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.

Implementation of theoretical non-photochemical quenching (NPQ) 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) was introduced for rapid estimation, which could be suitable for High-throughput Phenotyping.

High-Throughput Spike Detection in Greenhouse Cultivated Grain Crops with Attention Mechanisms-Based Deep Learning Models.

Detection of spikes is the first important step toward image-based quantitative assessment of crop yield. However, spikes of grain plants occupy only a tiny fraction of the image area and often emerge in the middle of the mass of plant leaves that exhibit similar colors to spike regions. Consequently, accurate detection of grain spikes renders, in general, a non-trivial task even for advanced, state-of-the-art deep neural networks (DNNs).

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.

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.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions.

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation.

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.

SWEET11b transports both sugar and cytokinin in developing barley grains.

Even though Sugars Will Eventually be Exported Transporters (SWEETs) have been found in every sequenced plant genome, a comprehensive understanding of their functionality is lacking. In this study, we focused on the SWEET family of barley (Hordeum vulgare). A radiotracer assay revealed that expressing HvSWEET11b in African clawed frog (Xenopus laevis) oocytes facilitated the bidirectional transfer of not only just sucrose and glucose, but also cytokinin.

Dissection of a grain yield QTL from wild emmer wheat reveals sub-intervals associated with culm length and kernel number.

Genetic diversity in wheat has been depleted due to domestication and modern breeding. Wild relatives are a valuable source for improving drought tolerance in domesticated wheat. A QTL region on chromosome 2BS of wild emmer wheat ( ssp.

Precision phenotyping across the life cycle to validate and decipher drought-adaptive QTLs of wild emmer wheat ( ssp. ) introduced into elite wheat varieties.

Drought events or the combination of drought and heat conditions are expected to become more frequent due to global warming, and wheat yields may fall below their long-term average. One way to increase climate-resilience of modern high-yielding varieties is by their genetic improvement with beneficial alleles from crop wild relatives. In the present study, the effect of two beneficial QTLs introgressed from wild emmer wheat and incorporated in the three wheat varieties BarNir, Zahir and Uzan was studied under well-watered conditions and under drought stress using non-destructive High-throughput Phenotyping (HTP) throughout the life cycle in a single pot-experiment.

Deep Learning Based Greenhouse Image Segmentation and Shoot Phenotyping (DeepShoot).

Background: Automated analysis of large image data is highly demanded in high-throughput plant phenotyping. Due to large variability in optical plant appearance and experimental setups, advanced machine and deep learning techniques are required for automated detection and segmentation of plant structures in complex optical scenes.

Methods: Here, we present a GUI-based software tool (DeepShoot) for efficient, fully automated segmentation and quantitative analysis of greenhouse-grown shoots which is based on pre-trained U-net deep learning models of arabidopsis, maize, and wheat plant appearance in different rotational side- and top-views.

Comparative Molecular and Metabolic Profiling of Two Contrasting Wheat Cultivars under Drought Stress.

Drought is one of the most important threats to plants and agriculture; therefore, understanding of the mechanisms of drought tolerance is crucial for breeding of new tolerant varieties. Here, we assessed the effects of a long-term water deficit stress simulated on a precision phenotyping system on some morphological criteria and metabolite traits, as well as the expression of drought associated transcriptional factors of two contrasting drought-responsive African wheat cultivars, Condor and Wadielniel. The current study showed that under drought stress Wadielniel exhibits significant higher tillering and height compared to Condor.

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm.

Wheat ( sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult.

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.

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

Well-characterized genetic resources are fundamental to maintain and provide the various genotypes for pre-breeding programs for the production of new cultivars (e.g., wild relatives, unimproved material, landraces).

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.

A two-step registration-classification approach to automated segmentation of multimodal images for high-throughput greenhouse plant phenotyping.

Background: Automated segmentation of large amount of image data is one of the major bottlenecks in high-throughput plant phenotyping. Dynamic optical appearance of developing plants, inhomogeneous scene illumination, shadows and reflections in plant and background regions complicate automated segmentation of unimodal plant images. To overcome the problem of ambiguous color information in unimodal data, images of different modalities can be combined to a virtual multispectral cube.

Automated Spike Detection in Diverse European Wheat Plants Using Textural Features and the Frangi Filter in 2D Greenhouse Images.

Spike is one of the crop yield organs in wheat plants. Determination of the phenological stages, including heading time point (HTP), and area of spike from non-invasive phenotyping images provides the necessary information for the inference of growth-related traits. The algorithm previously developed by Qiongyan et al.

Adjustment of photosynthetic activity to drought and fluctuating light in wheat.

Drought is a major cause of losses in crop yield. Under field conditions, plants exposed to drought are usually also experiencing rapid changes in light intensity. Accordingly, plants need to acclimate to both, drought and light stress.

Comparison of feature point detectors for multimodal image registration in plant phenotyping.

With the introduction of multi-camera systems in modern plant phenotyping new opportunities for combined multimodal image analysis emerge. Visible light (VIS), fluorescence (FLU) and near-infrared images enable scientists to study different plant traits based on optical appearance, biochemical composition and nutrition status. A straightforward analysis of high-throughput image data is hampered by a number of natural and technical factors including large variability of plant appearance, inhomogeneous illumination, shadows and reflections in the background regions.

Comparison and extension of three methods for automated registration of multimodal plant images.

With the introduction of high-throughput multisensory imaging platforms, the automatization of multimodal image analysis has become the focus of quantitative plant research. Due to a number of natural and technical reasons (e.g.