Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes for direct human consumption. Currently, 60% of its production is estimated to be at risk due to drought. However, the genetic basis of common bean's drought resistance is poorly understood. To this end, we assessed the genetic architecture of drought-responsive changes in a whole genome-sequenced population of 218 common bean accessions. Using multi-omics-based trait evaluation, including lipidomics, photosynthetic and agronomic traits, followed by multi-omics genome-wide association studies (moGWAS), yielded in the detection of a myriad of moQTL for photosynthesis and yield, as well as the levels of various lipids. QTL associated with glycolipids, which are integral to photosynthesis, since they constitute the major membrane components of chloroplasts, were identified. In addition, we molecularly validated several lipid-related candidate genes via P. vulgaris hairy root transformation as well as transient expression in tobacco. In particular, a lipoxygenase and an allene oxide synthase were identified as explaining the variation in triacylglycerol by oxylipin production. These data provide a blueprint for multi-omics-assisted improvement of crop water stress resilience. ### Competing Interest Statement The authors have declared no competing interest.

Phaseolus vulgaris (common bean) is one of the most economically important members of the Fabaceae family and a crop of high nutritional value. Seed and leaf morphological traits are key determinants of yield, shaped by genetic and environmental factors. In this study, we characterized a diversity panel of 434 P. vulgaris accessions for morphological and colorimetric traits. Using genome-wide association studies based on both single-nucleotide polymorphisms and structural variants, we identified 73 high-confidence quantitative trait locus (QTL). In total, we present 114 candidate genes within 25 quantitative trait loci linked to seed and leaf morphology and color, including an OVATE Family Protein 5 (PvOFP5), which was functionally validated as a key regulator of seed size in common bean. We employed a heterologous approach by overexpressing the inferior (Mesoamerican) and superior (Andean) alleles of PvOFP5 in Arabidopsis thaliana wild-type and knockout lines, and confirmed the key role of PvOFP5 in determining seed area. This work provides a comprehensive atlas of genetic associations for bean morphology and color, and highlights PvOFP5 as a promising target for marker-assisted breeding aimed at optimizing seed size.

Cereal-legume intercropping is a cornerstone of agroecological systems because interactions between species can enhance agroecosystem resilience. Yet, the mechanisms underlying these interactions remain poorly understood. To address this gap, we investigated the maize-bean association under low-input conditions. We conducted a two-year intercropping experiment with 200 climbing bean lines grown alongside three maize landraces in France and Romania. We evaluated bean phenotypic responses above- and below-ground to 3 maize landraces, treated as distinct biotic environments (E). Direct and indirect genetic effects were assessed by mapping bean and maize phenotypic traits onto the bean genome (G), with G-by-E interactions tested using contrasts among maize landraces. Competitive interactions dominated, maize acting as the stronger competitor. Maize landraces created distinct biotic environments affecting bean traits. Best-performing partners varied across experimental fields, with no evidence of bean local adaptation. The most productive and balanced mixtures were obtained with the traditionally intercropped maize landrace. Genome-wide association analyses identified loci underlying direct and indirect genetic effects, including candidate genes associated with neighbor perception. These findings reveal the genetic complexity of maize-bean interactions and highlight competitive tolerance in bean and reduced aggressiveness in maize as key traits for improving cereal-legume intercrop performance.

The common bean (Phaseolus vulgaris L.) is a major food legume and an important plant genetic resource for sustainable agriculture. Effective use of this diversity requires integrated evaluation of phenotypic variation and agronomic performance, with preliminary assessments of line performance across seasons. In this study, phenotypic diversity was evaluated in a subsample of the INCREASE R-core collection, a large and well-defined core set of common-bean SSD lines derived from heterogeneous germplasm lines. A total of 507 lines were characterized using 57 agro-morphological traits. Multivariate analyses revealed wide phenotypic diversity structured mainly by growth habit, phenology, and yield-related traits, with clear differentiation among lines. Mixed-data clustering identified cluster 4 as the main phenotypic group associated with higher seed- and yield-related performance and composed predominantly of indeterminate climbing landraces. Multi-trait selection indices generally ranked lines from this group highest, while early, small-seeded types tended to show lower overall performance. Evaluation of a selected subset of 19 lines across two growing seasons revealed marked year-to-year variation in yield performance, indicating contrasting responses among otherwise high-performing lines. The multi-trait genotype-ideotype distance index further distinguished lines with balanced performance across traits and years. Overall, this study shows that large-scale phenotypic characterization combined with multi-trait evaluation can provide a useful exploratory basis for identifying breeding-relevant ideotypes and promising lines for further validation for common-bean improvement.

Crops based on mixtures of species or genotypes support yield stability by pro-viding multiple ecosystem services. However, the genetic, molecular, and evolu-tionary dynamics underlying co-adaptation within such mixtures must be understood to optimize beneficial plant-plant interactions. We therefore propose agroecological genomics as an integrated quantitative and population genetics approach that can be combined with cutting-edge omics methods and participa-tory science. This strategy embraces the heterogeneity of agroecosystems de-rived from interactions between biotic and physical environmental components such as climate, crop management, and socio-cultural factors by exploiting decentralized research. The integration of such results will reveal the whole-genome patterns of co-adaptation in crop mixtures, leading to greater knowledge of the key traits that drive adaptation as well as to the development of innovative tools for mixed-crop breeding.

Common yew (Taxus baccata L.) is a long-living European species, with significant ecological importance. Climate change and severe droughts threaten its growth, emphasizing the need for preserving genetic diversity. By combining dendroecology and genetics, we aimed to identify groups of trees most resilient to changing climatic conditions. We analysed radial growth trends from 1951 to 2018 in three populations located in two mountain areas of central Italy with different rainfall regimes. From 298 selected yew trees, needles were collected for DNA extraction, and tree-ring cores were obtained for dendrochronological analysis. We assessed the relationship between tree growth and drought using the Standardized Precipitation Evapotranspiration Index (SPEI). The studied populations clustered in two distinct genetic groups, corresponding to the driest and wettest areas. At the rainiest site, in the period 1951-2018 yew growth was less constrained by evapotranspiration rates than at the driest area, but climate-growth analysis on moving windows indicates an increasing impact of drought. Growth recovery time after the 2003 drought was longer in individuals at the rainiest area compared to the more xeric sites. The yew trees of the driest area, which were further subdivided in two genetically distinct but spatially intermingled sub-groups, appeared to be better adapted to drought events and therefore more suitable for future warmer scenarios. This study highlights the climate sensitivity of common yew, showing that summer droughts can limit growth, and suggests the advantages of using a dendrogenetic approach to delve deeper into ecophysiological responses to be exploited for reforestation and conservation efforts.

Lentil ( Lens culinaris Medik) is a globally important grain legume valued for its high protein content and nutritional quality. However, the genetic and environmental factors influencing protein and amino acid composition, particularly the role of genotype × environment interaction (GEI), remain partially uncovered. This study evaluated 15 diverse lentil genotypes across seven agronomic trials spanning multiple years, sowing seasons, and locations to assess the effects of genotype, environment, and GEI on crude protein (CP), crude protein yield (CPY), total amino acids (TAA), and total amino acid yield (TAAY). Advanced statistical models such as AMMI, GGE, and WAASB were employed to dissect the contributions of genetic and environmental components and to identify stable, high-performing genotypes. Results revealed significant phenotypic variation for CP, Amino Acids (AA), and TAA among genotypes. Seasonal variation, especially between autumn and spring sowings, was the primary environmental driver of GEI for both CP and CPY. Notably, some landraces (PI\_431710\_LSP, PI\_431739\_LSP, PI\_431753\_LSP, IG_1959) demonstrated both high productivity and stability across environments, while others excelled in specific mega-environments identified through GGE analysis. Our findings emphasize the importance of integrating into lentil breeding programs, stability and adaptability, and a more comprehensive approach to measure the yield (e.g., CPY, MegaJoule, ammino acid composition and TAAY), which takes into account the quality and the effective energetic production of a crop. From this perspective, we highlight landraces as valuable sources of genetic diversity for improving yield. This work provides a foundation for targeted breeding strategies aimed at developing lentil varieties with enhanced protein content, balanced amino acid profiles, and resilience to environmental variability ### Competing Interest Statement The authors have declared no competing interest. The research has been partially funded by the National Operational Programme on Research and Innovation (PON “RICERCA E INNOVAZIONE”) 2014-2020 Project “RESO - REsilienza e SOstenibilità delle filiere ortofrutticole e cerealicole per valorizzare i territori”, ARS01_01224 - CUP B34I20000320005.

Lentil cultivation and consumption promote human health and sustainable agriculture, making a significant contribution to the transition toward a plant-based diet. In Europe, lentil yields are still unstable, and the lack of breeding efforts limits the choice of farmers to few varieties. Here, we characterized 46 lentil genotypes, including local cultivars and landraces from diverse geographic origins, in Mediterranean agro-environments for flowering, architectural and production traits in seven field trials, over 3 years (2019-2021), in two localities (central and southern Italy) and during two sowing seasons (autumn and spring). We estimated the genetic merit of each genotype and identified outperforming genotypes for all traits. Indian ILL 11557AGL and Argentinian IL 4605AGL domesticated varieties resulted superior for earliness. Italian landraces and French cultivars achieved the highest values for first pod height, while landraces and breeding materials from Ethiopia, Syria and Iran were the best-yielding. Data from all seven trials were available for 16 genotypes, so we analyzed the genotype, environment and genotype × environment interaction (GEI) to identify specific genotypic adaptations. European cultivars performed well for architectural traits, whereas the best-yielding genotypes were Middle Eastern and Ethiopian landraces. Environmental effect on yield related to sowing season and locality was detected, with an overall higher yield in autumn compared to spring sowing trials and in central rather than southern Italy. By dissecting the GEI structure using additive main effect and multiplicative interaction (AMMI) analysis and Weighted Average of Absolute Scores (WAASB) index, we identified a group of Iranian landraces (PI 431633 AGL and PI 432033 LSP AGL) adapted to both autumn and spring sowing and one Ethiopian landrace (IG 1959 AGL) showing high yield stability across all environmental conditions. These findings provide a foundation to unlock the full potential of lentil cultivation in European and Mediterranean systems by identifying adapted, high-performing genotypes. ### Competing Interest Statement The authors have declared no competing interest.

Grain legumes are important for sustainable agriculture due to their agronomic and nutritional properties. In this study, a rapid, high-throughput, non-destructive seed screening was performed on 835 lines of Phaseolus vulgaris , Lupinus albus and L. mutabilis grown under a sub-alpine climate. The lines were analysed for seed size characteristics (thousand seed weight – TSW, width and length) using a MARVIN analyser and for protein and moisture content using near-infrared transmittance spectroscopy. The results showed a strong correlation between TSW and seed size in all species, while protein content varied inversely with moisture content, especially in the Lupinus species . Regression analysis identified moisture content as a key factor for protein content, which explained up to 86.2% of the variance in L. mutabilis . Principal component analysis showed that trait variation was more strongly influenced by genetic and other environmental factors than by geographical origin. Lines selected based on normalised rank (NR) and weighted trait index (WTI) methods were characterised by balanced trait profiles, such as high TSW and protein content with optimal moisture contents. These results underline the importance of integrating non-destructive screening methods into pre-breeding programs. In this way, breeders can efficiently select legume seeds with superior agronomic and nutritional traits, such as optimal seed size, high protein content and adequate moisture. This approach not only improves the selection process, but also ensures the development of legume varieties that meet both agricultural and nutritional standards.

BACKGROUND:Lupinus albus is a food grain legume recognized for its high levels of seed protein (30-40%) and oil (6-13%), and its adaptability to different climatic and soil conditions. The availability of well-characterized, genetically and phenotypically diverse germplasm will facilitate the development of next-generation L. albus cultivars, encourage biodiversity conservation, and promote the sustainable utilization of this species. RESULTS:We evaluated more than 2000 L. albus accessions based on 35 agro-morphological traits and passport data to establish Intelligent Collections. The Reference-CORE (R-CORE), covering global diversity, exemplified the genotypic variation among accessions differing in biological status (cultivars, breeding/research materials, landraces, and wild relatives). The Training-CORE (T-CORE), a subset of 300 R-CORE accessions, represents the diversity of the entire collection. Principal component analysis showed that the L. albus R-CORE encompasses four phenotypic groups (A1, A2, A3, and B), and that groups A3 and B can be characterized by the main phenotypic traits of pod shattering and seed ornamentation, respectively. The coefficient of total genetic variation differed across morphological traits, phenotypic groups, geographic regions, and according to biological status. CONCLUSIONS:The core collections established in this study will facilitate agricultural research by providing the broad phenotypic data needed for crop improvement programs and by shedding light on the undiscovered biodiversity of L. albus genetic resources. Understanding the variation found in such resources will allow us to develop sustainable tools and technologies that address global challenges such as the provision of healthy and sustainable diets for all and the mitigation of climate change.

The higher adaptation of landraces to local agroclimatic conditions resulting from natural and moderate artificial selection by farmers within specific environments makes them a crucial source of alleles and genotypes for cultivation and breeding programs. Unlike modern cultivars, which have been developed under more intense artificial selective pressures, landraces exhibit a broader genetic base that has been documented in landrace collections for many crops. This review provides an overview of the importance of genetic resource valorisation in legume species, focusing on cultivated species of the Lupinus genus, particularly white lupin (Lupinus albus). On the one hand, legumes, including Lupins, are considered a crucial alternative source of protein within the framework of more sustainable agriculture. On the other hand, they are often neglected species in terms of breeding efforts, despite receiving increasing attention in recent years. Here, we also report on the latest advances in the development of genomic tools, such as the novel pangenome of white lupin and the identification of markers and loci for target adaptation traits, such as tolerance to alkaline soils, which can effectively support the breeding of Lupinus albus, especially for the introgression of desirable alleles from locally adapted varieties.

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.

The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals similar to 234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

Lupinus albus is a food grain legume recognized for its high levels of seed protein (30[ndash]40%) and oil (6[ndash]13%), and its adaptability to different climatic and soil conditions. To develop the next generation of L. albus cultivars, we need access to well-characterized, genetically and phenotypically diverse germplasm. Here we evaluated more than 2000 L. albus accessions with passport data based on 35 agro-morphological traits to develop Intelligent CORE Collections. The reference CORE (R-CORE), representing global diversity, exemplified the genotypic variation of cultivars, breeding/research materials, landraces and wild relatives. A subset of 300 R-CORE accessions was selected as a training CORE (T-CORE), representing the diversity in the entire collection. We divided the L. albus R-CORE into four phenotypic groups (A1, A2, A3 and B) based on principal component analysis, with groups A3 and B distinguished by pod shattering and seed ornamentation, respectively. The coefficient of additive genetic variation differed across morphological traits, phenotypic groups, geographic regions, and according to biological status. These CORE collections will facilitate agricultural research by identifying the genes responsible for desirable traits in crop improvement programs, and by shedding light on the use of orphan genetic resources for origin and domestication studies in L. albus. Understanding the variation in these genetic resources will allow us to develop sustainable tools and technologies that address global challenges such as providing healthy and sustainable diets for all, and contrasting the current climate change crisis. ### Competing Interest Statement The authors have declared no competing interest.

Non-photochemical quenching (NPQ) is a protective mechanism for dissipating excess energy generated during photosynthesis in the form of heat. The accelerated relaxation of the NPQ in fluctuating light can lead to an increase in the yield and dry matter productivity of crops. Since the measurement of NPQ is time-consuming and requires specific light conditions, theoretical NPQ (NPQ(T)) was introduced for rapid estimation, which could be suitable for High-throughput Phenotyping. We investigated the potential of NPQ(T) to be used for testing plant genetic resources of chickpea under drought stress with non-invasive High-throughput Phenotyping complemented with yield traits. Besides a high correlation between the hundred-seed-weight and the Estimated Biovolume, significant differences were observed between the two types of chickpea desi and kabuli for Estimated Biovolume and NPQ(T). Desi was able to maintain the Estimated Biovolume significantly better under drought stress. One reason could be the effective dissipation of excess excitation energy in photosystem II, which can be efficiently measured as NPQ(T). Screening of plant genetic resources for photosynthetic performance could take pre-breeding to a higher level and can be implemented in a variety of studies, such as here with drought stress or under fluctuating light in a High-throughput Phenotyping manner using NPQ(T).

The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions. Nitrogen had a pivotal role in tetraploid wheat domestication and adaptive responses, leading to diverse impacts on gene expression and selection signatures during primary and secondary domestication.

### Competing Interest Statement The authors have declared no competing interest.

In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.

Anthracnose, white mold, powdery mildew, and root rot caused by Colletotrichum lindemuthianum, Scletorinia sclerotiorum, Erysiphe spp., and Pythium ultimum, respectively, are among the most frequent diseases that cause significant production losses worldwide in common bean (Phaseolus vulgaris L.). Reactions against these four fungal diseases were investigated under controlled conditions using a diversity panel of 311 bean lines for snap consumption (Snap bean Panel). The genomic regions involved in these resistance responses were identified based on a genome-wide association study conducted with 16,242 SNP markers. The highest number of resistant lines was observed against the three C. lindemuthianum isolates evaluated: 156 lines were resistant to CL124 isolate, 146 lines resistant to CL18, and 109 lines were resistant to C531 isolate. Two well-known anthracnose resistance clusters were identified, the Co-2 on chromosome Pv11 for isolates CL124 and CL18, and the Co-3 on chromosome Pv04 for isolates CL124 and C531. In addition, other lesser-known regions of anthracnose resistance were identified on chromosomes Pv02, Pv06, Pv08, and Pv10. For the white mold isolate tested, 24 resistant lines were identified and the resistance was localized to three different positions on chromosome Pv08. For the powdery mildew local isolate, only 12 resistant lines were identified, and along with the two previous resistance genes on chromosomes Pv04 and Pv11, a new region on chromosome Pv06 was also identified. For root rot caused by Pythium, 31 resistant lines were identified and two main regions were located on chromosomes Pv04 and Pv05. Relevant information for snap bean breeding programs was provided in this work. A total of 20 lines showed resistant or intermediate responses against four or five isolates, which can be suitable for sustainable farm production and could be used as resistance donors. Potential genes and genomic regions to be considered for targeted improvement were provided, including new or less characterized regions that should be validated in future works. Powdery mildew disease was identified as a potential risk for snap bean production and should be considered a main goal in breeding programs.