Comprehensive leaf size traits dataset for seven plant species from digitised herbarium specimen images covering more than two centuries

Genetic diversity and agro-morphological characterization of cassava varieties provides insight for breeding and crop improvement

The lack of knowledge about genetic variation in cassava is a problem for Fiji's efforts to improve its genetics. Using agro-morphological features, this study aimed to assess the genetic diversity and interrelationships among 33 cassava cultivars. A field investigation was conducted at the Dobuilevu Research Station using a randomized complete block design. Morphological analysis, based on qualitative and quantitative characteristics, divided the germplasm into three groups. In both the qualitative and quantitative trait datasets, two principal components were found to account for 36.31% and 43.45% of the total genetic variance, respectively. Qualitative features, such as branching habit and stem cortex color (r = 0.19), petiole color and root cortex color (r = 0.32), and leaf color and root shape (r = 0.40) were shown to have significant positive correlations. Similarly, quantitative parameters like starch content (r = 0.25) and the number of leaf lobes with yield (r = 0.17) showed significant associations. Based on morphological and genetic similarities, hierarchical clustering grouped the cultivars into three qualitative and five quantitative clusters. While the quantitative traits emphasized variability in yield, starch content, and iron content. The qualitative traits' descriptive statistics revealed diverse phenotypic expressions, with dark green leaf color and cylindrical root form being the most common. These results demonstrate significant genetic variation across cassava cultivars, which can be used for genetic improvement initiatives, germplasm conservation, and short-term varietal release programs. To facilitate the development of more resilient and productive cassava cultivars, targeted breeding efforts aimed at improving yield, quality, and stress tolerance are recommended based on the significant phenotypic and genetic variation observed.

Effects of Drought Stress on Leaf Functional Traits and Biomass Characteristics of Atriplex canescens

Drought is a critical factor constraining plant growth in arid regions. However, the performance and adaptive mechanism of Atriplex canescens (A. canescens) under drought stress remain unclear. Hence, a three-year experiment with three drought gradients was performed in a common garden, and the leaf functional traits, biomass and biomass partitioning patterns of A. canescens were investigated. The results showed that drought stress had significant effects on A. canescens leaf functional traits. A. canescens maintained the content of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD), but the peroxidase (POD) and catalase (CAT) activity decreased, and the content of proline (Pro) and soluble sugar (SS) increased only under heavy drought stress. Under drought stress, the leaves became smaller but denser, the specific leaf area (SLA) decreased, but the dry matter content (LDMC) maintained stability. Total biomass decreased 60% to 1758 g under heavy drought stress and the seed and leaf biomass was only 10% and 20% of non-stress group, but there had no significant difference on root biomass. More biomass was allocated to root under drought stress. The root biomass allocation ratio was doubled from 9.62% to 19.81% under heavy drought, and the root/shoot ratio (R/S) increased from 0.11 to 0.25. The MDA was significantly and negatively correlated with biomass, while the SPAD was significantly and positively correlated with total and aboveground organs biomass. The POD, CAT, Pro and SS had significant correlations with root and seed allocation ratio. The leaf morphological traits related to leaf shape and weight had significant correlations with total and aboveground biomass and biomass allocation. Our study demonstrated that under drought stress, A. canescens made tradeoffs between growth potential and drought tolerance and evolved with a conservative strategy. These findings provide more information for an in-depth understanding of the adaption strategies of A. canescens to drought stress and provide potential guidance for planting and sustainable management of A. canescens in arid and semi-arid regions.

From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2

Premise

Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets.

Methods

LeafMachine2 was trained on 494,766 manually prepared annotations from 5648 herbarium images obtained from 288 institutions and representing 2663 species; it employs a set of plant component detection and segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, and roots. Our landmarking network automatically identifies and measures nine pseudo-landmarks that occur on most broadleaf taxa. Text labels and barcodes are automatically identified by an archival component detector and are prepared for optical character recognition methods or natural language processing algorithms.

Results

LeafMachine2 can extract trait data from at least 245 angiosperm families and calculate pixel-to-metric conversion factors for 26 commonly used ruler types.

Discussion

LeafMachine2 is a highly efficient tool for generating large quantities of plant trait data, even from occluded or overlapping leaves, field images, and non-archival data sets. Our project, along with similar initiatives, has made significant progress in removing the bottleneck in plant trait data acquisition from herbarium specimens and shifted the focus toward the crucial task of data revision and quality control.

Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.

Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae

Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.