Communication in oncology between healthcare providers, patients, the scientific community, and the media: recommendations from the Italian Association of Medical Oncology (AIOM).

AIM: To identify barriers between health and communication in oncology in order to promote the best possible practice. The areas of communication to be focused on are communication directly with the patient, communication within the scientific community, and communication with the media. MATERIAL AND METHODS: A working group including eminent experts from the national mass media, healthcare system, and patients' advocacy has been established on behalf of the Italian Association of Medical Oncology (AIOM), with the aim of developing suitable recommendations for the best communication in oncology. A literature search has been conducted selecting primary studies related to the best practices applied to communication in oncology. Subsequent to having identified the most representative statements, through a consensus conference using the RAND/University of California Los Angeles modified Delphi method, the panel evaluated the relevance of each statement to support useful strategies to develop effective communication between oncologist physicians and patients, communication within the scientific community, and communication with media outlets, including social media. RESULTS: A total of 292 statements have been extracted from 100 articles. Following an evaluation of relevance, it was found that among the 142 statements achieving the highest scores, 30 of these have been considered of particular interest by the panel. CONCLUSIONS: This consensus and the arising document represent an attempt to strengthen the strategic alliance between key figures in communication, identifying high-impact recommendations for the management of communication in oncology with respect to patients, the wider scientific community, and the media.

Adaptive gene loss in the common bean pan-genome during range expansion and domestication.

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 ~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.

Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication.

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.

Implementation of theoretical non-photochemical quenching (NPQ(T)) to investigate NPQ of chickpea under drought stress with High-throughput Phenotyping.

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).

Screening for resistance to four fungal diseases and associated genomic regions in a snap bean diversity panel.

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.

Business continuity plan in the management and operations of hospitals: First experience to certify the PDTA processes with the requirements defined by ISO 22301:2019 in emergency medical services.

BACKGROUND: A business continuity plan (BCP) facilitates the performance of primary functions during emergencies or other situations that can disrupt normal operations. If risk management is done analytically, a business impact analysis (BIA), according to ISO 22301 certification, makes it possible to define the best strategy for supporting the company's assets and image, optimizing the operational efficiency of service recovery and redesigning spaces for health. Since 2015, our healthcare company has embarked on a certification process for all sectors and activities through the implementation and development of diagnostic and therapeutic paths for operational diagnos-tic-therapeutic-assistance pathways (PDTAs). PDTA processes are all certified by the ISO 9001:2015 management system hospital. Our hospital is the first healthcare company to have obtained ISO 22301:2019 certification concerning PDTA processes, offering patients the highest standards of quality and safety of care in emergency medical services. METHODS: The formal BCP process includes several steps prior to the creation of a BCP: create a BCP team, conduct a BIA, determine the continuity plan by using the results of the analyses, and conduct training and exercises to educate staff and improve the BCP. RESULTS: From the BIA analysis, the team identified the time-employee PDTAs in company paths under emergency and urgency: acute ST-elevation myocardial infarction (STEMI), TRAUMA, and STROKE, providing for a planning path that took advantage of the duration of approximately 12 months. This path included the creation of structural procedures, the redefinition and updating of the PDTA in the light of the BCP, the preparation of exercises aimed at guaranteeing the business continuity objectives, and, finally, the awareness of our stakeholders regarding its correct application. CONCLUSIONS: With a business continuity management (BCM) system, companies take preventative measures to ensure they can start operations again quickly in an emergency. An exhaustive BIA in a hospital company reveals the effects when processes fail, how critical each process is for the company, and the amount of time required to get up and running again, thus providing the organization with important information for risk management. The measures for handling risks derived from this analysis are incorporated into a BCM system where the emergency plans are defined, too, so that business operations continue even in the event of an emergency.

Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System.

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.

Genetic control of pod morphological traits and pod edibility in a common bean RIL population.

KEY MESSAGE: QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.

Molecular Tumour Board (MTB): From Standard Therapy to Precision Medicine.

Background: In the metastatic setting, cancer patients may not benefit from standard care regimes and their diseases undergo drug resistance due to tumour cell heterogeneity and genomic landscape complexity. In recent years, there have been several attempts to personalise the diagnostic-therapeutic path and to propose novel strategies based on not only histological test results but also on each patient's clinical history and molecular biology. Profiling molecular tests allows physicians to investigate the single tumour genomic landscape and to promote targeted approaches. The Molecular Tumour Board (MTB) is a multidisciplinary committee dedicated to selecting individualised and targeted therapeutic strategies appropriate for patients suffering from diseases that present resistance to standard care. Materials and Methods: Our MTB settled in "Azienda Ospedaliero Universitaria delle Marche", Ancona (AN), Italy, and includes oncologists, molecular biologists, geneticists, and other specialists. Clinical cases are referred by physicians to the MTB, through the Cancer and Research Centre of the Marche Region (CORM), through a telemedicine platform. Four possible molecular profiles are available: FoundationOne® CDx e FoundationOne®Liquid CDx and two local Next Generation Sequencing (NGS) panels, with 16 DNA genes and 10 RNA genes respectively. The resulting genetic mutations and their analyses are evaluated by all the members of the Board and a report for each patient is provided with medical recommendations. Results: from June 2021 to May 2023, we collected data from 97 referral patients (M: 49, F: 48). The mean age was 60.6 years (range 22-83 years). 90 cases were approved for testing. Only seven patients were not eligible for genomic profiling. In two patients who were eligible, molecular profiling was not performed because a tissue sample was not available. Off-label therapy was recommended for three patients. 5% of cases (5/88) showed addressable driver mutations associated with an existing targeted therapy and were immediately enrolled. Conclusions: MTB presents a powerful tool for offering precise medical goals. Our Department of Clinical Oncology also takes advantage of the important role of multidisciplinary teams, through the establishment of CORM and MTB meetings, within which there is the chance to perform NGS-based analyses. It will be important in the future to implement the use of genomic profiling to improve personalised care and to guide the choice of suitable therapies and more appropriate management of patients.

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies.

Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.

Engaging Precision Phenotyping to Scrutinize Vegetative Drought Tolerance and Recovery in Chickpea Plant Genetic Resources.

Precise and high-throughput phenotyping (HTP) of vegetative drought tolerance in chickpea plant genetic resources (PGR) would enable improved screening for genotypes with low relative loss of biomass formation and reliable physiological performance. It could also provide a basis to further decipher the quantitative trait drought tolerance and recovery and gain a better understanding of the underlying mechanisms. In the context of climate change and novel nutritional trends, legumes and chickpea in particular are becoming increasingly important because of their high protein content and adaptation to low-input conditions. The PGR of legumes represent a valuable source of genetic diversity that can be used for breeding. However, the limited use of germplasm is partly due to a lack of available characterization data. The development of HTP systems offers a perspective for the analysis of dynamic plant traits such as abiotic stress tolerance and can support the identification of suitable genetic resources with a potential breeding value. Sixty chickpea accessions were evaluated on an HTP system under contrasting water regimes to precisely evaluate growth, physiological traits, and recovery under optimal conditions in comparison to drought stress at the vegetative stage. In addition to traits such as Estimated Biovolume (EB), Plant Height (PH), and several color-related traits over more than forty days, photosynthesis was examined by chlorophyll fluorescence measurements on relevant days prior to, during, and after drought stress. With high data quality, a wide phenotypic diversity for adaptation, tolerance, and recovery to drought was recorded in the chickpea PGR panel. In addition to a loss of EB between 72% and 82% after 21 days of drought, photosynthetic capacity decreased by 16-28%. Color-related traits can be used as indicators of different drought stress stages, as they show the progression of stress.

Decreased metabolic diversity in common beans associated with domestication revealed by untargeted metabolomics, information theory, and molecular networking.

The process of crop domestication leads to a dramatic reduction in the gene expression associated with metabolic diversity. Genes involved in specialized metabolism appear to be particularly affected. Although there is ample evidence of these effects at the genetic level, a reduction in diversity at the metabolite level has been taken for granted despite having never been adequately accessed and quantified. Here we leveraged the high coverage of ultra high performance liquid chromatography-high-resolution mass spectrometry based metabolomics to investigate the metabolic diversity in the common bean (Phaseolus vulgaris). Information theory highlights a shift towards lower metabolic diversity and specialization when comparing wild and domesticated bean accessions. Moreover, molecular networking approaches facilitated a broader metabolite annotation than achieved to date, and its integration with gene expression data uncovers a metabolic shift from specialized metabolism towards central metabolism upon domestication of this crop.

A comprehensive metabolomics and lipidomics atlas for the legumes common bean, chickpea, lentil and lupin.

Legumes represent an important component of human and livestock diets; they are rich in macro- and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst several health-promoting and anti-nutritional properties have been associated with grain content, in-depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) and pearl lupin (Lupinus mutabilis), at the tissue level. We were able to detect and quantify over 3400 metabolites covering major nutritional and anti-nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics-assisted crop breeding and facilitate metabolite-based genome-wide association studies to dissect the genetic and biochemical bases of metabolism in legume species.

The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event.

Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.

CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.

High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genome-wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods because of the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR-Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-seq data. The novel depletion method removed ∼40% of reads mapping to repeats, increasing those mapping to single-copy regions by ∼2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of ∼10-fold compared to nondepleted libraries. In the same condition, we were also able to identify ∼12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed because of low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely related species (L. orientalis). Our results showed that CRISPR-Cas9-driven repeat depletion focuses sequencing data on single-copy regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.

Selection and adaptive introgression guided the complex evolutionary history of the European common bean.

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.

Legume byproducts as ingredients for food applications: Preparation, nutrition, bioactivity, and techno-functional properties.

The demand for high-quality alternative food proteins has increased over the last few decades due to nutritional and environmental concerns, leading to the growing consumption of legumes such as common bean, chickpea, lentil, lupin, and pea. However, this has also increased the quantity of non-utilized byproducts (such as seed coats, pods, broken seeds, and wastewaters) that could be exploited as sources of ingredients and bioactive compounds in a circular economy. This review focuses on the incorporation of legume byproducts into foods when they are formulated as flours, protein/fiber or solid/liquid fractions, or biological extracts and uses an analytical approach to identify their nutritional, health-promoting, and techno-functional properties. Correlation-based network analysis of nutritional, technological, and sensory characteristics was used to explore the potential of legume byproducts in food products in a systematic manner. Flour is the most widely used legume-based food ingredient and is present at levels of 2%-30% in bakery products, but purified fractions and extracts should be investigated in more detail. Health beverages and vegan dressings with an extended shelf-life are promising applications thanks to the techno-functional features of legume byproducts (e.g., foaming and emulsifying behaviors) and the presence of polyphenols. A deeper exploration of eco-friendly processing techniques (e.g., fermentation and ohmic treatment) is necessary to improve the techno-functional properties of ingredients and the sensory characteristics of foods in a sustainable manner. The processing of legume byproducts combined with improved legume genetic resources could enhance the nutritional, functional, and technological properties of ingredients to ensure that legume-based foods achieve wider industrial and consumer acceptance.

CRISPR/Cas9-Mediated Enrichment Coupled to Nanopore Sequencing Provides a Valuable Tool for the Precise Reconstruction of Large Genomic Target Regions.

Complete and accurate identification of genetic variants associated with specific phenotypes can be challenging when there is a high level of genomic divergence between individuals in a study and the corresponding reference genome. We have applied the Cas9-mediated enrichment coupled to nanopore sequencing to perform a targeted de novo assembly and accurately reconstruct a genomic region of interest. This approach was used to reconstruct a 250-kbp target region on chromosome 5 of the common bean genome (Phaseolus vulgaris) associated with the shattering phenotype. Comparing a non-shattering cultivar (Midas) with the reference genome revealed many single-nucleotide variants and structural variants in this region. We cut five 50-kbp tiled sub-regions of Midas genomic DNA using Cas9, followed by sequencing on a MinION device and de novo assembly, generating a single contig spanning the whole 250-kbp region. This assembly increased the number of Illumina reads mapping to genes in the region, improving their genotypability for downstream analysis. The Cas9 tiling approach for target enrichment and sequencing is a valuable alternative to whole-genome sequencing for the assembly of ultra-long regions of interest, improving the accuracy of downstream genotype-phenotype association analysis.

The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.).

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

Shift in beneficial interactions during crop evolution.

Plant domestication can be viewed as a form of co-evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here, we ask how this plant-human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on beneficial interactions resulting from three main mechanisms that can be promoted by manipulating genetic diversity in agrosystems: niche partitioning, facilitation, and kin selection. We show that a combination of factors has impacted either directly or indirectly plant-plant interactions during domestication and breeding, with a trend toward reduced benefits arising from niche partitioning and facilitation. Such factors include marked decrease of molecular and functional diversity of crops and other organisms present in the agroecosystem, mass selection, and increased use of chemical inputs. For example, the latter has likely contributed to the relaxation of selection pressures on nutrient-mobilizing traits such as those associated to root exudation and plant nutrient exchanges via microbial partners. In contrast, we show that beneficial interactions arising from kin selection have likely been promoted since the advent of modern breeding. We highlight several issues that need further investigation such as whether crop phenotypic plasticity has evolved and could trigger beneficial interactions in crops, and whether human-mediated selection has impacted cooperation via kin recognition. Finally, we discuss how plant breeding and agricultural practices can help promoting beneficial interactions within and between species in the context of agroecology where the mobilization of diversity and complexity of crop interactions is viewed as a keystone of agroecosystem sustainability.