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Automatic segmentation of stem and leaf components and individual maize plants in field terrestrial LiDAR data using convolutional neural networks
No full textHigh-throughput maize phenotyping at both organ and plant levels plays a key role in molecular breed-ing for increasing crop yields. Although the rapid development of light detection and ranging (LiDAR) pro-vides a new way to characterize three-dimensional (3D) plant structure, there is a need to develop robust algorithms for extracting 3D phenotypic traits from LiDAR data to assist in gene identification and selec-tion. Accurate 3D phenotyping in field environments remains challenging, owing to difficulties in seg-mentation of organs and individual plants in field terrestrial LiDAR data. We describe a two-stage method that combines both convolutional neural networks (CNNs) and morphological characteristics to segment stems and leaves of individual maize plants in field environments. It initially extracts stem points using the PointCNN model and obtains stem instances by fitting 3D cylinders to the points. It then segments the field LiDAR point cloud into individual plants using local point densities and 3D morpho-logical structures of maize plants. The method was tested using 40 samples from field observations and showed high accuracy in the segmentation of both organs (F-score =0.8207) and plants (F -score =0.9909). The effectiveness of terrestrial LiDAR for phenotyping at organ (including leaf area and stem position) and individual plant (including individual height and crown width) levels in field environ-ments was evaluated. The accuracies of derived stem position (position error =0.0141 m), plant height (R2 >0.99), crown width (R2 >0.90), and leaf area (R2 >0.85) allow investigating plant structural and func-tional phenotypes in a high-throughput way. This CNN-based solution overcomes the major challenges in organ-level phenotypic trait extraction associated with the organ segmentation, and potentially con-tributes to studies of plant phenomics and precision agriculture. (c) 2022 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC -ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Trans-Beringial Distribution of Platimeliphyllum (Platanaceae) in the Eocene of Eastern Asia and Western North America
No full textPremise of research. Our concept of the former diversity and geographic spread of Platanaceae continues to expand. Unlobed platanaceous leaves have been poorly known in the fossil record of western North America. New information on the extinct Paleogene genus Platimeliphyllum and its associated reproductive structures is helping to unravel the biogeographic and evolutionary history of Platanaceae.Methodology. We studied leaves of Platimeliphyllum and associated platanaceous inflorescences and infructescences from the Eocene of western North America and northeastern China. Epidermal anatomy was obtained from cuticle fragments macerated in Schultze solution and studied using transmitted light and epifluorescence microscopy. In situ pollen from inflorescences was studied using light microscopy and SEM.Pivotal results. We provide new evidence supporting the platanaceous affinity of Platimeliphyllum and document its occurrence in the Eocene of western North America as well as in eastern Asia. We present the new combinations Platimeliphyllum durhamensis (Wolfe) comb. nov. from Washington and Oregon and Platimeliphyllum fushunensis (Chen) comb. nov. from Fushun, Liaoning Province, northeastern China. This extends the geographic range of a genus previously known mainly from the Paleocene and Eocene of Russia and Kazakhstan. The ovate, unlobed, simple laminae correspond to Platanaceae in their marginal teeth with rounded sinuses, straight secondary veins, agrophic veins, and orthogonal tertiary and quaternary venation. The association of these leaves with platanaceous inflorescences further confirms their affinities with Platanaceae.Conclusions. Platimeliphyllum likely spread between North America and Asia via the Bering Land Bridge in the Paleocene or Eocene. Previous climate estimates of the Fushun flora based on the coexistence approach need reevaluation with the updated taxonomy of the flora. The co-occurrence of Platimeliphyllum with Macginitiea, Platanites, and Platanus indicates that an array of platanaceous lineages coexisted during the Eocene in western North America
Function of pH-dependent transcription factor PacC in regulating development, pathogenicity, and mycotoxin biosynthesis of phytopathogenic fungi
No full textpH, as one of the most important environmental factors, affects various biological processes in pathogenic fungi. Sensing and responding to fluctuations in ambient pH are essential for these fungi to complete their life cycle. Fungi have evolved a complicated and conserved system, the so-called Pal-pH pathway, to regulate genes and adapt to alterations in ambient pH. PacC is the dominant transcription factor in the Pal-pH pathway and regulates various biological processes. The regulatory mode of PacC has been extensively studied in Aspergillus nidulans and is generally conserved in other fungal species, including numerous phytopathogenic fungi. However, species-specific alterations have been reported. This review summarizes recent advances in the regulatory mechanisms of PacC and its role in controlling development, pathogenicity, and mycotoxin biosynthesis in phytopathogenic fungi. Potential applications of these findings and some unresolved questions are also discussed
High-level nitrogen additions accelerate soil respiration reduction over time in a boreal forest
No full textIncreased nitrogen (N) inputs are widely recognised to reduce soil respiration (Rs), but how N deposition affects the temporal dynamics of Rs remains unclear. Using a decade-long fertilisation experiment in a boreal larch forest (Larix gmelini) in northeast China, we found that the effects of N additions on Rs showed a temporal shift from a positive effect in the short-term (increased by 8% on average in the first year) to a negative effect over the longer term (decreased by 21% on average in the 11th year). The rates of decrease in Rs for the higher N levels were almost twice as high as those of the low N level. Our results suggest that the reduction in Rs in response to increased N input is accelerated by high-level N additions, and experimental high N applications are likely to overestimate the contribution of N deposition to soil carbon sequestration in a boreal forest
Plant genome size modulates grassland community responses to multi-nutrient additions
No full textGrassland ecosystems cover c. 40% of global land area and contain c. 40% of soil organic carbon. Understanding the effects of adding nutrients to grasslands is essential because they provide much of our food, support diverse ecosystem services and harbor rich biodiversity. Using the meadow steppe (grassland) study site of Inner Mongolia, we manipulated seven key nutrients and a cocktail of micronutrients to examine their effects on grassland biomass productivity and diversity. The results, explained in structural equation models, link two previously disparate hypotheses in grassland ecology: (1) the light asymmetry competition hypothesis and (2) the genome size-nutrient interaction hypothesis. We show that aboveground net primary productivity increases predominantly from species with large genome sizes with the addition of nitrogen, and nitrogen plus phosphorus. This drives an asymmetric competition for light, causing a decline in species richness mainly in species with small genome sizes. This dynamic is likely to be caused by the nutrient demands of the nucleus and/or the scaling effects of nuclear size on cell size which impact water use efficiency. The model will help inform the best management approaches to reverse the rapid and unprecedented degradation of grasslands globally
First record of Aquilegia grubovii (Ranunculaceae) for Russia and key to all currently known species in the country
No full textWe report the first record of Aquilegia grubovii (Ranunculaceae) for Russia, a rare species previously known from five lo-calities in Mongolia. The species belongs to A. sect. Aquilegia subsect. Aquilegia and is characterized by curved or hooked spurs slightly longer than the limb of petals, 2-2.8 mm long, straight only at the top diverging fruits with stylodia 2 times shorter than follicles, smooth or tuberculate seed surface and stems covered with simple and glandular hairs. The new records of Aquilegia grubovii are located in the Azas Nature Reserve, which is situated in the central part of the Todzha basin, Tuva Republic (a large intermountain trough within the Altai-Sayan mountain region) of south-central Asia about 500 km west of Lake Baikal. We provide an assessment of the conservation status, geographical distribution and habitat of Aquilegia grubovii, along with an identification key to all species from Russia
Notes on Glossadelphus M. Fleisch. (Hypnaceae, Bryophyta) in China
No full textThe genus Glossadelphus has been replaced by Phyllodon. However, Glossadelphus and Phyllodon are still used simultaneously in moss checklist of China. Total of 19 taxa of China published as members of the genus Glossadelphus are examined in this study. Our analyses show that only one species of Phyllodon (P. lingulatus) is recognized in China; twelve taxa of Glossadelphus in China are transferred to other genera (Bryocrumia, Ectropothecium, Entodon, Taxiphyllum); five taxa are excluded from the flora of China, and one species remains uncertain. Among them, two new combinations are proposed, Ectropothecium anomalum comb. nov. and E. falcatulum comb. nov. Myurella brevicosta is newly reduced to a synonym of Bryocrumia vivicolor. Glossadelphus isopterygioides is verified as a synonym of Entodon obtusatus. We newly designate lectotypes for G. anomalus and G. falcatulus. A list of 19 taxa of Glossadelphus of China is provided with their present status
A common whole-genome paleotetraploidization in Cucurbitales
No full textCucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families. The previously identified Cucurbitaceae common paleotetraploidization is shared by Cucurbitales and Begoniaceae
Cereal Endosperms: Development and Storage Product Accumulation
No full textThe persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death
High potential of stable carbon sequestration in phytoliths of China's grasslands
No full textPhytolith carbon (C) sequestration plays a key role in mitigating global climate change at a centennial to millennial time scale. However, previous estimates of phytolith-occluded carbon (PhytOC) storage and potential in China's grasslands have large uncertainties mainly due to multiple data sources. This contributes to the uncertainty in predicting long-term C sequestration in terrestrial ecosystems using Earth System Models. In this study, we carried out an intensive field investigation (79 sites, 237 soil profiles [0-100 cm], and 61 vegetation assessments) to quantify PhytOC storage in China's grasslands and to better explore the biogeographical patterns and influencing factors. Generally, PhytOC production flux and soil PhytOC density in both the Tibetan Plateau and the Inner Mongolian Plateau had a decreasing trend from the Northeast to the Southwest. The aboveground PhytOC production rate in China's grassland was 0.48 x 10(6) t CO2 a(-1), and the soil PhytOC storage was 383 x 10(6) t CO2. About 45% of soil PhytOC was stored in the deep soil layers (50-100 cm), highlighting the importance of deep soil layers for C stock assessments. Importantly, the Tibetan Plateau had the greatest contribution (more than 70%) to the PhytOC storage in China's grasslands. The results of multiple regression analysis indicated that altitude and soil texture significantly influenced the spatial distribution of soil PhytOC, explaining 78.1% of the total variation. Soil phytolith turnover time in China's grasslands was mainly controlled by climatic conditions, with the turnover time on the Tibetan Plateau being significantly longer than that on the Inner Mongolian Plateau. Our results offer more accurate estimates of the potential for phytolith C sequestration from ecological restoration projects in degraded grassland ecosystems. These estimates are essential to parameterizing and validating global C models