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.

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.

HIV and AIDS in the state of Paraná, Brazil, 2007-2022: trends and spatiotemporal distribution.

Objective: The aim of this study was to analyze the spatiotemporal evolution of the incidence rates of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) in the state of Paraná, Brazil.

Methods: An ecological study with an analytical component of time series analysis was conducted in the state of Paraná from 2007 to 2022. The data source was the Notifiable Diseases Information System.

Challenges and Opportunities behind the Use of 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. 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.

Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis.

Introduction: The recent boosting of genomic data in durum wheat ( subsp. ) offers the opportunity to better understand the effects of breeding on the genetic structures that regulate the expression of traits of agronomic interest. Furthermore, the identification of DNA markers useful for marker-assisted selection could also improve the reliability of technical protocols used for variety protection and registration.

Phenotypic evolution in durum wheat ( Desf.) based on SNPs, morphological traits, UPOV descriptors and kernel-related traits.

Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors.

Thermal desorption direct analysis in real-time high-resolution mass spectrometry and machine learning allow the rapid authentication of ground black pepper and dried oregano: A proof-of-concept study.

Thermal desorption direct analysis in real-time high-resolution mass spectrometry (TD-DART-HRMS) approaches have gained popularity for fast screening of a variety of samples. With rapid volatilization of the sample at increasing temperatures outside the mass spectrometer, this technique can provide a direct readout of the sample content with no sample preparation. In this study, TD-DART-HRMS's utility for establishing spice authenticity was examined.

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.

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.

Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Chickpea.

Here we present the approach used to develop the INCREASE "Intelligent Chickpea" Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single-seed-descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed-increase purposes.

The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems.

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.

Characterization of Nutritional Quality Traits of a Common Bean Germplasm Collection.

Food legumes are at the crossroads of many societal challenges that involve agriculture, such as climate change and food sustainability and security. In this context, pulses have a crucial role in the development of plant-based diets, as they represent a very good source of nutritional components and improve soil fertility, such as by nitrogen fixation through symbiosis with rhizobia. The main contribution to promotion of food legumes in agroecosystems will come from plant breeding, which is guaranteed by the availability of well-characterized genetic resources.

Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Common Bean.

The optimal use of legume genetic resources represents a key prerequisite for coping with current agriculture-related societal challenges, including conservation of agrobiodiversity, agricultural sustainability, food security, and human health. Among legumes, the common bean (Phaseolus vulgaris) is the most economically important for human consumption, and its evolutionary trajectories as a species have been crucial to determining the structure and level of its present and available genetic diversity. Genomic advances are considerably enhancing the characterization and assessment of important genetic variants.

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections.

The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein.

Comparative Analysis Based on Transcriptomics and Metabolomics Data Reveal Differences between Emmer and Durum Wheat in Response to Nitrogen Starvation.

Mounting evidence indicates the key role of nitrogen (N) on diverse processes in plant, including development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies: emmer and durum wheat. We found that durum wheat exhibits broader and stronger response in comparison to emmer as seen from the expression pattern of both genes and metabolites and gene enrichment analysis.

Pod indehiscence in common bean is associated with the fine regulation of PvMYB26.

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.

Evaluation of Occupational Exposure to Perchlorethylene in a Group of Italian Dry Cleaners Using Noninvasive Exposure Indices.

Recent data suggest a general trend in decreased occupational exposure to perchlorethylene (PCE) in the dry-cleaning sector. The aims of this study were to confirm this trend to lower exposure levels in a group of Italian dry cleaners and to evaluate the current occupational PCE exposure in these works using noninvasive biological indices. Environmental exposure was assessed by personal sampling in 60 operators working in 21 dry cleaning shops in North Italy.

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

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.

Convergent Evolution of the Seed Shattering Trait.

Loss of seed shattering is a key trait in crop domestication, particularly for grain crops. For wild plants, seed shattering is a crucial mechanism to achieve greater fitness, although in the agricultural context, this mechanism reduces harvesting efficiency, especially under dry conditions. Loss of seed shattering was acquired independently in different monocotyledon and dicotyledon crop species by 'convergent phenotypic evolution', leading to similar low dehiscent and indehiscent phenotypes.

Genomic dissection of pod shattering in common bean: mutations at non-orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species.

The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of 'pod shattering' in Phaseolus vulgaris is achieved here using a population of introgression lines and next-generation sequencing techniques.

Molecular Genotyping (SSR) and Agronomic Phenotyping for Utilization of Durum Wheat ( Desf.) Ex Situ Collection from Southern Italy: A Combined Approach Including Pedigreed Varieties.

In South Italy durum wheat ( Desf.) has a long-time tradition of growing and breeding. Accessions collected and now preserved ex situ are a valuable genetic resource, but their effective use in agriculture and breeding programs remains very low.