency, number of pods per plant, number of grains per plant and number of grains per pod. Glyphosate dose of 7.2 g a.e. ha-1 provided a 23% increase in grain yield in winter season, and the dose of 36.0 g a.e. ha-1 provided a 109% increase in grain yield in wet season. To our knowledge, this is the first report on effect of glyphosate at low doses and sowing season to obtain yield increases in common bean of early cycle.

GWAS of pod morphological and color characters in common bean.

BACKGROUND: Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS. RESULTS: Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color. CONCLUSIONS: GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.

Genome-wide association mapping reveals new loci associated with light-colored seed coat at harvest and slow darkening in carioca beans.

BACKGROUND: Common bean (Phaseolus vulgaris L.) is a legume whose grain can be stored for months, a common practice among Brazilian growers. Over time, seed coats become darker and harder to cook, traits that are undesirable to consumers, who associate darker-colored beans with greater age. Like commercial pinto and cranberry bean varieties, carioca beans that have darker seeds at harvest time and after storage are subject to decreased market values. RESULTS: The goal of our study was to identify the genetic control associated with lightness of seed coat color at harvest (HL) and with tolerance to post-harvest seed coat darkening (PHD) by a genome-wide association study. For that purpose, a carioca diversity panel previously validated for association mapping studies was used with 138 genotypes and 1,516 high-quality SNPs. The panel was evaluated in two environments using a colorimeter and the CIELAB scale. Shelf storage for 30 days had the most expressive results and the L* (luminosity) parameter led to the greatest discrimination of genotypes. Three QTL were identified for HL, two on chromosome Pv04 and one on Pv10. Regarding PHD, results showed that genetic control differs for L* after 30 days and for the ΔL* (final L*-initial L*); only ΔL* was able to properly express the PHD trait. Four phenotypic classes were proposed, and five QTL were identified through six significant SNPs. CONCLUSIONS: Lightness of seed coat color at harvest showed an oligogenic inheritance corroborated by moderate broad-sense heritability and high genotypic correlation among the experiments. Only three QTL were significant for this trait - two were mapped on Pv04 and one on Pv10. Considering the ΔL, six QTL were mapped on four different chromosomes for PHD. The same HL QTL at the beginning of Pv10 was also associated with ΔL* and could be used as a tool in marker-assisted selection. Several candidate genes were identified and may be useful to accelerate the genetic breeding process.

Regulation of flowering under short photoperiods based on transcriptomic and metabolomic analysis in Phaseolus vulgaris L.

Common bean (Phaseolus vulgaris L.) is a short-day plant and its flowering time, and consequently, pod yield and quality is influenced by photoperiod. In this study, the photoperiodic-sensitive variety 'Hong jin gou', which flowers 31 days (d) earlier in short-day than in long-day, was used as the experimental material. Samples were collected to determine the growth and photosynthetic parameters in each daylength treatment, and transcriptome and metabolome data were conducted. We identified eight genes related to flowering by further screening for differentially expressed genes. These genes function to regulate the biological clock. The combination of differentially expressed genes and metabolites, together with the known regulation network of flowering time and the day-night expression pattern of related genes allow us to speculate on the regulation of flowering time in the common bean and conclude that TIMING OF CAB EXPRESSION1 (TOC1) plays a pivotal role in the network and its upregulation or downregulation causes corresponding changes in the expression of downstream genes. The regulatory network is also influenced by gibberellic acid (GA) and jasmonic acid (JA). These regulatory pathways jointly comprise the flowering regulatory network in common bean.