Physiological analysis of common bean (Phaseolus vulgaris L.) cultivars uncovers characteristics related to terminal drought resistance

Phenotypic and yield responses of common bean (Phaseolus vulgaris l.) varieties to different soil moisture levels

BACKGROUND

Morphological plasticity is one of the capacities of plants to modify their morphological appearance in response to external stimuli. A plant's morphology and physiology are constantly tuned to its variable surroundings by complex interactions between environmental stimuli and internal signals. In most of plant species,, such phenotypic and physiological expression varies among different varieties based on their levels of particular environmental stress conditions. However, the morphological and yield responses of common bean varieties to different environmental conditions are not well known. The purpose of the study was to evaluate morphological and yield response of common bean to soil moisture stress and to investigate the morphological mechanism by which common bean varieties tolerate fluctuations in moisture stress.

METHODS

A pot experiment was carried out to investigate the effects of different moisture levels on the phenotypic and yield responses of common bean varieties. A factorial combination of five common bean varieties (Hirna, kufanzik, Awash-1, Ado, and Chercher) and three moisture levels (control, waterlogging stress, and moisture deficit stress) was used in three replications. Moisture stress treatments were started 20 days after planting, at the trifoliate growth stage. To evaluate the response of each variety, morphological and yield data were collected at week intervals.

MAIN RESULTS

The results indicated that moisture levels and varieties had a significant influence on all growth parameters. Crop phenology was significantly influenced by the interaction effect of moisture level and variety. Exposing Hirna variety to moisture stress led to extended flowering and pod setting by 23 and 24 days, respectively, compared to the other treatments. The results showed that the phenotypic responses to moisture deficit and waterlogging stress varied between varieties. Waterlogging stress had a stronger reduction effect on the fresh weight, dry weight and leaf area of common bean varieties than moisture deficit and the control. Pods per plant, seeds per plant, grain yield per plant, and harvest index were significantly influenced by the varieties, moisture stress levels and their interaction. Except for Chercher and Hirna. However, varieties Ado, kufanzik and Awasha-1 did not show significant differences on the time of flower initiation due to moisture level. Biomass and growth in leaf fresh weight, leaf dry weight, leaf area, leaf number and plant height were significantly influenced by moisture level. When moisture deficit and waterlogging stress occurred, Ado and Awash-1 were more responsive to moisture stress than Hirna, Chercher, and Kufanzik.

CONCLUSION

Hence, Hirna and Kufanzik varieties were found to be tolerant because they produced higher yields than the Chercher, Awash-1, and Ado varieties.

Dissecting the genetic basis of drought responses in common bean using natural variation

The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional "stay-green" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes.

Metabolome profile variations in common bean (Phaseolus vulgaris L.) resistant and susceptible genotypes incited by rust (Uromyces appendiculatus)

The causal agent of rust, Uromyces appendiculatus is a major constraint for common bean (Phaseolus vulgaris) production. This pathogen causes substantial yield losses in many common bean production areas worldwide. U. appendiculatus is widely distributed and although there have been numerous breakthroughs in breeding for resistance, its ability to mutate and evolve still poses a major threat to common bean production. An understanding of plant phytochemical properties can aid in accelerating breeding for rust resistance. In this study, metabolome profiles of two common bean genotypes Teebus-RR-1 (resistant) and Golden Gate Wax (susceptible) were investigated for their response to U. appendiculatus races (1 and 3) at 14- and 21-days post-infection (dpi) using liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-qTOF-MS). Non-targeted data analysis revealed 71 known metabolites that were putatively annotated, and a total of 33 were statistically significant. Key metabolites including flavonoids, terpenoids, alkaloids and lipids were found to be incited by rust infections in both genotypes. Resistant genotype as compared to the susceptible genotype differentially enriched metabolites including aconifine, D-sucrose, galangin, rutarin and others as a defence mechanism against the rust pathogen. The results suggest that timely response to pathogen attack by signalling the production of specific metabolites can be used as a strategy to understand plant defence. This is the first study to illustrate the utilization of metabolomics to understand the interaction of common bean with rust.

Meta-QTL Analysis for Yield Components in Common Bean (Phaseolus vulgaris L.)

Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.

N 6-Methyladenosine and physiological response divergence confer autotetraploid enhanced salt tolerance compared to its diploid Hordeum bulbosum

Polyploid species have played an essential role in plant evolution, exemplified by adaptive advantages to abiotic stress. N 6-Methyladenosine (m6A) is suggested to play an important role in stress response. However, whether genome doubling affects m6A to increase autopolyploids stress tolerance is still unclear. This study aims to compare physiological (maintaining osmoregulatory homeostasis) and m6A changes between autotetraploid and diploid wild barley (Hordeum bulbosum) in response to salt (NaCl) stress. Results showed that autotetraploids physiologically had enhanced stress tolerance based on the measured parameters of relative water content, water loss, proline, H2O2, and chlorophyll. Diploid H. bulbosum experienced an excessive abundance of proline following salt stress where tetraploids had beneficial proline accumulation and thus enhanced osmoregulation. The significantly higher level of proline and H2O2 in diploid than in autotetraploid implies that diploids suffered higher osmotic stress than autotetraploid. Autotetraploid produced enough proline to protect stress, but not so much to cause toxicity. m6A in total RNA showed no significant difference between ploidies in controls, but was significantly higher in autotetraploids than in diploids during stress and recovery. These results suggest that increased m6A might be one of molecular mechanisms that increases salt tolerance in autotetraploid H. bulbosum compared to diploids, which enhances the adaptation of autopolyploids.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01260-x.

Response characteristics of highland barley (Hordeum vulgare) seedlings to the stress of salinity and artemisinin under freeze–thaw environment

In Qinghai-Tibet Plateau, crops are commonly subjected to freeze-thaw and salt stress factors simultaneously, and allelopathy is common, which affects the growth of highland barley (Hordeum vulgare L.), the largest food crop in Tibet. In order to explore the effects of artemisinin, salt and freeze-thaw (FAS) stress on physiological characteristics of highland barley seedlings, hydroponic experiment was carried out with the addition of 20mg/L artemisinin and 150mMNaCl as well as the simulation of freeze-thaw environment. The results suggested that under combined stress, the soluble protein content in combined stresses of artemisinin, FAS increased by 97.8%, the variation of relative conductivity in FAS group was lower than that in combined salt and freeze-thaw stress (FS), the relative water content decreased significantly (P <0.05), the malondialdehyde (MDA), H2 O2 and soluble sugar content in FAS group accumulated but less than those in FS group, and the superoxide dismutase (SOD) activity in combined artemisinin and freeze-thaw stress (FA) and FAS groups decreased. In addition, after freeze-thaw treatment, photosynthesis was weakened, and internal CO2 conentration (C i ) in FAS group significantly decreased (P <0.05). This study proved that appropriate amount of artemisinin can alleviate the damage of salt and freeze-thaw stress on barley seedlings.

The Evaluation of Common Bean (Phaseolus vulgaris L.) Genotypes under Water Stress Based on Physiological and Agronomic Parameters

Drought affects common bean productivity, and the severity of its impact is expected to increase due to climate change. The use of versatile genotypes could contribute to securing future bean production. This study investigates the adaptability of 10 common bean genotypes of indeterminate growth type under water scarcity conditions by measuring agronomic and physiological parameters. The evaluation occurs under irrigation treatments applied at two different phenological stages (anthesis (WDA) and seed filling initiation (WDSF)). The recorded adaptabilities of the genotypes (G) showed that G10 produced the highest overall seed yield in the normal irrigation (NI) (197.22 g plant−1) and WDA (192.78 g plant−1), while the G6 had the highest yield at WDSF (196.71 g plant−1). For the genotype’s average mean, chlorophyll content decreased by 10.5% under drought at WDSF. Net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (E) were reduced at WDA by 53%, 80.8%, and 61.4% and at WDSF by 43.75%, 57.7%, and 36%, respectively, while relative water content (RWC) reduced by 16.48%, on average, for both stages. G10 and G6 showed adaptability when water scarcity occurred at an early (WDA) or later stage (WDSF), respectively, providing insights into using germplasm resources to cope with the drought effect.

Contrasting Phaseolus Crop Water Use Patterns and Stomatal Dynamics in Response to Terminal Drought

Terminal drought stress affects more than half of the areas planted with common bean (Phaseolus vulgaris), the main food legume globally, generating severe yield losses. Phenotyping water deficit responses and water use are central strategies to develop improved terminal drought resilience. The exploration and exploitation of genetic diversity in breeding programs are gaining importance, with a particular interest in related species with great adaptation to biotic and abiotic factors. This is the case with tepary beans (Phaseolus acutifolius), a bean that evolved and was domesticated in arid conditions and is considered well adapted to drought and heat stress. Under greenhouse conditions, using one genotype of tepary beans (resistant to drought) and two of common beans (one resistant and one susceptible to terminal drought), we evaluated phenotypic differences in traits such as water use efficiency (WUE), transpiration efficiency, rate of photosynthesis, photosynthetic efficiency, stomatal density, stomatal index, stomatal size, and the threshold for transpiration decline under well-watered and terminal drought conditions. Our results indicate two different water use strategies in drought-resistant genotypes: one observed in common bean aimed at conserving soil water by closing stomata early, inhibiting stomatal development, and limiting growth; and the other observed in tepary bean, where prolonged stomatal opening and higher carbon fixation, combined with no changes in stomata distribution, lead to higher biomass accumulation. Strategies that contribute to drought adaptation combined with other traits, such as greater mobilization of photoassimilates to the formation of reproductive structures, confer bean drought resistance and are useful targets in breeding programs.

Water Shortage Affects Vegetative and Reproductive Stages of Common Bean (Phaseolus vulgaris) Chilean Landraces, Differentially Impacting Grain Yield Components

Water availability for agricultural use is currently a global problem that worsens with climate change in several regions of the world. Among grain legumes, common bean (Phaseolus vulgaris) is the most cultivated in the worldwide. The Chilean germplasm of common bean is characterized by tolerance to water stress. Here, we analyzed a selection of nine ancient Chilean landraces in regard to their drought tolerance, simulating optimal (OW) and restricted watering (RW) in a Mediterranean environment. Phenological, growth, and yield traits were recorded, and correlation analysis was performed. Accordingly, leaf temperature and osmotic potential were higher under RW, while the leaf chlorophyll content decreased in all landraces. Physiological maturity days and seed-filling days were lower in RW than in OW. This similarly occurred with the grain yield. The % yield reduction was negatively correlated with the % pod reduction and the relative rate of leaf expansion (RLAE) reduction. However, the 100-seed weight value was not significantly modified by water treatment (p > 0.05). For instance, landraces that preferred to fill the grain with a lower rate of leaf expansion showed a lower loss in grain yield under drought conditions. These results suggest that the resource partitioning between growing leaves, flowers, and developing pods in Chilean landraces is variable, affecting the common bean drought tolerance.

Effect of Drought on Bean Yield Is Mediated by Intraspecific Variation in Crop Mixtures

Increasing plant diversity in agricultural systems provides promising solutions for sustainably increasing crop yield. It remains unclear; however, how plant-plant interactions in diverse systems are mediated by plant genetic variation. We conducted a greenhouse experiment in which we grew three varieties of common beans with three companion plant species (chickpeas, sorghum, and sunflower) in different combinations (crop mixtures, bean cultivar mixtures, and monocultures), with and without drought stress. We hypothesized that under drought stress, the effect of companion plant species on bean yield would be mediated by the drought tolerance potential of the species. We further hypothesized that this effect would vary across different bean cultivars. Overall, we show that the effect of companion plant species on bean yield was not influenced by drought stress; instead, it was dependent on the identity of the bean variety. This could partially be explained by variation in growth rate between bean varieties, where the fastest growing variety recorded the highest yield increase in plant mixtures. The effect of companion plant species on chickpea biomass, however, was potentially influenced by chickpea drought tolerance potential; chickpea biomass was recorded to be higher in plant mixtures than in its monoculture under drought conditions. Our study highlights that to develop plant mixtures, it is not only important to consider the functional traits of the interacting plant species, but also those of the different plant varieties. We further suggest that stress tolerance can be a useful trait for initial selection of plant varieties when developing crop mixtures.

Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia

Common bean (Phaseolus vulgaris L.) is sensitive to different types of abiotic stresses (drought, high temperature, low soil fertility, and acid soil), and this may limit its adaptation and consequently to its yield under stress. Because of this, a sister species, tepary bean (Phaseolus acutifolius A. Gray), has recently gained attention in breeding for improved abiotic stress tolerance in common bean. In this study, we evaluated the adaptation of 302 accessions of tepary bean (Phaseolus acutifolius A. Gray) and its wild relatives (grouped in four types of tepary bean genetic resource: cultivated, acutifolius regressive, acutifolius wild, tenuifolius wild) when grown under high temperature and acid soil conditions with aluminum toxicity in the Amazon region of Colombia. Our objective was to determine differences among four types of tepary bean genetic resource in their morpho-phenological, agronomic, and physiological responses to combined high temperature and acid soil stress conditions. We found that cultivated P. acutifolius var acutifolius presented a greater number of pods per plant, as well as larger seeds and a greater number of seeds per pod. Some traits, such as root biomass, days to flowering and physiological maturity, specific leaf area, and stomatal density, showed significant differences between types of tepary bean genetic resource, probably contributing to difference in adaptation to combined stress conditions of high temperature and acid soil conditions. The photochemical quenching (qP) was higher in cultivated P. acutifolius var. acutifolius, while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in acutifolius regressive and tenuifolius wild accessions. We have identified 6 accessions of cultivated and 19 accessions of tenuifolius wild that exhibited grain yields above 1800 kg ha⁻¹. These accessions could be suitable to use as parents to improve dry seed production of tepary bean under combined stress conditions of high temperature and acid soil.

Productivity versus drought adaptation in olive leaves: Comparison of water relations in a modern versus a traditional cultivar

The physiological traits that set the tradeoff between productivity and drought adaptation in plants are still under debate. To reveal these traits, we compared the water relations of two olive (Olea europaea) cultivars: "Barnea"-a highly productive modern cultivar; and "Souri"-a drought-adapted traditional cultivar. We hypothesized that Souri has lower hydraulic conductivity and lower hydraulic vulnerability. The hypothesis was tested at the leaf level. The soil volumetric water content (θ), stem water potential (Ψ_S ), and gas exchange were measured in both cultivars while they dried until a significant reduction in their maximal photochemical potential (F_v /F_m  < 0.6) was obtained. Additionally, pressure-volume relations, leaf hydraulic vulnerability, and the petiole xylem architecture were evaluated. To our surprise, Souri's leaf hydraulic conductivity was more vulnerable to low Ψ_S , approaching zero at -8 MPa compared with <-10 MPa in "Barnea." At the same time, Souri's higher osmotic content and cell rigidity enabled it to sustain 1.4 MPa lower Ψ_S , while maintaining near optimal (F_v /F_m ). However, both cultivars significantly reduced their F_v /F_m (<0.6) at the same θ, suggesting that the capability to sustain a low θ is not the issue. Instead, Souri's lower transpiration enabled it to withstand a longer drought while avoiding low θ. Barnea's larger xylem vessels and hydraulic conductivity supported higher stomatal conductance (g_s ) and assimilation rate, which nurtured its higher productivity but resulted in quick depletion of θ. These results suggest that hydraulic resistance or the ability to sustain low θ do not set the tradeoff between productivity and drought adaptation in olive leaves.

Target-Based Physiological Modulations and Chloroplast Proteome Reveals a Drought Resilient Rootstock in Okra (Abelmoschus esculentus) Genotypes

As climate changes increase, drought stress is becoming a problem for all major horticultural crops; among them is okra (Abelmoschus esculentus). Despite its superior resilience to heat stress and high nutritional content, it is still underutilized in contrast to other vegetable crops. Moreover, the drought-resistant and drought-sensitive genotypes of okra are also not well known and require further exploration to improve their productivity. To investigate this in more detail, we performed comparative physiological and large-scale chloroplast proteomics on drought-stressed genotypes of okra. We evaluated four major genotypes of okra, viz., NS7774, NS7772, Green Gold, and OH3312 for drought resilient rootstock. The physiological modulations demonstrated a significant change by 50-76% in biomass, net-photosynthetic machinery, water transport, and absorption both in early and late stages of drought stress compared to well-watered crops in all genotypes. Maximum oxidative damage due to drought stress was observed for the genotypes NS7772, Green Gold and OH3312 as depicted by H2O2 and O2- determination. Greater oxidative stress was correlated to lesser antioxidant activity and expression of antioxidant enzymes, such as catalase and ascorbate peroxidase under stress in okra genotypes. The overall photosynthetic pigments, such as total chlorophyll, and total carotenoid content, were also decreased, and stomatal guard cells were disrupted and appeared closed compared to the control for the above three mentioned genotypes, except NS7774. A subsequent tissue-specific proteome analysis of chloroplasts and thylakoids analyzed by BN-PAGE (blue native polyacrylamide gel electrophoresis) revealed either over or under expression of specific proteins, such as ATPase, PSI, PSII core dimer, PSII monomer and ATP synthase. The expression of multiprotein complex proteins, including PSII-core dimer and PSII-core monomer, was slightly higher for the genotype NS7774 when compared to three other genotypes for both 5 and 10 days of drought stress. Further identification of specific proteins obtained in second dimension BN-PAGE provided descriptive detail of seven proteins involved in drought resistance across all genotypes. The identified proteins are majorly involved in photosynthesis under drought stress, suggesting NS7774 as a drought tolerant genotype. Further, the proteomic results were confirmed using Immunoblot by selecting specific protein such as PsaA. Overall, from our physiological modulations and chloroplast proteomics in all genotypes, we summarized NS7774 as a resilient rootstock and the other three genotypes (NS7772, OH3312, and Green Gold) as sensitive ones.

Adaptation of Interspecific Mesoamerican Common Bean Lines to Acid Soils and High Temperature in the Amazon Region of Colombia

Knowledge of the physiological basis for improved genetic adaptation of common bean (Phaseolus vulgaris L.) lines to acid soils and high temperature conditions in the Amazon region of Colombia is limited. In this study, we evaluated the differences among 41 common bean lines in energy use, leaf cooling, photosynthate partitioning to pod formation and grain filling, and grain yield over two seasons under acid soil and high temperature stress in the Amazon region of Colombia. Common bean lines evaluated included medium and large seeded interspecific lines of Mesoamerican and Andean gene pools with different levels of adaptation to abiotic stress conditions and some lines are improved for iron and zinc (biofortified) concentration in seeds. We found three bean lines (GGR 147, SMG 21 and SMG 12) that were superior in their photosynthetic response, leaf cooling, photosynthate partitioning ability to pod formation and grain filling, resulting in grain yields exceeding 1900 kg ha-1 under acid soil and high temperature stress conditions. The superior photosynthetic performance was attributed to the efficient use of absorbed energy on the electron level in thylakoids, which is mainly oriented to a higher quantum yield of PSII (ΦII), lower energy dissipation in the form of heat (ΦNPQ), high linear electron flow (LEF) and high fraction of PSI centers in open state (PSIopen). We speculate that these photosynthetic and photosynthate partitioning responses of superior bean lines are part of the genetic adaptation to acidic soils and high temperature stress conditions. Among the evaluated bean lines, three lines (GGR 147, SMG 21 and SMG 12) combined the desirable attributes for genetic improvement of stress tolerance and biofortification. These lines can serve as parents to further improve traits (energy use efficiency and multiple stress resistance) that are important for bean production in the Amazon region.

Determining relevant traits for selecting landrace accessions of Phaseolus lunatus L. for insect resistance

Plant-insect interactions are a determining factor for sustainable crop production. Although plants can resist or tolerate herbivorous insects to varying degrees, even with the use of pesticides, insects can reduce plant net productivity by as much as 20%, so sustainable strategies for pest control with less dependence on chemicals are needed. Selecting plants with optimal resistance and photosynthetic traits can help minimize damage and maintain productivity. Here, 27 landrace accessions of lima beans, Phaseolus lunatus L., from the Yucatan Peninsula were evaluated in the field for morphological resistance traits, photosynthetic characteristics, insect damage and seed yield. Variation was found in physical leaf traits (number, area, and dry mass of leaves; trichome density, specific leaf thickness and hardness) and in physiological traits (photosynthetic rate, stomatal conductance, intercellular carbon, water-use efficiency, and transpiration). Five accessions (JMC1325, JMC1288, JMC1339, JMC1208 and JMC1264) had the lowest index for cumulative damage with the highest seed yield, although RDA analysis uncovered two accessions (JMC1339, JMC1288) with strong positive association of seed yield and the cumulative damage index with leaf production, specific leaf area (SLA) and total leaf area. Leaf traits, including SLA and total leaf area are important drivers for optimizing seed yield. This study identified 12 important morphological and physiological leaf traits for selecting landrace accessions of P. lunatus for high yields (regardless of damage level) to achieve sustainable, environmentally safe crop production.

Correlation between leaf epicuticular wax composition and structure, physio-biochemical traits and drought resistance in glaucous and non-glaucous near-isogenic lines of rye

The objective of this research was to investigate the differences between glaucous and non-glaucous near-isogenic lines (NILs) of winter rye (Secale cereale L.) in terms of epicuticular wax layer properties (weight, composition, and crystal morphology), selected physiological and biochemical responses, yield components, above-ground biomass, and plant height under soil drought stress. An important aspect of this analysis was to examine the correlation between the above characteristics. Two different NIL pairs were tested, each consisting of a typical glaucous line and a non-glaucous line with a recessive mutation. The drought experiment was conducted twice (2015-2016). Our study showed that wax accumulation during drought was not correlated with higher leaf hydration and glaucousness. Environmental factors had a large impact on the response of the lines to drought in individual years, both in terms of physiological and biochemical reactions, and the composition of epicuticular leaf wax. The analysed pairs displayed significantly different responses to drought. Demonstration of the correlation between the components of rye leaf wax and the physiological and biochemical parameters of rye NILs is a significant achievement of this work. Interestingly, the study showed a correlation between the wax components and the content of photosynthetic pigments and tocopherols, whose biosynthesis, similarly to the biosynthesis of wax precursors, is mainly located in chloroplasts. This suggests a relationship between wax biosynthesis and plant response to various environmental conditions and drought stress.

Chloride nutrition improves drought resistance by enhancing water deficit avoidance and tolerance mechanisms

Chloride (Cl-), traditionally considered harmful for agriculture, has recently been defined as a beneficial macronutrient with specific roles that result in more efficient use of water (WUE), nitrogen (NUE), and CO2 in well-watered plants. When supplied in a beneficial range of 1-5 mM, Cl- increases leaf cell size, improves leaf osmoregulation, and reduces water consumption without impairing photosynthetic efficiency, resulting in overall higher WUE. Thus, adequate management of Cl- nutrition arises as a potential strategy to increase the ability of plants to withstand water deficit. To study the relationship between Cl- nutrition and drought resistance, tobacco plants treated with 0.5-5 mM Cl- salts were subjected to sustained water deficit (WD; 60% field capacity) and water deprivation/rehydration treatments, in comparison with plants treated with equivalent concentrations of nitrate, sulfate, and phosphate salts. The results showed that Cl- application reduced stress symptoms and improved plant growth during water deficit. Drought resistance promoted by Cl- nutrition resulted from the simultaneous occurrence of water deficit avoidance and tolerance mechanisms, which improved leaf turgor, water balance, photosynthesis performance, and WUE. Thus, it is proposed that beneficial Cl- levels increase the ability of crops to withstand drought, promoting a more sustainable and resilient agriculture.

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.

Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar

BACKGROUND

Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes.

RESULTS

As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified.

CONCLUSIONS

Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r ² _sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r ² from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.

Sensitivity of leaflet growth rate to drought predicts yield in common bean (Phaseolus vulgaris)

Although drought limits yield by decreasing photosynthesis and therefore biomass accumulation, biomass is not the strongest predictor of yield under drought in common beans (Phaseolus vulgaris L.). Instead, resource partitioning from pod walls into seeds is a stronger correlate. Our aim was to determine whether growth rates of developing leaflets and pods, as independent indicators of sink strength, predict resource partitioning into seeds. Using 20 field-grown genotypes, we paired biomass, yield, and resource partitioning data with leaflet and pod growth rates under well-watered and droughted conditions. We hypothesised that genotypes with faster growing leaflets and pods under drought would fill seeds better. However, we found that leaflet and pod growth rates did not predict partitioning to seeds; rather, sensitivity of leaflet growth rate to drought was a good predictor of yield reduction. Further, plants with rapidly growing leaves under well-watered conditions were most vulnerable to decreases in leaflet growth rate under drought. This suggests that lines that inherited a conservative growth strategy were better able to maintain yield by allocating resources to seeds. Our findings indicate that inherent sensitivity of leaflet growth rate to drought may be used as a predictor of partitioning and yield in common beans.

Effect of Water Deficit on Morphoagronomic and Physiological Traits of Common Bean Genotypes with Contrasting Drought Tolerance

Water deficit is considered one of the most limiting factors of the common bean. Understanding the adaptation mechanisms of the crop to this stress is fundamental for the development of drought-tolerant cultivars. In this sense, the objective of this study was to analyze the influence of water deficit on physiological and morphoagronomic traits of common bean genotypes with contrasting drought tolerance, aiming to identify mechanisms associated with tolerance to water deficit. The experiment was carried out in a greenhouse, arranged in a randomized complete block 4 × 2 factorial design, consisting of four common bean genotypes under two water regimes (with and without water stress), with six replications. The morphoagronomic and physiological traits of four cultivars, two drought-tolerant (IAPAR 81 and BAT 477) and two drought-sensitive (IAC Tybatã and BRS Pontal), were measured for 0, 4, 8, and 12 days, under water deficit, initiated in the phenological stage R5. Water-deficit induced physiological changes in the plants, altering the evaluated morphoagronomic traits. The drought tolerance of cultivar BAT 477 is not only a direct result of the low influence of water deficit on its yield components, but also a consequence of the participation of multiple adaptive physiological mechanisms, such as higher intrinsic water use efficiency, net photosynthesis rate, transpiration, carboxylation efficiency, stomatal conductance, and intracellular concentration of CO2 under water deficit conditions. On the other hand, cultivar IAPAR 81 can be considered drought-tolerant for short water-deficit periods only, since after the eighth day of water deficit, the physiological activities decline drastically.

Genetic Parameters and QTLs for Total Phenolic Content and Yield of Wheat Mapping Population of CSDH Lines under Drought Stress

A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse. Genetic parameters, such as additive and epistatic effects, affecting total phenolic content, were estimated for eight year-by-drought combinations. Twenty-one markers showed a significant additive effect on total phenolic content in all eight year-by-drought combinations. These markers were located on chromosomes: 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, and 4D. A region on 4AL with a stable QTL controlling the phenolic content, confirmed by various statistical methods is particularly noteworthy. In all years and treatments, three markers significantly linked to QTLs have been identified for both phenols and yield. Thirteen markers were coincident with candidate genes. Our results indicated the importance of both additive and epistatic gene effects on total phenolic content in eight year-by-drought combinations.

Association of Shoot and Root Responses to Water Deficit in Young Faba Bean (Vicia faba L.) Plants

Water deficit may occur at any stage of plant growth, with any intensity and duration. Phenotypic acclimation and the mechanism of adaptation vary with the evolutionary background of germplasm accessions and their stage of growth. Faba bean is considered sensitive to various kinds of drought. Hence, we conducted a greenhouse experiment in rhizotrons under contrasting watering regimes to explore shoot and root traits and drought avoidance mechanisms in young faba bean plants. Eight accessions were investigated for shoot and root morphological and physiological responses in two watering conditions with four replications. Pre-germinated seedlings were transplanted into rhizotron boxes filled with either air-dried or moist peat. The water-limited plants received 50-ml water at transplanting and another 50-ml water 4 days later, then no water was given until the end of the experimental period, 24 days after transplanting. The well-watered plants received 100 ml of water every 12 h throughout the experimental period. Root, stem, and leaf dry mass, their mass fractions, their dry matter contents, apparent specific root length and density, stomatal conductance, SPAD value, and Fv/Fm were recorded. Water deficit resulted in 3-4-fold reductions in shoot biomass, root biomass, and stomatal conductance along with 1.2-1.4-fold increases in leaf and stem dry matter content and SPAD values. Total dry mass and apparent root length density showed accession by treatment interactions. Accessions DS70622, DS11320, and ILB938/2 shared relatively high values of total dry mass and low values of stomatal conductance under water deficit but differed in root distribution parameters. In both treatments, DS70622 was characterized by finer roots that were distributed in both depth and width, whereas DS11320 and ILB938/2 produced less densely growing, thicker roots. French accession Mélodie/2 was susceptible to drought in the vegetative phase, in contrast to previous results from the flowering phase, showing the importance of timing of drought stress on the measured response. Syrian accession DS70622 explored the maximum root volume and maintained its dry matter production, with the difference from the other accessions being particularly large in the water-limited treatment, so it is a valuable source of traits for avoiding transient drought.

Using of Microbial Fertilizer as Biostimulant Alleviates Damage from Drought Stress in Guar (<i>Cyamopsis Tetragonoloba</i> (L.) Taub.) Seedlings

Drought is a significant environmental stress that limits plant growth and yield. In this study, an investigation of guar, grown under different drought level conditions [(S0: 100% of field capacity), S1 (depletion of 75% the available water holding capacity), S2 (depletion of 50% the available water holding capacity), S3 (depletion of 25% the available water holding capacity), S4 (no applied irrigation water)] with regards to the impact of Chlorella vulgaris based microbial fertilizer on physiological, morphological, and enzymatic activity was performed. Microbial fertilizer applications significantly increased shoot length, fresh and dry weight of the shoot and root, and leaf number and area of guar plants compared to the only drought stress treatments. In addition, following the above-mentioned procedures, there were significant increases in the relative water content, total phenolic and flavonoid contents, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutation reductase (GR) activity. However, the malondialdehyde (MDA) content were significantly decreased. Hence, the results support the administration of a foliar application to the microbial fertilizer containing microalgae in order to increase the guar plant’s defense system, enabling it to tolerate the negative effects resulting from drought stress.

Improved protocol for isolation of high-quality total RNA from different organs of Phaseolus vulgaris L

A modified protocol was developed to obtain high-quality total RNA from various mature organs, including leaves, seeds, pods and testae, from different cultivars of Phaseolus vulgaris L. grown under optimal conditions or subjected to severe drought; stress conditions leading to the accumulation of numerous secondary metabolites can affect RNA quality. This modified procedure is based on CTAB extraction protocols. Modifications in this protocol prevent oxidation of phenolic complexes, the precipitation of proteins, DNA and degradation of RNA; also, it is effective at removing secondary metabolites. The RNA obtained following this procedure showed high quality as revealed by a high RNA integrity number and high 260/280 nm (>2) ratio, the requirements needed to increase reliability of diverse molecular analyses.

Relationship between fluorescence yield and photochemical yield under water stress and intermediate light conditions

The dynamics between fluorescence (Fs) yield and photochemical (P) yield in a changing environment are essential for understanding the relationship between photosynthesis and fluorescence. The ratio of Fs yield and P yield tends to be constant under high light intensity, but the relationship between these two yields, and its response to environmental conditions, need to be explored further under intermediate and low light. In this study, we performed leaf-scale measurements of fluorescence parameters by pulse-amplitude modulation (PAM) technology in summer maize (Zea mays L.) plants grown under intermediate light conditions in a climate chamber. Plants were treated as moderately water stressed and non-water stressed. Results showed that a decrease in P yield was accompanied by increases in Fs yield and non-photochemical quenching (NPQ) yield in response to moderate water stress under intermediate and low light conditions. Fs yield was negatively correlated with P yield under intermediate and low light conditions when there was sufficient soil water in the root zone. Under water stress, the correlation between Fs yield and P yield was negative in low light, but became positive under higher light levels. Fs yield was negatively related to P yield when NPQ yield was low; however, they were synergistically and positively associated when excessive light dissipation was dominated by NPQ.

Physiological characterization of common bean (Phaseolus vulgaris L.) under abiotic stresses for breeding purposes

In the Brazilian wet and dry seasons, common beans (Phaseolus vulgaris L.) are grown under rainfed conditions with unexpected episodes of drought and high temperatures. The objective of this study was to evaluate the physiological mechanisms associated with drought adaptation traits in landraces and line/cultivars of beans from the Andean and Mesoamerican gene pools. Twenty-five genotypes, contrasting in terms of drought tolerance, were evaluated in a phenotyping platform under irrigated and rainfed conditions. Agronomic and physiological parameters such as grain yield, shoot structures, gas exchange, water potential, and osmotic adjustment were evaluated. The stress intensity was estimated to be 0.57, and the grain yield reduction ranged from 22 to 89%. Seven accessions, representative of the Andean and Mesoamerican germplasm (CF 200012, CF 240056, CF 250002, CF 900004, CNF 4497, CNF 7382, and SEA 5), presented superior performance in grain yield with and without stresses. The physiological responses under abiotic stresses were highly variable among the genotypes, and two Mesoamerican accessions (CF 200012 and SEA 5) showed more favorable adaptive responses. As the main secondary physiological traits, gas exchange and osmotic adjustment should be evaluated together with the grain yield to increase the selection efficiency of abiotic stresses-tolerant common bean lines.

Physiological, biochemical and morphoagronomic characterization of drought-tolerant and drought-sensitive bean genotypes under water stress

Water deficit is one of the main factors that reduce grain yield. A better understanding of the mechanisms related to this abiotic stress is a key aspect to design and act upon drought tolerance improvement in crop plants. Therefore, the major objective of this study was to investigate four common bean genotypes for drought tolerance and to establish their tolerance mechanisms. The experiment was carried out in a greenhouse, using the completely randomized design in a factorial arrangement (2 × 4), composed by 2 water conditions (well-watered and water deficit) and 4 cultivars, with six replicates per treatment. The four cultivars, two drought-sensitive (IAC Tybatã and BRS Pontal) and two drought-tolerant (IAPAR 81 and BAT 477), were evaluated for some physiological, biochemical and morphoagronomic traits. Drought promoted physiological and metabolic changes in the plants, reflecting on the morphoagronomic traits. Under water deficit, the genotype IAPAR 81 stood out from the others in terms of physiological characters, however, it presented a low efficiency concerning biochemical activities and a significant reduction in the morphoagronomic characters. The cultivar BAT 477 demonstrated to be drought-adapted presenting more efficient biochemical and morphoagronomic adaptions and the genotype BRS Pontal obtained morphoagronomic values similar to BAT 477, thus it may be classified as moderately tolerant to drought.

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean

Arbuscular mycorrhizal fungi (AMF) colonization in plants promotes both local and systemic changes in the gene expression profiles of the host that might be relevant for drought-stress perception and response. Drought-tolerant common bean plants (cv. BAT 477), colonized by a mixture of AMF (Glomus clarum, Acaulospora scrobiculata, and Gigaspora rosea), were exposed to a water deprivation regime of 96 h during pre-flowering. Root transcriptomes were accessed through RNA-Seq revealing a set of 9,965 transcripts with significant differential regulation in inoculated plants during a water deficit event, and 10,569 in non-inoculated. These data include 1,589 transcripts that are exclusively regulated by AMF-inoculation, and 2,313 under non-inoculation conditions. Relative gene expression analyses of nine aquaporin-related transcripts were performed in roots and leaves of plants harvested at initial stages of treatment. Significant shifts in gene expression were detected in AM water deficit-treated roots, in relation to non-inoculated, between 48 and 72 h. Leaves also showed significant mycorrhizal influence in gene expression, especially after 96 h. Root cortical cells, harboring or not arbuscules, were collected from both inoculation treatments through a laser microdissection-based technique. This allowed the identification of transcripts, such as the aquaporin PvPIP2;3 and Glucan 1,3 β-Glucosidase, that are unique to arbuscule-containing cells. During the water deficit treatment, AMF colonization exerted a fine-tune regulation in the expression of genes in the host. That seemed to initiate in arbuscule-containing cells and, as the stressful condition persisted, propagated to the whole-plant through secondary signaling events. Collectively, these results demonstrate that arbuscular mycorrhization leads to shifts in common bean's transcriptome that could potentially impact its adaptation capacity during water deficit events.

Dehydration survival of crop plants and its measurement

Dehydration survival under drought stress is defined in this review as the transition from plant activity into a quiescent state of life preservation, which will be terminated by either recovery or death, depending on the stress regime and the plant's resilience. Dehydration survival is a popular phenotype by which functional genomics attempts to test gene function in drought resistance and survival. The available reports on phenotyping and genotyping of dehydration survival in genomic studies indicate that the measurement of this trait is often biased to the extent that misguided interpretations are likely to occur. This review briefly discusses the physiological basis of dehydration survival in resurrection plants and crop plants, and concludes that in phenotyping dehydration survival there is a need to distinguish between dehydration avoidance and dehydration tolerance (also termed desiccation tolerance) in affecting survival and recovery. Without this distinction, functional genomics studies of the trait might be biased. Survival due to dehydration avoidance is expressed by the capacity to maintain a relatively high plant water status as the plant is desiccated. Survival due to dehydration tolerance is expressed by delayed mortality (mortality at a relatively low plant water status) as affected by the resilience of plant metabolism. The common test of dehydration survival, using the relative recovery after a given number of stress days, is therefore insufficient because it is mainly driven by dehydration avoidance and so ignores a possible role for dehydration tolerance. Conceivable methods for more accurate phenotyping of the two components of dehydration survival are proposed and discussed.

Comparative analysis of drought responses in Phaseolus vulgaris (common bean) and P. coccineus (runner bean) cultivars

Genetic improvement of crop drought tolerance has become an urgent need for increasing agricultural yields and food production, to feed a growing human population in the context of global climate change. To get insights into the most relevant mechanisms underlying drought resistance in beans, we have analysed the responses to water deficit of three Phaseolus vulgaris (common bean) and one P. coccineus (runner bean) cultivars, focusing on the accumulation of specific osmolytes, a conserved response to abiotic stress in plants. Changes in osmolyte levels were correlated with the relative tolerance to water stress of the studied cultivars. Drought tolerance in Phaseolus largely depends on the accumulation of myo-inositol; glycine betaine may also contribute to tolerance in P. coccineus (but not in P. vulgaris). Proline, another common osmolyte, is a reliable marker of the level of stress affecting bean plants, but is not directly involved in tolerance mechanisms, as its drought-dependent accumulation is lowest in the most tolerant cultivar. We suggest that, by measuring the levels of proline and myo-inositol in water-stressed plants, a large number of cultivars could be easily and rapidly screened to select promising candidates to be used in breeding programmes for improving drought tolerance in beans.

The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought

Recent studies have identified microRNAs as post-transcriptional regulators involved in stress responses. miR1514a is a legume microRNA that is induced in response to drought stress in Phaseolus vulgaris (common bean) and shows differential accumulation levels in roots during water deficit in two cultivars with different drought tolerance phenotypes. A recent degradome analysis revealed that miR1514a targets the transcripts of two NAC transcription factors (TFs), Phvul.010g121000 and Phvul.010g120700. Furthermore, expression studies and small RNA-seq data indicate that only Phvul.010g120700 generates phasiRNAs, which also accumulate under water deficit conditions. To confirm these results, we over-expressed miR1514a in transgenic hairy roots, and observed a reduced accumulation of Phvul.010g120700 and an increase in NAC-derived phasiRNAs; inhibition of miR1514a activity resulted in the opposite effect. Moreover, we determined that a NAC-derived phasiRNA associates with ARGONAUTE 1 (AGO1), suggesting that it is functional. In addition, a transcriptome analysis of transgenic hairy roots with reduced miR1514a levels revealed several differentially expressed transcripts, mainly involved in metabolism and stress responses, suggesting they are regulated by the NAC TF and/or by phasiRNAs. This work therefore demonstrates the participation of miR1514 in the regulation of a NAC transcription factor transcript through phasiRNA production during the plant response to water deficit.

Insights into the function of the phasiRNA-triggering miR1514 in response to stress in legumes

We recently described the activity of miR1514a in response to water deficit in Phaseolus vulgaris. Pvu-miR1514a targets a NAC transcription factor mRNA for cleavage and subsequently triggers NAC-derived phasiRNA formation. Here we show that accumulation and activity of miR1514a are also conserved in the model legume Medicago truncatula. Consistently, we identified Mtr-miR1514a and detected its increased accumulation in response to stress conditions, targeting a NAC TF mRNA for cleavage and triggering phasiRNA production. In P. vulgaris, miR1514a inhibition in transgenic hairy roots was reported to increase NAC 700 mRNA levels and to affect expression patterns of several genes, including that of a Sec 14 homolog. We report here that in adult plant roots exposed to dehydration conditions, where miR1514a levels increased and NAC 700 mRNA decreased, there was a reduction of Sec 14 homolog mRNA levels, suggesting a direct transcriptional effect. The functions of miR1514a, NAC 700 and derived phasiRNAs have just begun to be elucidated in common bean; future understanding of their activities in this and other legumes species will advance our knowledge of microRNA functions in plants.

Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23-24 × SEA 5 of Common Bean

Drought is the major abiotic stress factor limiting yield of common bean (Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23-24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod harvest index, and seed number per area could serve as useful selection criteria for assessing sink strength and for genetic improvement of drought resistance in common bean.

Genome-wide Association Analysis for Drought Tolerance and Associated Traits in Common Bean

A genome-wide association study explored the genetic basis of variation for drought tolerance and related traits in a Middle American diversity panel comprising 96 common bean ( L.) genotypes. The panel was grown under irrigated and rainfed conditions and single nucleotide polymorphism (SNP) data were used to explore the genetic diversity and ancestry of the panel. Varying levels of admixtures and distinctly divergent individuals were observed. Estimations of genome-wide heterozygosity revealed that, on average, greater diversity is present in individuals with Mesoamerica (3.8%) ancestry, followed by admixed individuals (2.3%). The race Durango had the lowest level of heterozygosity (1.4%). We report 27 significant marker-trait associations based on best linear unbiased predictors. These associations include seven markers for shoot biomass at harvest under irrigation and five markers under rainfed conditions on () chromosome 11, two markers for shoot biomass at flowering under irrigation on 02 and 08, two markers for seed size under irrigated and rainfed conditions on 09, seven markers for lodging score under irrigation on 02 and 07, one marker for leaf elongation rate on 03 and one for wilting score on 11. Positional candidate genes, including on 11, associated with wilting, were identified. The SNP ss715639327 marker was located in the exon region of the gene, which codes for an aquaporin associated with water movement in beans. Significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate genetic improvement of drought tolerance in common bean.

Effective Use of Water and Increased Dry Matter Partitioned to Grain Contribute to Yield of Common Bean Improved for Drought Resistance

Common bean (Phaseolus vulgaris L.) is the most important food legume in the diet of poor people in the tropics. Drought causes severe yield loss in this crop. Identification of traits associated with drought resistance contributes to improving the process of generating bean genotypes adapted to these conditions. Field studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia, to determine the relationship between grain yield and different parameters such as effective use of water (EUW), canopy biomass, and dry partitioning indices (pod partitioning index, harvest index, and pod harvest index) in elite lines selected for drought resistance over the past decade. Carbon isotope discrimination (CID) was used for estimation of water use efficiency (WUE). The main objectives were: (i) to identify specific morpho-physiological traits that contribute to improved resistance to drought in lines developed over several cycles of breeding and that could be useful as selection criteria in breeding; and (ii) to identify genotypes with desirable traits that could serve as parents in the corresponding breeding programs. A set of 36 bean genotypes belonging to the Middle American gene pool were evaluated under field conditions with two levels of water supply (irrigated and drought) over two seasons. Eight bean lines (NCB 280, NCB 226, SEN 56, SCR 2, SCR 16, SMC 141, RCB 593, and BFS 67) were identified as resistant to drought stress. Resistance to terminal drought stress was positively associated with EUW combined with increased dry matter partitioned to pod and seed production and negatively associated with days to flowering and days to physiological maturity. Differences in genotypic response were observed between grain CID and grain yield under irrigated and drought stress. Based on phenotypic differences in CID, leaf stomatal conductance, canopy biomass, and grain yield under drought stress, the lines tested were classified into two groups, water savers and water spenders. Pod harvest index could be a useful selection criterion in breeding programs to select for drought resistance in common bean.

Chloride regulates leaf cell size and water relations in tobacco plants

Chloride (Cl(-)) is a micronutrient that accumulates to macronutrient levels since it is normally available in nature and actively taken up by higher plants. Besides a role as an unspecific cell osmoticum, no clear biological roles have been explicitly associated with Cl(-) when accumulated to macronutrient concentrations. To address this question, the glycophyte tobacco (Nicotiana tabacum L. var. Habana) has been treated with a basal nutrient solution supplemented with one of three salt combinations containing the same cationic balance: Cl(-)-based (CL), nitrate-based (N), and sulphate+phosphate-based (SP) treatments. Under non-saline conditions (up to 5 mM Cl(-)) and no water limitation, Cl(-) specifically stimulated higher leaf cell size and led to a moderate increase of plant fresh and dry biomass mainly due to higher shoot expansion. When applied in the 1-5 mM range, Cl(-) played specific roles in regulating leaf osmotic potential and turgor, allowing plants to improve leaf water balance parameters. In addition, Cl(-) also altered water relations at the whole-plant level through reduction of plant transpiration. This was a consequence of a lower stomatal conductance, which resulted in lower water loss and greater photosynthetic and integrated water-use efficiency. In contrast to Cl(-), these effects were not observed for essential anionic macronutrients such as nitrate, sulphate, and phosphate. We propose that the abundant uptake and accumulation of Cl(-) responds to adaptive functions improving water homeostasis in higher plants.

Photosynthesis and chloroplast genes are involved in water-use efficiency in common bean

A recent proposal to mitigate the effects of climatic change and reduce water consumption in agriculture is to develop cultivars with high water-use efficiency. The aims of this study were to characterize this trait as a differential response mechanism to water-limitation in two bean cultivars contrasting in their water stress tolerance, to isolate and identify gene fragments related to this response in a model cultivar, as well as to evaluate transcription levels of genes previously identified. Keeping CO2 assimilation through a high photosynthesis rate under limited conditions was the physiological response which allowed the cultivar model to maintain its growth and seed production with less water. Chloroplast genes stood out among identified genetic elements, which confirmed the importance of photosynthesis in such response. ndhK, rpoC2, rps19, rrn16, ycf1 and ycf2 genes were expressed only in response to limited water availability.

De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes

The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean.

Development of plasmid DNA reference material for the quantification of genetically modified common bean embrapa 5.1

The genetically modified (GM) common bean Embrapa 5.1 was recently approved for commercialization. The reliable detection and quantification of GM organisms is strongly dependent on validated methods as well as calibration systems. This work presents the development of a calibrant plasmid for Embrapa 5.1 common bean detection. The reaction parameters were determined and compared for both the plasmid DNA (pDNA) and the genomic DNA (gDNA). PCR efficiencies for pDNA were 81% for the construction-specific assays and 76% for the taxon-specific assay, whereas for gDNA efficiencies were 94 and 93%, respectively. The limits of detection (LOD) in both qPCR assays were 10(2) and 10(3) copies of gDNA and pDNA per PCR reaction, respectively. This is sufficient to detect 0.067 and 0.67% of GM common bean in 100 ng of DNA, respectively, which is in agreement with detecting the 1% GM content required by the Brazilian legislation.

Phenotyping common beans for adaptation to drought

Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation.

Root hydrotropism: an update

While water shortage remains the single-most important factor influencing world agriculture, there are very few studies on how plants grow in response to water potential, i.e., hydrotropism. Terrestrial plant roots dwell in the soil, and their ability to grow and explore underground requires many sensors for stimuli such as gravity, humidity gradients, light, mechanical stimulations, temperature, and oxygen. To date, extremely limited information is available on the components of such sensors; however, all of these stimuli are sensed in the root cap. Directional growth of roots is controlled by gravity, which is fixed in direction and intensity. However, other environmental factors, such as water potential gradients, which fluctuate in time, space, direction, and intensity, can act as a signal for modifying the direction of root growth accordingly. Hydrotropism may help roots to obtain water from the soil and at the same time may participate in the establishment of the root system. Current genetic analysis of hydrotropism in Arabidopsis has offered new players, mainly AHR1, NHR1, MIZ1, and MIZ2, which seem to modulate how root caps sense and choose to respond hydrotropically as opposed to other tropic responses. Here we review the mechanism(s) by which these genes and the plant hormones abscisic acid and cytokinins coordinate hydrotropism to counteract the tropic responses to gravitational field, light or touch stimuli. The biological consequence of hydrotropism is also discussed in relation to water stress avoidance.