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.

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.

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.

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. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterization of chickpea seeds for seed-trait descriptors Basic Protocol 2: Characterization of chickpea lines for plant-trait descriptors specific for primary seed increase.