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Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean ( Phaseolus vulgaris L . ) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris , which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

Beans (Phaseolus spp.) are one of the most important legumes for their nutritional value and health benefits in many world regions. In addition to Phaseolus vulgaris, there are four additional species that are cultivated in many regions of the world and are a source of food for human consumption: P. lunatus, P. coccineus, P. polyanthus, and P. acutifolius. In this work, phenolic compounds, antioxidant activity, and anti-nutritional compounds of 18 bean accessions, corresponding to four different species of the genus Phaseolus, were analyzed. In addition, their physical characteristics, proximate composition, and amino acid content were determined in order to compare their phytochemical composition and nutritional value. The species closest to each other in terms of essential amino acid content were P. polyanthus with P. vulgaris and P. lunatus with P. coccineus. Furthermore, there was a strong positive correlation between antioxidant activity and flavonoids, anthocyanins, and lectins with all the accessions collected. Significant differences in the content of phenolic compounds were found among the bean species studied. Therefore, in addition to P. vulgaris, other species such as P. coccineus and P. lunatus have high biological and antioxidant potential that could be beneficial to human health when consumed as nutraceutical foods.

Common bean variety choice by farmers in Uganda is driven by seed yield plus end-use quality traits like market class and cooking time. Limited genotype by environment information is available for traits valued by consumers. This research evaluated yield, seed size, hydration properties, and cooking time of 15 common bean genotypes within market classes recognized by consumers along with three farmers’ checks at nine on-farm locations in Uganda for two seasons. Yield ranged from 71 to 3,216 kg ha −1 and was largely controlled by location (21.5% of Total Sums of Squares [TSS]), plus the interaction between location and season (48.6% of TSS). Cooking time varied from 19 to 271 minutes with the genotypes Cebo Cela and Ervilha consistently cooking fastest in 24 and 27 minutes respectively. Comparatively, the local checks (NABE-4, NABE-15, and Masindi yellow) took 35 to 45 minutes to cook. Cooking time was largely controlled by genotype (40.6% of TSS). A GGE biplot analysis uncovered the presence of two mega-environments for yield and one mega-environment for cooking time. Identification of mega-environments for these traits will help expedite common bean breeding, evaluation, and variety selection through reduction of number of test environments needed for phenotype evaluations. The high yielding and fast cooking genotypes from this study can be targeted as parental materials to improve existing common bean germplasm for these important traits.

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs.

Key message The origin of common bean was investigated throughout chloroplast and nuclear WGS data considering recombination events. Our results support the Mesoamerican origin of common bean. The remarkable evolutionary history of the common bean ( Phaseolus vulgaris L. ) has led to the emergence of three wild main gene pools corresponding to three different eco-geographical areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios, and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris . Here we shed light on the origin of P. vulgaris by analyzing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms including a large collection of Mesoamerican and Andean individuals. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador gene pools occurred ~ 0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account the genetic rearrangements produced by recombination when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genusGlycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.

Iron (Fe) and zinc (Zn) stress significantly affects fundamental metabolic and physiological processes in plants that results in reduction of plant growth and development. In the present study, common bean variety; Shalimar French Bean-1 (SFB-1) was used as an experimental material. Four different MGRL media i.e. normal MGRL medium (Control), media without Fe (0-Fe), media without Zn (0-Zn) and media with excess Zn (300-Zn) were used for growing seeds of SFB-1 under in vitro condition for three weeks under optimum conditions. Three week old shoot and root tissues were harvested from the plants grown in these four different in vitro conditions and were, subjected to Fe and Zn estimation. Further, extraction of total RNA for differential gene expression of ten candidate genes selected based on our in silico investigation and their classification, phylogeny and expression pattern was unraveled. Expression analysis of three candidate genes (OPT3, NRAMP2 and NRAMP3) in roots revealed possible cross talk among Fe/Zn stress that was further confirmed by observing less accumulation of Fe in roots under both these conditions. However, we observed, higher accumulation of Fe in shoots under 0-Fe condition compared to control that suggests precise sensing for priority based compartmentalization and partitioning leading to higher accumulation of Fe in shoots. Furthermore, the expression analysis of IRT1, FRO1 and Ferritin 1 genes under Fe/Zn stress suggested their role in uptake/transport and signaling of Fe and Zn, whereas the expression of ZIP2, NRAMP1, HA2 and GLP1 genes were highly responsive to Zn in Phaseolus vulgaris . The identified genes highly responsive to Fe and Zn stress condition can be potential candidates for overcoming mineral stress in dicot crop plants.

Abstract The development of new cultivars is a strategy used in breeding programs to increase food production with environmental sustainability. The genotype × environment interaction is a great challenge in the identification and selection of superior genotypes for different edaphoclimatic conditions. Due to this interaction, it is essential to select and develop materials that can provide not only high productivity but also wide adaptability and production stability. Given the above, this work aims to select bean pre-cultivars regarding grain productivity, adaptability and stability for the State of Rio de Janeiro. In the 2018 harvest, two inbred lines competition trials were carried out and three in the 2019 harvest. Eleven black bean genotypes were evaluated in five environments, and the experiments were set up in a randomized block design with three replications. The adaptability and genotypic stability were assessed via the GGE Biplot, Eberhart and Russell and Lin and Binns methodologies, with the aid of the GENES and R software systems. The methodologies based on simple linear regression and non-parametric statistical analysis were concordant in the identification of genotypes with production stability (BRS Esteio, BRS FP 403 and CNFP 16459), responsive to environmental improvement (BRS Esteio) and adapted to unfavorable environments (BRS Esteio). Furthermore, BRS Esteio was classified as the ideotype and presented the best adaptability, high stability and performance above the general average. Thus, the adaptability and stability analysis methodologies proved to be effective and consistent in identifying superior genotypes. Resumo O desenvolvimento de novas cultivares é uma estratégia utilizada em programas de melhoramento genético para aumentar a produção de alimentos com sustentabilidade ambiental. A interação genótipos × ambientes é um grande desafio na identificação e seleção de genótipos superiores para diferentes condições edafoclimáticas. Devido a esta interação, é essencial selecionar e desenvolver materiais que possam proporcionar não apenas alta produtividade, mas também ampla adaptabilidade e estabilidade de produção. Diante do exposto, este trabalho tem como objetivo selecionar pré-cultivares de feijão quanto a produtividade de grãos, adaptabilidade e estabilidade para o Estado do Rio de Janeiro. Na safra de 2018 foram realizados dois ensaios de competição de linhagens e três na safra de 2019. Foram avaliados onze genótipos de feijão preto em cinco ambientes, sendo os experimentos instalados em delineamento de blocos casualizados com três repetições. A adaptabilidade e estabilidade fenotípica foram avaliadas através das metodologias GGE Biplot, Eberhart and Russell e Lin and Binns, com auxílio dos softwares GENES e R. As metodologias baseadas em regressão linear simples e análise estatística não paramétrica foram concordantes na identificação de genótipos com estabilidade produtiva (BRS Esteio, BRS FP 403 e CNFP 16459), responsivos à melhoria ambiental (BRS Esteio) e adaptados a ambientes desfavoráveis (BRS Esteio). Além disso, o BRS Esteio foi classificado como ideótipo e apresentou melhor adaptabilidade, alta estabilidade e desempenho acima da média geral. Assim, as metodologias de análise de adaptabilidade e estabilidade mostraram-se eficientes e concordantes na identificação de genótipos superiores.

Lima bean (Phaseolus lunatus L.) is a legume of high socioeconomic value with great potential to contribute to food security. However, it is increasingly affected by genetic erosion. In this study, 43 lima bean accessions from the germplasm collection of the Federal University of Piauí (PGB-UFPI, Brazil) were analyzed, comprising 27 domesticated and 16 wild accessions. Genetic characterization was performed using five chloroplast microsatellite markers (cpSSRs). All analyzed loci were polymorphic, each presenting two alleles per locus, resulting in the identification of eight distinct haplotypes. Analysis of molecular variance (AMOVA) revealed that 94% of genetic variation occurred between groups. Principal Coordinate Analysis (PCoA) indicated the formation of two distinct clusters, supporting the hypothesis of multiple domestication events and highlighting genetic differentiation between wild and domesticated accessions. Haplotype diversity was higher among wild accessions than among domesticated ones. The use of cpSSR markers was effectiveness for assessing the genetic diversity of lima beans, underscoring the need to conserve both wild and domesticated accessions. These findings provide essential insights for guiding genetic conservation strategies and strategic use of germplasm in breeding programs.