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Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

Adenine metabolism is important for common bean (Phaseolus vulgaris L.) productivity since this legume uses ureides derived from the oxidation of purine nucleotides as its primary nitrogen storage molecules. Purine nucleotides are produced from de novo synthesis or through salvage pathways. Adenine phosphoribosyl transferase (APRT) is the enzyme dedicated to adenine nucleobase salvage for nucleotide synthesis, but it can also convert active cytokinin bases into their inactive nucleotide forms. In common bean, APRT is encoded by four genes. Gene expression analysis, biochemical properties, and subcellular location indicated functional differences among the common bean APRT isoforms. CRISPR/Cas9 targeted down-regulation of two of the four PvAPRTs followed by metabolomic and physiological analyses of targeted hairy roots revealed that, although the two proteins have redundant functions, PvAPRT1 mostly participated in the salvage of adenine, whereas PvAPRT5 was the predominant form in the regulation of cytokinin homeostasis and stress responses with a high impact in root and nodule growth. [ABSTRACT FROM AUTHOR]

The dual challenges of global population explosion and environmental deterioration represent major hurdles for 21st Century agriculture culminating in an unprecedented demand for food security. In this Review, we revisit historical concepts of plasticity and canalization before integrating them with contemporary studies of genotype-environment interactions (G×E) that are currently being carried out at the genome-wide level. In doing so we address both fundamental questions regarding G×E and potential strategies to best secure yields in both current and future climate scenarios. Breeding environmental adaptive crop cultivars under the climate changing scenario is anything but easy. Here, the authors review the concepts of plasticity and canalization and their integration with contemporary studies of genotype-environmental interactions with the objective to facilitate crop breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: Because plants are immobile, they have developed intricate mechanisms to sense and absorb nutrients, adjusting their growth and development accordingly. Sulfur is an essential macroelement, but our understanding of its metabolism and homeostasis is limited. LSU (RESPONSE TO LOW SULFUR) proteins are plant‐specific proteins with unknown molecular functions and were first identified during transcriptomic studies on sulfur deficiency in Arabidopsis. These proteins are crucial hubs that integrate environmental signals and are involved in the response to various stressors. Herein, we report the direct involvement of LSU proteins in primary sulfur metabolism. Our findings revealed that the quadruple lsu mutant, q‐lsu‐KO, which was grown under nonlimiting sulfate conditions, exhibited a molecular response resembling that of sulfur‐deficient wild‐type plants. This led us to explore the interactions of LSU proteins with sulfate reduction pathway enzymes. We found that all LSU proteins interact with ATPS1 and ATPS3 isoforms of ATP sulfurylase, all three isoforms of adenosine 5´ phosphosulfate reductase (APR), and sulfite reductase (SiR). Additionally, in vitro assays revealed that LSU1 enhances the enzymatic activity of SiR. These results highlight the supportive role of LSU proteins in the sulfate reduction pathway. Significance Statement: This study demonstrates that the quadruple lsu mutant exhibits impaired sulfate assimilation and reduction at the transcript, metabolite, and long‐distance sulfur flux levels. Our subsequent research has revealed the molecular mechanism underlying these findings, showing a direct interaction between LSU proteins and enzymes involved in sulfate reduction, particularly sulfite reductase (SiR), with LSU1 enhancing SiR activity. [ABSTRACT FROM AUTHOR]

Summary: Drought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID‐INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP‐seq), we show that the sorghum BRI1‐EMS‐SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G‐box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1‐mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought. [ABSTRACT FROM AUTHOR]

Background/Objectives: The biostimulant SuperFifty, produced from the brown algae Ascophyllum nodosum, can improve crop quality and yield and mitigate stress tolerance in model and crop plants such as Arabidopsis thaliana, pepper, and tomato. However, the effect of SuperFifty on raspberries and strawberries has not been well studied, especially in terms of nutritional properties and yield. The aim of this study was to investigate the effect of SuperFifty on the quality and quantity of raspberry and strawberry fruits, with a focus on metabolic composition and essential elements, which together determine the nutritional properties and total yield of these two crops. Methods: Metabolome analysis was performed by liquid chromatography–mass spectrometry analysis (LC-MS), and essential elements analysis was performed by inductively coupled plasma-mass spectrometry (ICP-MS). Results: Here, we demonstrate that SuperFifty increases the fruit size of both raspberries and strawberries and enhances the yield in these two berry crops by 42.1% (raspberry) and 33.9% (strawberry) while preserving the nutritional properties of the fruits. Metabolome analysis of 100 metabolites revealed that antioxidants, essential amino acids, organic acids, sugars, and vitamins, such as glutathione, alanine, asparagine, histidine, threonine, serine, tryptophan, sucrose, citric acid, pantothenic acid (vitamin B5), as well as other primary metabolites, remain the same in the SuperFifty-primed fruits. Secondary metabolites, such as caffeic acid, p-coumaric acid, kaempferol, and quercetin, also maintained their levels in the SuperFifty-primed fruits. Analysis of essential elements demonstrated that elements important for human health, such as Zn, Mn, Fe, B, Cu, K, and Ca, maintain the same levels in the raspberry and strawberry fruits obtained from the biostimulant-primed plants. Magnesium, an important element known as a co-factor in many enzymatic reactions related to both plant physiology and human health, increased in both raspberry and strawberry fruits primed with SuperFifty. Finally, we discuss the potential financial and health benefits of the SuperFifty-induced priming for both growers and consumers. Conclusions: We demonstrate that SuperFifty significantly enhances the yield of both raspberries and strawberries, improves the marketable grade of the fruits (larger and heavier fruits), and enhances the nutritional properties by elevating Mg content in the fruits. Altogether, this biostimulant-induced molecular priming offers an environmentally friendly, efficient, and sustainable way to enhance the yield and quality of berry crops, with clear benefits to both berry producers and customers. [ABSTRACT FROM AUTHOR]

Summary: Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro‐ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd‐containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops. [ABSTRACT FROM AUTHOR]

Summary: Antibiotic resistance is now deemed a worldwide problem that puts public health at risk. The potential of Murraya (Murraya koenigii (L.) Spreng. and Murraya paniculata (L.) Jacq.) leaves and stems as antibacterial agents against multidrug‐resistant Acinetobacter baumannii (MDRAB) was assessed in our study. First, screening was performed by disc diffusion assay, and minimum inhibitory concentration values were then determined as compared to tigecycline. A. baumnii mouse model of infection was established to substantiate the antibacterial activity of Murraya species. Results revealed high antimicrobial activity for stem of both plants where leaves showed moderate to weak activity. Phytochemical characterisation revealed the identification of 129 metabolites belonging to different classes of compounds viz. coumarins, carbazole alkaloids, flavonoids, phenolic acids, and miscellaneous. In vivo data from the animal model supported the high efficiency of M. paniculata stems as promising extract for lead candidates against MDRAB pulmonary infections. Inhibition of its essential MurF (UDP‐N‐acetylmuramoyl‐tripeptide‐D‐alanyl‐d‐alanine ligase) protein has been reported as a potential target for broad‐spectrum drugs. In silico results after molecular docking to MurF from Acinetobacter baumannii (PDB ID: 4QF5) showed competitive binding mode to ATP ligand at the active site predicting antibacterial activity of the tested compounds. Furthermore, chlorogenic acid, caffeic acid, sinapic acid, feruloyl agmatine, and mahanimbidine were detected as the key discriminatory metabolites correlated with antibacterial activity. To our knowledge, this is the first in vivo anti‐MDRAB study for the investigated plant. Murraya plants have enormous possibility for the discovery of novel bioactive compounds which could combat against resistant microorganisms. [ABSTRACT FROM AUTHOR]

Background: Specialised anti-herbivory metabolites are abundant in the solanaceous genus Nicotiana. These metabolites include the large family of 17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs). Many HGL-DTGs occur exclusively within the Nicotiana genus, but information from the molecular model species N. tabacum, N. benthamiana, and the tree tobacco N. glauca is limited. Objectives: We studied HGL-DTG occurrence and complexity in these species with the aim of providing in-depth reference annotations and comprehensive HGL-DTG inventories. Methods: We analysed polar metabolite extracts in comparison to the previously investigated wild reference species N. attenuata using positive ESI(+) and negative ESI(-) mode electrospray ionisation LC-MS and MS/MS. Results: We provide annotations of 66 HGL-DTGs with in-source and MS/MS fragmentation spectra for selected HGL-DTGs with exemplary fragment interpretations of ESI(+) as well as less studied ESI(-) spectra. We assemble a potential biosynthesis pathway comparing the presence of HGL-DTGs in N. tabacum, N. glauca, and N. benthamiana to N. attenuata. Approximately one-third of HGL-DTGs are chromatographically resolved isomers of hexose, deoxyhexose, or malonate conjugates. The number of isomers is especially high for conjugates with low numbers of deoxyhexose moieties. Conclusions: We extend the number of known HGL-DTGs with a focus on Nicotiana model species and demonstrate that the HGL-DTG family of N. tabacum plants can be surprisingly complex. Our study provides an improved basis with detailed references to previous studies of wild Nicotiana species and enables inference of HGL-DTG pathways with required enzymes for the biosynthesis of this important family of specialised defence metabolites. [ABSTRACT FROM AUTHOR]