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Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and genome-wide association study (GWAS) results for part of the cowpea core collection of the United States Department of Agriculture (USDA) along with breeding line controls. Included in the analysis were a total of 373 accessions analyzed with 6880 Single Nucleotide Polymorphism (SNP) markers from Genotyping by Sequencing (GBS). Population structure differentiated accessions into two groups irrespective of geographical origin and formed three clusters based on taxa upon phylogenetic analysis. A total of 56 SNPs were significantly associated to nine traits including pod length (25 Quantitative Trait Nucleotides, QTNs), seed anti-oxidant content (7 QTNs), dry pod color (7 QTNs), plant maturity (5 QTNs), flower color (5 QTNs), seed weight (4 QTNs), tolerance to low phosphate (1 QTN), growth habit (1 QTN), and response to rock phosphate (1 QTN) using Bayesian-information, Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Fixed and random model Circulating Probability Unification (FarmCPU) association models. Key genes related to all significant SNPs were identified based on annotations of the cowpea reference genome, including a flavonoid gene controlling flower color (Vigun08g040200.1), a root nodulation regulator for tolerance to low phosphate (Vigun11g168000.1), and numerous genes involved in signaling, biosynthesis, metabolite transport, and abiotic stress. Our results highlight the importance of maintaining public phenotyping databases at USDA and strengthening collaborations for data collection in cowpea to maximize research impacts.

Abstract The species Vigna unguiculata L. (Walp), commonly known as cowpea, is a multi-purpose legume that has been selected into three subspecies that are divided into grain, fodder and pod (yardlong bean) types. However, genetic bases for distinctions are not well understood. The purpose of this study was to apply genotyping-by-sequencing (GBS) and current reference genome for V. unguiculata to distinguish three subspecies and identify signatures of divergence. The collection of 130 accessions included 128 cultivated from: 1) ssp. cylindrica, fodder type; 2) ssp. sesquipedalis, pod vegetable type; and 3) ssp. unguiculata, grain type. Two wilds genotypes from spp. dekindtiana and spp. pubescens, were used to anchor phylogeny. A total of 11,083 highly informative single nucleotide polymorphisms (SNPs) were discovered. Wild accessions showed distinct genetic fingerprints and were separated from cultivated subspecies. Principal component analysis showed closer relationship between ssp. unguiculata and ssp. cylindrica compared to ssp. sesquipedalis. Relative differentiation of cultivated subspecies (with Fixation Index, F ST ) indicated the existence of discrete signatures of selection. This work clarifies the population structure, phylogeny, and domestication of cultivated cowpeas. Furthermore, significant genetic differences between grain and pod vegetable types can provide valuable information for future breeding in three cowpea groups.

Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change.“I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.

Abstract Common bean (Phaseolus vulgaris) is grown in two growth types, bush and climbing beans. The latter are preferred in several regions in East and Southern African as well as in Latin America (dominant in Rwanda and Colombia), due to higher yields and resilience compared with bush type. Common bean productivity is reduced by several pests and diseases between them. Bean common mosaic virus (BCMV), which is the most common and destructive poty‐virus affecting bean production worldwide, and anthracnose, caused by the fungus Colletotrichum lindemuthianum, can cause yield losses as high as 95% in susceptible cultivars. Further important traits in common bean are high micro mineral contents to alleviate malnutrition and grain quality traits such as the canning quality of bean varieties, which is important for farmers to access the processing market. In this study, new climbing bean populations were generated (coded ENF/CGA) to combine high seed iron (SdFe) and multiple diseases resistance. Double and triple crosses between parents with virus and anthracnose resistance, high SdFe, and good agronomic traits were employed. In trials in Darien and Popayan, lines were identified that combine BCMNV/BCMV and anthracnose resistance with seed yields above 4000 kg/ha. Phenotypic evaluations validated the usefulness of SNP markers tagging the genes bc‐3 and I for BCMN and Co‐3 for anthracnose as a selection tool for field resistance. These results show the genetic potential of the lines that are now being tested in target regions to be delivered to smallholder farmers.

Genetic variation in wild relatives, GenBank accessions, landraces, and cultivars can unlock key alleles for the traits of interest for breeding programs. Breeding programs often utilize different strategies to quantify the source of heritable variation for target traits. One neglected area of study is the root traits of diverse genotypes, and this is especially the case for aluminum toxicity effects on legumes such as the common bean, which is the most used pulse for direct human consumption. This study evaluated 267 genotypes of common bean that were part of the global Andean Diversity Panel (ADP), consisting mainly of genotypes assembled from public and private breeding programs in Africa and North America, as well as elite lines and land races from the USDA. The ADP was evaluated for root traits at the seedling stage in the Tennessee State University (TSU) greenhouse using a hydroponic system with a standard nutrient solution with and without aluminum (Al). The recorded data on the roots per trial were fit to a linear mixed model for the analysis of variance in order to test for the genotype differences. Adjusted means considered replication and blocks within replication as random effects and genotypes as fixed effects. These were then used for Pearson correlation tests and for principal component analysis (PCA), where the first two vectors accounted for 94.5% and 93% of the explained variation under the control and Al-treatment conditions, respectively. Genotypes were clustered based on the morphology of roots in response to Al-toxicity treatment using the Euclidean distance and Ward’s hierarchical agglomerative clustering method, identifying four distinctive groups significant at p < 0.01. The intra-cluster distance was lower than the inter-cluster distances, which indicated a heterogeneous and homogeneous nature between and within clusters, respectively. The results suggest that crossing between accessions from two of the clusters would result in the maximum genetic segregation. One cluster was found to have a higher Al-toxicity tolerance than the others.

Seed uniformity and stability testing, and multiplication, are key steps in the seed supply chain of the common bean (Phaseolus vulgaris L.) and other crops. Optimizing agronomical practices in these phases can ultimately ensure seed quality and availability, and germplasm prospective utilization. However, farmers have rarely standardized seed testing and propagation protocols in local common bean landraces conserved in situ. An example of this is the Liborino variety (var.), a promising yellow Andean common bean known for its presumably high digestibility and adaptation to the local conditions of the Cauca river canyon (northwest Andes of Colombia), but likely experiencing genetic erosion after decades of suboptimal propagation. Therefore, this work intended to evaluate and select locally adapted genotypes of common bean var. Liborino for commercial use, to be later multiplied, evaluated by participatory breeding, and eventually shared with farmers. Specifically, we evaluated 44 accessions of var. Liborino common bean in six adaption and yield field trials in the Cauca river canyon at 1100 and 1400 m a.s.l, and in AGROSAVIA’s “La Selva” research station at 2100 m a.s.l. In parallel, we carried out standardized seed multiplication of a Liborino genotype using best practices to guarantee uniformity and stability. From the 44 accessions, nine were well adapted to the tested local conditions. Four of these accessions exhibited a bush type growth habit, while the remaining five were climbers. The trials revealed maximum average extrapolated yields of up to 1169.4 ± 228.4 kg ha−1 for the bush types (G8152) and up to 1720.0 ± 588.4 kg ha−1 for the climbers (G51018), both at 2100 m a.s.l. Three climbing accessions matched farmers’ expectations for seed coat color and shape, according to a participatory selection exercise. Uniform and stable seed of the selected genotype was delivered in 2022 to 39 farmers, ~6.5 kg of seeds per farmer. Our results will allow implementing bean genetic improvement pipelines, promoting var. Liborino commercialization, and boosting the economic and sustainable development of the rural communities in the Cauca river canyon. Seed uniformity testing and multiplication pipelines must be extended to other bean landraces conserved in situ.

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.

Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of its consumption for human health and nutrition. While mung bean is rich in a range of nutritional components, such as protein, carbohydrates and vitamins, it remains less well studied than other legume crops in terms of micronutrients. In addition, mung bean genomics and genetic resources are relatively sparse. The objectives of this research were three-fold, namely: to develop a genome-wide marker system for mung bean based on genotyping by sequencing (GBS), to evaluate diversity of mung beans available to breeders in the United States and finally, to perform a genome-wide association study (GWAS) for nutrient concentrations based on a seven mineral analysis using inductively coupled plasma (ICP) spectroscopy. All parts of our research were performed with 95 cultivated mung bean genotypes chosen from the USDA core collection representing accessions from 13 countries. Overall, we identified a total of 6,486 high quality single nucleotide polymorphisms (SNPs) from the GBS dataset and found 43 marker × trait associations (MTAs) with calcium, iron, potassium, manganese, phosphorous, sulfur or zinc concentrations in mung bean grain produced in either of two consecutive years’ field experiments. The MTAs were scattered across 35 genomic regions explaining on average 22% of the variation for each seed nutrient in each year. Most of the gene regions provided valuable candidate loci to use in future breeding of new varieties of mung bean and further the understanding of genetic control of nutritional properties in the crop. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) for nutritional improvement in mung bean and to analyze cultivars of mung bean.

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region.

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans (Xff), is a worldwide disease of common bean (Phaseolus vulgaris L.). Longyundou 5, a Chinese cultivar in the Mesoamerican gene pool of common bean, displays resistance to the Xff strain XSC3-1. To identify the genetic mechanisms behind this resistance, we crossed Long 5 with a susceptible genotype to develop a mapping population of F2 plants. Plant resistance to CBB was identified at 14 and 21 days after inoculation with Xff strain XSC3-1. A major QTL at 14 and 21 days after inoculation was mapped on chromosome Pv10 with LOD scores of 6.41 and 5.35, respectively. This locus was associated with SAP6, a previously-identified and much-used dominant marker, but in a 4.2 cM interval between new codominant markers BMp10s174 and BMp10s244. Ten candidate genes were found between markers BMp10s174 and BMp10s244 on chromosome Pv10 and could encode defense response proteins responding to CBB pathogens. Four pairs each of epistatic QTL for CBB resistance were detected at 14 and 21 days after inoculation. Phenotypic variation explained by the epistatic QTL ranged from 7.19% to 12.15% and 7.72% to 8.80% at 14 and 21 days after inoculation, respectively. These results confirmed the importance of epistasis in CBB resistance in common bean. The adjacent markers found may be more efficient for marker assisted selection in common bean breeding for CBB resistance owing to their closer linkage to the target QTL.

Drought stress linked with climate change is one of the major constraints faced by common bean farmers in Africa and elsewhere. Mitigating this constraint requires the selection of resilient varieties that withstand drought threats to common bean production. This study assessed the drought response of 64 small red-seeded genotypes of common bean grown in a lattice design replicated twice under contrasting moisture regimes, terminal drought stress and non-stress, in Ethiopia during the dry season from November 2014 to March 2015. Multiple plant traits associated with drought were assessed for their contribution to drought adaptation of the genotypes. Drought stress determined by a drought intensity index was moderate (0.3). All the assessed traits showed significantly different genotypic responses under drought stress and non-stress conditions. Eleven genotypes significantly (P ≤ 0.05) outperformed the drought check cultivar under both drought stress and non-stress conditions in seed yielding potential. Seed yield showed positive and significant correlations with chlorophyll meter reading, vertical root pulling resistance force, number of pods per plant, and seeds per pod under both soil moisture regimes, indicating their potential use in selection of genotypes yielding well under drought stress and non-stress conditions. Clustering analysis using Mahalanobis distance grouped the genotypes into four groups showing high and significant inter-cluster distance, suggesting that hybridization between drought-adapted parents from the groups will provide the maximum genetic recombination for drought tolerance in subsequent generations.

Exploring the genomic architecture of species and populations divergence aids understanding how lineages evolve and adapt, and ultimately can show the repeatability of evolutionary processes. Yet, the genomic signatures associated with divergence are still relatively unexplored, leading to a knowledge gap on whether species divergence ultimately differs in its genetic architecture from divergence at other spatial scales (i.e., populations, ecotypes). Our goal in this research was to determine whether genomic islands of speciation are more prone to harbor within-species differentiation due to genomic features, suppressed recombination, smaller effective population size or increased drift, across repeated hierarchically nested levels of divergence. We used two species of Phaseolus beans with strong genepool and population sub-structure produced by multiple independent domestications each especially in Andean and Mesoamerican / Middle American geographies. We genotyped 22,531 GBS-derived SNP markers in 209 individuals of wild and cultivated Phaseolus vulgaris and Phaseolus lunatus. We identified six regions for species-associated divergence. Out of these divergence peaks, 21% were recovered in the four within-species between-genepool comparisons and in the five within-genepool wild-cultivated comparisons (some of the latter did retrieve genuine signatures of the well described multiple domestication syndromes). However, genomic regions with overall high relative differentiation (measured by FST) coincided with regions of low SNP density and regions of elevated delta divergence between-genepools (ΔDiv), independent of the scale of divergence. The divergence in chromosome Pv10 further coincided with a between-species pericentric inversion. These convergences suggest that shared variants are being recurrently fixed at replicated regions of the genome, and in a similar manner across different hierarchically nested levels of divergence, likely as result of genomic features that make certain regions more prone to accumulate islands of speciation and within-species divergence. In summary, neighboring signatures of speciation, adaptation and domestication in Phaseolus beans are influenced by ubiquitous genomic constrains, which may continue to fortuitously shape genomic differentiation at various others scales of divergence.

Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations (GEA) in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using genotyping by sequencing (GBS) to discover single nucleotide polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1 Mb containing associated SNPs had more positive Tajima’s D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.

Understanding functional relations among plant traits and their modulation by growing conditions is imperative in designing selection strategies for breeding programs. This study assessed trait relationships among 196 common bean genotypes exposed to stresses for drought and field infestation of bean fly or bean stem maggot (BSM). The study was carried out at two locations and data was analyzed with linear correlation, path coefficient and genotype × trait biplot analyses. Multiple trait data related to mechanisms of drought and bean fly tolerance were collected on 196 genotypes grown under i) water deficit at mid-pod fill, or ii) unprotected against bean fly; iii) irrigated, well watered conditions, or iv) bean fly protection with chemicals. Seed yield exhibited positive and significant correlations with leaf chlorophyll content, vertical root pulling resistance, pod harvest index, pods per plant and seeds per pod at both phenotypic and genotypic levels under stress and non-stress conditions. Genotypic correlations of traits with seed yield were greater than their respective phenotypic correlations across environments indicating the greater contribution of genotypic factors to the trait correlation. Pods per plant and seeds per pod had high positive direct effects on seed yield both under stress and non-stress whereas pods per plant had the highest indirect effect on seed yield through pod harvest index under stress. In general, our results suggest that vertical root pulling resistance and pod harvest index are important selection objectives for improving seed yield in common beans under non-stress and stress conditions, and particularly useful for drought and BSM tolerance evaluation.

The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in grain amaranth accessions and close relatives from six Amaranthus species and determine genetic differences and similarities between groupings. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The majority of the SNPs were species specific with 4,568 and 3,082 for the two grain amaranths originating in Central America Amaranthus cruentus and A. hypochondriacus and 3,284 found amongst both A. caudatus, originally domesticated in South America, and its close relative, A. quitensis. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. The SNPs we discovered here can be used for marker development for future amaranth study.

Common beans are a warm-season, food legume cultivated in areas prone to water limitation throughout their growing season. This study assessed the magnitude and pattern of trait associations for a total of 202 common bean genotypes divided into panels of 81 Andean and 121 Mesoamerican gene pool accessions grown under contrasting treatments of well-watered, non-stress, and water-limited, terminal drought-stress conditions. Linear correlation, complex path coefficient, and genetic divergence analyses were used to dissect the relationship dynamics between traits and the relative contribution of adaptive traits to differentiation among gene pools and genotypes based on drought stress. Drought severity level for the trial was high and created the ideal condition to reveal genotypic differences, as seen by the differential response of the genotypes for the various traits measured. The value for phenotypic coefficients of variation for all traits was higher than the corresponding genotypic values. Seed yield had positive and strong genotypic and phenotypic correlation with pods per plant across gene pools and stress levels. The overall amount of genetic correlation was greater than the corresponding phenotypic correlation matrix for all the traits within the gene pool and across stress levels. Moreover, the results depicted the phenotypic correlation as equal or better than its genotypic counterpart in estimating drought tolerance in common bean plants. Clustering analysis with Mahanalobis's coefficient of generalized distance grouped genotypes with a differential level of drought adaptation into different classes within each panel. This indicates drought tolerance involves different mechanisms of plant response and is present separately in each gene pool panel. Pods per plant, seed weight, pod partitioning index, and harvest index are useful selection objectives to improve drought adaptation in common bean, but must be differentially weighted in each gene pool. The analysis of genetic variation and association between adaptive traits on the two panels provided useful insights on which traits could be used to improve common bean adaptation to low water availability during the growth season.

Purple passion fruit (Passiflora edulis Sims f. edulis) is a tropical juice source. The goal of this project was to evaluate photosynthetic and physiological variability for the crop with the hypotheses that landraces contain the diversity to adapt to higher elevation nontraditional growing environments and this is dependent on specific parameters of ecological adaptation. A total of 50 genotypes of this crop were chosen from divergent sources for evaluations of their eco-physiological responses in two equatorial locations at different altitudes in the Andes Mountains, a center of diversity for the species. The germplasm included 34 landraces, 8 commercial cultivars, and 8 genebank accessions. The two locations were contrasting in climates, representing mid and high elevations in Colombia. Mid-elevation valleys are typical regions of production for passion fruit while high elevation sites are not traditional. The location effects and variables that differentiated genotypes were determined. Results showed statistically significant differences between locations and importance of physiological parameters related to photosynthesis and water use efficiency. Some landraces exhibited better water status and gas exchange than commercial types. Parameters like maximum photosynthesis, points of light saturation and compensation, darkness respiratory rate, and apparent quantum yield varied between genotype groups. The landraces, commercial types, and genebank entries also differed in content of carotenoids and chlorophylls a and b. Meanwhile, photosynthesis measurements showed that altitudinal difference had an effect on genotype-specific plant growth and adaptation. An important conclusion was that landraces contained the diversity to adapt to the new growing environment at higher altitudes.

Nutrient transport to grain legume seeds is not well studied and can benefit from modern methods of elemental analysis including spectroscopic techniques. Some cations such as potassium (K) and magnesium (Mg) are needed for plant physiological purposes. Meanwhile, some minerals such as copper (Cu), iron (Fe), molybdenum (Mo) and zinc (Zn) are important micronutrients. Phosphorus (P) is rich in legumes, while sulfur (S) concentration is related to essential amino acids. In this research, the goal was to analyze a genetic mapping population of common bean (Phaseolus vulgaris L.) with inductively coupled plasma (ICP) spectrophotometry to determine concentrations of and to discover quantitative trait loci (QTL) for 15 elements in ground flour of whole seeds. The population was grown in randomized complete block design experiments that had been used before to analyze Fe and Zn. A total of 21 QTL were identified for 9 additional elements, of which four QTL were found for Cu followed by three each for Mg, Mn and P. Fewer QTL were found for K, Na and S. Boron (B) and calcium (Ca) had only one QTL each. The utility of the QTL for breeding adaptation to element deficient soils and association with previously discovered nutritional loci are discussed.

Expressed sequence tags (ESTs) have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA) libraries from root tissues of common beans ( L.) grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP) citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

Amaranthus L. is genus of C4 dicotyledonous herbaceous plants comprising approximately 70 species, with three subgenera, which contains both cultivated and wild types, where cultivated ones are used for food grains, leafy vegetables, potential forages and ornamentals. Grain amaranth are pseudocereals from three species domesticated in North and South America and are notable for containing high amount of protein and minerals and balanced amino acid in their small seeds. Genetic diversity analysis of amaranths is important for development of core set of germplasm with widely diverse population and effective utilization of plant genetic resources. In this study, we evaluated a germplasm collection of 260 amaranth accessions from United State Department of Agriculture (USDA) and 33 accessions from Seed Savers’ Exchange (SSE). We evaluated morphological traits like blade pigmentation, blade shape, petiole pigmentation, branching index, flower color, stem color, inflorescence density, inflorescence shape, terminal inflorescence attitude, plant height and yield characteristics across all 293 accessions. We compared clustering within the USDA and SSE collection and across both collections. Data analysis of morphological data showed significant difference of petiole pigmentation, stem color, blade pigmentation, blade shape and flower color across different clusters of accessions of USDA unlike among different clusters of SSE where we found significant difference of only blade pigmentation, blade shape and flower color. The relationship depicted by neighbor-joining dendogram using the morphological markers was consistent with some but not all of the differences observed between species. Some divisions were found between cultivated and weedy amaranths that was substantiated by morphological characteristics but no separation of South and Central American species was observed. Substantial phenotypic plasticity limits the use of morphological analysis for phylogenetic analysis but does show that important morphological traits such as inflorescence type and plant architecture can cross species boundaries. Similarly, color variants for leaves, flowers and seeds are not exclusive to one cluster in our study nor to one species and can be used widely for breeding any of the cultigens, but not to species identification. Our findings will help in germplasm conservation of grain amaranths and facilitate in this crop’s improvement. It will also help on developing effective breeding programs involving different plant characteristics and morphological traits of Amaranths.

Microsatellite markers or simple sequence repeat (SSR) loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC) end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs) from the G19833 common bean ( L.) library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]). Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR)-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

Se utilizó la información generada por 29 microsatélites en 63 accesiones del acervo andino de P. vulgaris para elaborar agrupamientos y calcular índices de prevalencia. Las accesiones formaron grupos que correspondieron a las razas Nueva Granada, Chile y Perú. Se determinó la existencia de notoria introgresión en genotipos de las razas Chile y Perú

Se evaluó el tipo de faseolina en 180 accesiones cultivadas de Phaseolus vulgaris del Caribe de la colección del Centro Internacional de Agricultura Tropical (CIAT). En fríjoles de Cuba (25 accesiones) predominó el tipo S (68%, semilla pequeña, roja o negra y hábito de crecimiento de tipos II y III), seguidos por fríjoles con faseolina T (20 %) y con un bajo porcentaje los tipos B, CH y Sd. En Haití (108 accesiones) las faseolinas más comunes fueron T (48.1%, semilla grande, rojo moteado y hábito arbustivo) y S (42.6%, semilla pequeña, negra), y unas pocas mostraron faseolinas B, Sb y Sd. En los fríjoles de Puerto Rico (21 accesiones) las faseolinas más comunes fueron T (57.14%, semilla grande, rojo moteada) y S (42.86%, semilla pequeña amarilla, negra o blanca). En los de República Dominicana (21 accesiones) abundó el tipo T (85.7%, semilla grande o mediana rojomoteada). En los fríjoles de Jamaica (5) predominaron las faseolinas T y B (40% de cada una). Los patrones de faseolina indicaron la prevalencia tanto de fríjoles Mesoamericanos como Andinos.

Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the domestication syndrome. Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. MYB transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa colour in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defence against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on structural and chemical aspects.

Common beans (Phaseolus vulgaris L.), like many legumes, are rich in iron, zinc and certain other microelements that are generally found to be in low concentrations in cereals, other seed crops, and root or tubers and therefore are good candidates for biofortification. But a quandary exists in common bean biofortification: namely that the distribution of iron has been found to be variable between the principal parts of seed; namely the cotyledonary tissue, embryo axis and seed coat. The seed coat represents ten or more percent of the seed weight and must be considered specifically as it accumulates much of the anti-nutrients such as tannins that effect mineral bioavailability. Meanwhile the cotyledons accumulate starch and phosphorus in the form of phytates. The goal of this study was to evaluate a population of progeny derived from an advanced backcross of a wild bean and a cultivated Andean bean for seed coat versus cotyledonary minerals to identify variability and predict inheritance of the minerals. We used wild common beans because of their higher seed mineral concentration compared to cultivars and greater proportion of seed coat to total seed weight. Results showed the most important gene for seed coat iron was on linkage group B04 but also identified other QTL for seed coat and cotyledonary iron and zinc on other linkage groups, including B11 which has been important in studies of whole seed. The importance of these results in terms of physiology, candidate genes and plant breeding are discussed.