Breeding crops for high yield and superior adaptability to new and variable climates is imperative to ensure continued food security, biomass production, and ecosystem services. Advances in genomics ...and phenomics are delivering insights into the complex biological mechanisms that underlie plant functions in response to environmental perturbations. However, linking genotype to phenotype remains a huge challenge and is hampering the optimal application of high-throughput genomics and phenomics to advanced breeding. Critical to success is the need to assimilate large amounts of data into biologically meaningful interpretations. Here, we present the current state of genomics and field phenomics, explore emerging approaches and challenges for multiomics big data integration by means of next-generation (Next-Gen) artificial intelligence (AI), and propose a workable path to improvement.
The integration of genomics and phenomics will speed the development of climate resilient crops; however, these omics technologies are generating large, heterogeneous, and complex data much faster than currently can be analyzed.First-generation AI is being used in surveying and classifying omics data; however, it is designed to solve well-defined tasks of single-omics datasets that do not require integration of data across multiple modalities.Next-generation AI can change the dynamics of how experiments are planned, thus enabling better data integration, analysis, and interpretation.There is a critical need to develop means by which to open the black boxes prevalent in many current AI approaches so that they can be interpreted meaningfully from a complex biological perspective. AI decisions and outputs can be explained by breeders and researchers via human–computer interaction.
Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, ...breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby
L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F
partially inbred population (termed here 'POP6'), whose F
was obtained from an intraspecific
controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature (
) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype variability under drought stress conditions.
derived from aerial thermal imagery presented a good correlation with ground-truth stomatal conductance (
) in both segmentation techniques. Interestingly, the HTFP approach was instrumental to detect drought-tolerant response in 25% of the population. This study shows the potential of UAV-based thermal imaging for field phenomics of poplar and other tree species. This is anticipated to have tremendous implications for accelerating forest tree genetic improvement against abiotic stress.
Megafauna (terrestrial vertebrate herbivores > 5 kg) can have disproportionate direct and indirect effects on forest structure, function, and biogeochemical cycles. We reviewed the literature ...investigating these effects on tropical forest dynamics and biogeochemical cycles in relation to ecology, paleoecology, and vegetation modelling. We highlight the limitations of field‐based studies in evaluating the long‐term consequences of loss of megafauna. These limitations are due to inherent space‐time restrictions of field‐studies and a research focus on seed dispersal services provided by large animals. We further present evidence of a research gap concerning the role of megafauna in carbon cycling in tropical ecosystems. Specifically, changes in aboveground biomass might not be noticeable in short‐term studies because of slow vegetation dynamics requiring decades to respond to disturbance (i.e. defaunation). Nutrient cycling has received even less attention in relation to the role of megafauna in tropical forests. We present an approach to investigate the effects of megafauna from new perspectives and with various tools (notably, vegetation models), which can simulate long‐term dynamics in different environmental and megafauna density scenarios. Vegetation models could facilitate interaction between plant–animal ecology and biogeochemistry research. We present practical examples on how to integrate plant–animal interactions in vegetation models to further our understanding of the role of large herbivores in tropical forests.
To evaluate the phytoremediation capability of some poplar and willow clones a hydroponic screening for cadmium tolerance, accumulation and translocation was performed. Rooted cuttings were exposed ...for 3 weeks to 50 μM cadmium sulphate in a growth chamber and morpho-physiological parameters and cadmium content distribution in various parts of the plant were evaluated. Total leaf area and root characteristics in clones and species were affected by cadmium treatment in different ways. Poplar clones showed a remarkable variability whereas willow clones were observed to be more homogeneous in cadmium accumulation and distribution. This behaviour was further confirmed by the calculation of the bio-concentration factor (BCF) and the translocation factor (T
f
). Mean values of all the clones of the two Salicaceae species showed that willows had a far greater ability to tolerate cadmium than poplars, as indicated by the tolerance index (T
i
), calculated on the dry weight of roots and shoots of plants. As far as the mean values of T
f
was concerned, the capacity of willows to translocate was double that of poplars. On the contrary, the mean values of total BCF in poplar clones was far higher with respect to those in willows. The implications of these results in the selection of Salicaceae clones for phytoremediation purposes were discussed.
•Large trees are more prone to bear TreMs and hence considered habitat trees.•The richness of TreMs does not increase in tall trees.•Tree species composition impacts on TreMs occurrence and ...richness.•Combined-objective forestry ensures high level of TreMs occurrence in mature forests.•Close-to-nature forestry enhances TreMs richness.
Mediterranean forests are important sources of income for society and represent biodiversity hotspots, characterized by a mosaic of forest structures, from short-rotation even-aged stands to old-growth forests. However, such increased complexity requires forest management to balance timber production with biodiversity conservation at various spatial scales. This study investigated the impacts of forest structures and management alternatives on the occurrence and richness of Tree-related Microhabitats (TreMs) – as proxies for forest biodiversity – in three Mediterranean forests in Italy. The generalized linear mixed model was applied to assess the relationship between a large set of forest structural parameters and the occurrence and richness of TreMs at the tree level, and resulted in an overall model accuracy higher than 80%. The same model was then implemented in hypothetical forest structures, resulting from no management, close-to-nature forestry and combined management system. Results show that at early developmental stages of the stand, no management slightly anticipates the occurrence of TreMs, while in mature forests, the combined forest management system effectively balances forest productivity with biodiversity conservation. The close-to-nature management system is recommended for promoting TreMs richness. Such findings might be used to support sustainable forest management and valorise the multifunctional role of Mediterranean forests.
This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach ...based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier's Scopus database over the period 1980-2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1% (N = 17) during the period 1980-1989 and they reached 3% (N = 69) in the time slice 1990-1994. Since 1995, the number of publications increased exponentially, thus reaching 55% (N = 1,476) during the period 2010-2014. Within the thirty-four years considered, the retrieved publications were published by 88 countries. Among them, Spain was the most productive country, publishing 44% (N = 1,178) of total publications followed by Italy (18%, N = 482) and France (12%, N = 336). These countries also host the ten most productive scientific institutions in terms of number of publications in Mediterranean forest subjects. Forest Ecology and Management and Annals of Forest Science were the most active journals in publishing research in Mediterranean forest. During the period 1980-1994, the research topics were poorly characterized, but they become better defined during the time slice 1995-1999. Since 2000s, the clusters become well defined by research topics. Current status of Mediterranean forest research (20092014) was represented by four clusters, in which different research topics such as biodiversity and conservation, land-use and degradation, climate change effects on ecophysiological responses and soil were identified. Basic research in Mediterranean forest ecosystems is mainly conducted by ecophysiological research. Applied research was mainly represented by land-use and degradation, biodiversity and conservation and fire research topics. The citation analyses revealed highly cited terms in the Mediterranean forest research as they were represented by fire, biodiversity, carbon sequestration, climate change and global warming. Finally, our analysis also revealed the multidisciplinary role of climate change research. This study provides a first holistic view of the Mediterranean forest research that could be useful for researchers and policy makers as they may evaluate and analyze its historical evolution, as well as its structure and scientific production. We concluded that Mediterranean forest research represents an active scientific field.
In light of impending water and arable land shortages, population growth and climate change, it is more important than ever to examine how forest tree domestication can be accelerated to sustainably ...meet future demands for wood, biomass, paper, fuel and biomaterials. Because of long breeding cycles, tree domestication cannot be rapidly achieved through traditional genetic improvement methods alone. Integrating modern genetic and genomic techniques with conventional breeding will expedite tree domestication. Breeders will only embrace these technologies if they are cost-effective and readily accessible, and forest landowners will only adopt end-products that meet with regulatory approval and public acceptance. All parties involved must work together to achieve these objectives for the benefit of society.
A Landsat time series has been recognized as a viable source of information for monitoring and assessing forest disturbances and for continuous reporting on forest dynamics. This study focused on ...developing automated procedures for detecting disturbances in Mediterranean coppice forests which are characterized by rapid regrowth after a cut. Specifically, new methods specific to Mediterranean coppice forests are needed for mapping clearcut disturbances over time and for estimating related indicators in the context of Sustainable Forest Management and Biodiversity International monitoring frameworks. The aim of this work was to develop a new change detection algorithm for mapping clearcut disturbances in Mediterranean coppice forests with Landsat time series (LTS) using a short time window. Accuracy for the new algorithm, characterized as the Two Thresholds Method (TTM), was evaluated using an independent clearcut reference dataset over a temporal period of the 13 years between 2001 and 2013. TTM was also evaluated against two benchmark approaches: (i) LandTrendr, and (ii) the forest loss category of the Global Forest Change Map. Overall Accuracy for LandTrendr and TTM were greater than 0.94. Meanwhile, smaller accuracies were always obtained for the GFC. In particular, Producer’s Accuracy ranged between 0.45 and 0.84 for TTM and between 0.49 and 0.83 for LT, while for the GFC, PA ranged between 0 and 0.38. User’s Accuracy ranged between 0.86 and 0.96 for TTM and between 0.73 and 0.91 for LT, while for the GFC UA ranged between 0.19 and 1.00. Moreover, to illustrate the utility of TTM for mapping clearcut disturbances in Mediterranean coppice forests, we applied TTM to a Landsat scene that covered almost the entirety of the Tuscany region in Italy.
To combat global deforestation, monitoring forest disturbances at sub-annual scales is a key challenge. For this purpose, the new Planetscope nano-satellite constellation is a game changer, with ...a revisit time of 1 day and a pixel size of 3-m.
We present a near-real time forest disturbance alert system based on PlanetScope imagery: the Thresholding Rewards and Penances algorithm (TRP). It produces a new forest change map as soon as a new PlanetScope image is acquired.
To calibrate and validate TRP, a reference set was constructed as a complete census of five randomly selected study areas in Tuscany, Italy. We processed 572 PlanetScope images acquired between 1 May 2018 and 5 July 2019.
TRP was used to construct forest change maps during the study period for which the final user's accuracy was 86% and the final producer's accuracy was 92%. In addition, we estimated the forest change area using an unbiased stratified estimator that can be used with a small sample of reference data. The 95% confidence interval for the sample-based estimate of 56.89 ha included the census-based area estimate of 56.19 ha.
Three different formulations of bio-based polyurethane (PU), varying the weight ratio between Organosolv lignin and a commercial isocyanate, were synthesized. The coating formulations were ...characterized by SEM, pyrolysis-GC/MS, FTIR spectroscopy and FTIR mapping, which confirmed the successful formation of urethane bonds between commercial isocyanate and hydroxyl groups deriving from lignin. The coatings were applied on beech wood samples to measure color and contact angles, and eventually FTIR mapping of the coated wood samples was performed. FTIR mapping is an interesting tool to monitor the distribution of PU chemical bonds on the coating surface and to evaluate the homogeneity of the applied coating films. Increasing the lignin content of the PU coatings results in more red-yellow and darker tones, while the commercial PU coating is transparent. For a higher lignin concentration, the solid content as well as the weight gain of the applied coatings increase. A higher percentage of lignin in the prepared PU formulations leads to superficial cracks and therefore higher coating permeability compared to the commercial PU, but the prepared lignin-based PU coating still makes a raw wood surface significantly more hydrophobic. Apparently, additives such as film-formers with low surface tension to counteract cracks' formation are necessary to improve the performance of lignin-based PU coatings.
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