ResearchPad - plant-anatomy https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis]]> https://www.researchpad.co/article/elastic_article_13837 In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive considerations of program efficiency and method selection. In order to reduce the complexity of scRNA-seq data analysis, we present scedar, a scalable Python package for scRNA-seq exploratory data analysis. The package provides a convenient and reliable interface for performing visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering on large-scale scRNA-seq datasets. The analytical methods are efficient, and they also do not assume that the data follow certain statistical distributions. The package is extensible and modular, which would facilitate the further development of functionalities for future requirements with the open-source development community. The scedar package is distributed under the terms of the MIT license at https://pypi.org/project/scedar.

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<![CDATA[Imaging dataset of fresh hydrous plants obtained by field-emission scanning electron microscopy conducted using a protective NanoSuit]]> https://www.researchpad.co/article/elastic_article_7644 Although scanning electron microscopy (SEM) can generate high-resolution images of nanosized objects, it requires a high vacuum to do so, which precludes direct observations of living organisms and often produces unwanted structural changes. It has previously been reported that a simple surface modification gives rise to a nanoscale layer, termed the “NanoSuit”, which can keep small animals alive under the high vacuum required for field-emission scanning electron microscopy (FE-SEM). We have previously applied this technique to plants, and successfully observed healthy petals in a fully hydrated state using SEM. The flower petals protected with the NanoSuit appeared intact, although we still lack a fundamental understanding of the images of other plants observed using FE-SEM. This report presents and evaluates a rich set of images, acquired using the NanoSuit, for a taxonomically diverse set of plant species. This dataset of images allows the surface features of various plants to be analyzed and thus provides a further complementary morphological profile. Image data can be accessed and viewed through Figshare (https://doi.org/10.6084/m9.figshare.c.4446026.v1).

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<![CDATA[Uptake and speciation of zinc in edible plants grown in smelter contaminated soils]]> https://www.researchpad.co/article/N21b4cc8f-fdc5-4198-8cfa-2868c1971919

Heavy metal accumulation in edible plants grown in contaminated soils poses a major environmental risk to humans and grazing animals. This study focused on the concentration and speciation of Zn in different edible plants grown in soils contaminated with smelter wastes (Spelter, WV, USA) containing high levels of the metals Zn, Cu, Pb, Cd. Their accumulation was examined in different parts (roots, stem, and leaves) of plants and as a function of growth stage (dry seed, sprouting seed, cotyledon, and leaves) in the root vegetables radish, the leafy vegetable spinach and the legume clover. Although the accumulation of metals varied significantly with plant species, the average metal concentrations were [Zn] > [Pb] > [Cu] > [Cd]. Metal uptake studies were complemented with bulk and micro X-ray absorption spectroscopy (XAS) at Zn K-edge and micro X-ray fluorescence (μXRF) measurements to evaluate the speciation and distribution of Zn in these plant species. Dynamic interplay between the histidine and malate complexation of Zn was observed in all plant species. XRF mapping of spinach leaves at micron spatial resolution demonstrated the accumulation of Zn in vacuoles and leaf tips. Radish root showed accumulation of Zn in root hairs, likely as ZnS nanoparticles. At locations of high Zn concentration in spinach leaves, μXANES suggests Zn complexation with histidine, as opposed to malate in the bulk leaf. These findings shed new light on the dynamic nature of Zn speciation in plants.

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<![CDATA[Identification and expression analysis of miRNAs and elucidation of their role in salt tolerance in rice varieties susceptible and tolerant to salinity]]> https://www.researchpad.co/article/N52f944dc-26d8-4e67-9222-1bf646d955e0

Soil salinization is a serious problem for cultivation of rice, as among cereals rice is the most salt sensitive crop, and more than 40% of the total agricultural land amounting to approximately 80 million ha the world over is salt affected. Salinity affects a plant in a varieties of ways, including ion toxicity, osmotic stress and oxidative damage. Since miRNAs occupy the top place in biochemical events determining a trait, understanding their role in salt tolerance is highly desirable, which may allow introduction of the trait in the rice cultivars of choice through biotechnological interventions. High throughput sequencing of sRNAs in the root and shoot tissues of the seedlings of the control and NaCl treated Pokkali, a salt-tolerant rice variety, identified 75 conserved miRNAs and mapped 200 sRNAs to the rice genome as novel miRNAs. Expression of nine novel miRNAs and two conserved miRNAs were confirmed by Northern blotting. Several of both conserved and novel miRNAs that expressed differentially in root and/or shoot tissues targeted transcription factors like AP2/EREBP domain protein, ARF, NAC, MYB, NF-YA, HD-Zip III, TCP and SBP reported to be involved in salt tolerance or in abiotic stress tolerance in general. Most of the novel miRNAs expressed in the salt tolerant wild rice Oryza coarctata, suggesting conservation of miRNAs in taxonomically related species. One of the novel miRNAs, osa-miR12477, also targeted L-ascorbate oxidase (LAO), indicating build-up of oxidative stress in the plant upon salt treatment, which was confirmed by DAB staining. Thus, salt tolerance might involve miRNA-mediated regulation of 1) cellular abundance of the hormone signaling components like EREBP and ARF, 2) synthesis of abiotic stress related transcription factors, and 3) antioxidative component like LAO for mitigation of oxidative damage. The study clearly indicated importance of osa-miR12477 regulated expression of LAO in salt tolerance in the plant.

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<![CDATA[Production of a rabbit monoclonal antibody for highly sensitive detection of citrus mosaic virus and related viruses]]> https://www.researchpad.co/article/Nfb5e596f-2980-40fa-8fa6-576f474cd99c

Citrus mosaic virus (CiMV) is one of the causal viruses of citrus mosaic disease in satsuma mandarins (Citrus unshiu). Prompt detection of trees infected with citrus mosaic disease is important for preventing the spread of this disease. Although rabbit monoclonal antibodies (mAbs) exhibit high specificity and affinity, their applicability is limited by technical difficulties associated with the hybridoma-based technology used for raising these mAbs. Here, we demonstrate a feasible CiMV detection system using a specific rabbit mAb against CiMV coat protein. A conserved peptide fragment of the small subunit of CiMV coat protein was designed and used to immunize rabbits. Antigen-specific antibody-producing cells were identified by the immunospot array assay on a chip method. After cloning of variable regions in heavy or light chain by RT-PCR from these cells, a gene set of 33 mAbs was constructed and these mAbs were produced using Expi293F cells. Screening with the AlphaScreen system revealed eight mAbs exhibiting strong interaction with the antigen peptide. From subsequent sequence analysis, they were grouped into three mAbs denoted as No. 4, 9, and 20. Surface plasmon resonance analysis demonstrated that the affinity of these mAbs for the antigen peptide ranged from 8.7 × 10−10 to 5.5 × 10−11 M. In addition to CiMV, mAb No. 9 and 20 could detect CiMV-related viruses in leaf extracts by ELISA. Further, mAb No. 20 showed a high sensitivity to CiMV and CiMV-related viruses, simply by dot blot analysis. The anti-CiMV rabbit mAbs obtained in this study are envisioned to be extremely useful for practical applications of CiMV detection, such as in a virus detection kit.

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<![CDATA[Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice]]> https://www.researchpad.co/article/N3fbe67d9-408b-4f07-a6d8-c659dfb628bd

Rice seed germination is a critical step that determines its entire life circle, with seeds failing to germinate or pre-harvest sprouting both reduce grain yield. Nevertheless, the mechanisms underlying this complex biological event remain unclear. Previously, gibberellin has been shown to promote seed germination. In this study, a delayed seed germination rice mutant was obtained through screening of the EMS induced mutants. Besides of delayed germination, it also shows semi-dwarfism phenotype, which could be recovered by exogenous GA. Through re-sequencing on the mutant, wild-type and their F2 populations, we identified two continuous mutated sites on ent-kaurene oxidase 1 (OsKO1) gene, which result in the conversion from Thr to Met in the cytochrome P450 domain. Genetic complementary analysis and enzyme assay verified that the mutations in OsKO1 gene block the biosynthesis of GA and result in the defect phenotypes. Further analyses proved that OsKO1 could catalyze the reaction from ent-kaurene into ent-kaurenoic acid in GA biosynthesis mainly at seed germination and seedling stages, and the mutations decrease its activity to catalyze the step from ent-kaurenol to ent-kaurenoic acid in this reaction. Transcriptomic and proteomic data indicate that the defect on GA biosynthesis decreases its ability to mobilize starch and attenuate ABA signaling, therefore delay the germination process. The results provide some new insights into both GA biosynthesis and seed germination regulatory pathway in rice.

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<![CDATA[Sugar, amino acid and inorganic ion profiling of the honeydew from different hemipteran species feeding on Abies alba and Picea abies]]> https://www.researchpad.co/article/Neb889307-c28f-4dcd-8ba6-6ff5a5f28e34

Several hemipteran species feed on the phloem sap of plants and produce large amounts of honeydew that is collected by bees to produce honeydew honey. Therefore, it is important to know whether it is predominantly the hemipteran species or the host plant to influence the honeydew composition. This is particularly relevant for those botanical and zoological species from which the majority of honeydew honey originates. To investigate this issue, honeydew from two Cinara species located on Abies alba as well as from two Cinara and two Physokermes species located on Picea abies were collected. Phloem exudates of the host plants were also analyzed. Honeydew of all species contained different proportions of hexoses, sucrose, melezitose, erlose, and further di- and trisaccharides, whereas the phloem exudates of the host trees contained no trisaccharides. Moreover, the proportions of sugars differed significantly between hemipteran species feeding on the same tree species. Sucrose hydrolysis and oligosaccharide formation was shown in whole-body homogenates of aphids. The type of the produced oligosaccharides in the aphid-extracts correlated with the oligosaccharide composition in the honeydew of the different aphid species. The total contents of amino acids and inorganic ions in the honeydew were much lower than the sugar content. Glutamine and glutamate were predominant amino acids in the honeydew of all six hemipteran species and also in the phloem exudates of both tree species. Potassium was the dominant inorganic ion in all honeydew samples and also in the phloem exudate. Statistical analyses reveal that the sugar composition of honeydew is determined more by the hemipteran species than by the host plant. Consequently, it can be assumed that the sugar composition of honeydew honey is also more influenced by the hemipteran species than by the host tree.

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<![CDATA[Sap flow of Salix psammophila and its principal influencing factors at different slope positions in the Mu Us desert]]> https://www.researchpad.co/article/N9e08a49c-6957-422b-bc2c-73a7e35a95db

The changes in sap flow of Salix psammophila growing on a gentle slope (lower slope, P1), a middle slope (P2), and an upper slope (P3), and the response of sap flow to meteorological factors at the different slope positions were studied using the continuous and synchronized observations, the instrument were wrapped stem flowmeter EMS 62 sap-flow heat-balance-based system and the LSI-LASTEM automatic weather station. The results revealed that the soil moisture content was the highest and the growth conditions of Salix psammophila were the best at P1, followed by P2. At P3, however, although good apical dominance was observed, the proportion of dead branches was the highest. Furthermore, the daily variation patterns of sap flow on the three slopes presented as multi-peak bell-shaped curves. The daily accumulation changes in sap flow showed a trend of P1 > P3 > P2, and within the same diameter range, the sap flow at P1 was significantly different from that at P2 and P3, whereas the sap flow at P2 and P3 did not vary significantly. All the three slopes showed a significant and positive correlation with photosynthetically active radiation, atmospheric temperature, and vapor pressure difference, and a significant and negative correlation with relative humidity; however, the degrees of correlation varied slightly. The stepwise regression analysis showed that, at different slopes, different variables were selected for different branch diameters, but photosynthetically active radiation and atmospheric temperature played dominant roles on all slopes. This study reveals the sap flow pattern of Salix psammophila on different slopes and its response mechanism to meteorological factors, which was essential for understanding the restoration ability, physiological adaptability, and ecosystem stability of Salix psammophila communities.

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<![CDATA[A δ2H Isoscape of blackberry as an example application for determining the geographic origins of plant materials in New Zealand]]> https://www.researchpad.co/article/Nea2d9f77-f900-4107-8de8-5a146688a563

In this investigation, two previously reported precipitation δ2H isoscapes for New Zealand were used to develop a δ2H isoscape for blackberry (Rubus sp.) leaf. These isoscapes were calibrated using the measured δ2H values of 120 authentic blackberry leaf samples collected from across the country. A regression model based on environmental variables available for New Zealand was also determined to predict δ2H values measured from blackberry leaves without initially modelling the precipitation δ2H values. The three models were compared for their accuracy and precision when assigning 10 samples of blackberry leaves for their geographic location based on their measured δ2H values. One of the models based on a precipitation isoscape was similar in accuracy and precision of assignment to the model determined from the environmental variables and provides an approach for determining valid isoscapes for future plant materials.

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<![CDATA[Using morphological attributes for the fast assessment of nutritional responses of Buddhist pine (Podocarpus macrophyllus [Thunb.] D. Don) seedlings to exponential fertilization]]> https://www.researchpad.co/article/N5094337c-fdbe-414d-8545-a46f7fbb230f

Culturing slowly growing tree seedlings is a potential approach for managing the conflict between the increasing demand for ornamental stock and the decreasing area of farmlands due to urbanization. In this study, Buddhist pine (Podocarpus macrophyllus [Thunb.] D. Don) seedlings were raised in multishelves with light-emitting diode lighting in the spectrum of 17:75:8 (red:green:blue) at 190–320 μmol m-2 s-1 with controlled temperature and relative humidity at 19.5°C and 60%, respectively. Seedlings were fed by exponential fertilization (EF) (nitrogen [N]-phosphorus [P]2O5-K2O, 10-7-9) at eight rates of 0 (control), 20 (E20), 40 (E40), 60 (E60), 80 (E80), 100 (E100), 120 (E120), and 140 (E140) mg N seedling-1 for four months through 16 fertilizer applications. The nutritional responses of Buddhist pine seedlings can be identified and classified into various stages in response to increasing doses, up to and over 120 N seedling-1. Morphological traits, i.e., the green color index and leaf area (LA) obtained by digital analysis and the fine root growth, all remained constant in response to doses that induced steady nutrient loading. LA had a positive relationship with most of the nutritional parameters. A dose range between 60 and 120 mg N seedling-1 was recommended for the culture of Buddhist pine seedlings. At this range of fertilizer doses, measuring the leaf area through digital scanning can easily and rapidly indicate the inherent nutrient status of the seedlings.

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<![CDATA[Plant begomoviruses subvert ubiquitination to suppress plant defenses against insect vectors]]> https://www.researchpad.co/article/5c784ff3d5eed0c4840079a5

Most plant viruses are vectored by insects and the interactions of virus-plant-vector have important ecological and evolutionary implications. Insect vectors often perform better on virus-infected plants. This indirect mutualism between plant viruses and insect vectors promotes the spread of virus and has significant agronomical effects. However, few studies have investigated how plant viruses manipulate plant defenses and promote vector performance. Begomoviruses are a prominent group of plant viruses in tropical and sub-tropical agro-ecosystems and are transmitted by whiteflies. Working with the whitefly Bemisia tabaci, begomoviruses and tobacco, we revealed that C2 protein of begomoviruses lacking DNA satellites was responsible for the suppression of plant defenses against whitefly vectors. We found that infection of plants by tomato yellow leaf curl virus (TYLCV), one of the most devastating begomoviruses worldwide, promoted the survival and reproduction of whitefly vectors. TYLCV C2 protein suppressed plant defenses by interacting with plant ubiquitin. This interaction compromised the degradation of JAZ1 protein, thus inhibiting jasmonic acid defense and the expression of MYC2-regulated terpene synthase genes. We further demonstrated that function of C2 protein among begomoviruses not associated with satellites is well conserved and ubiquitination is an evolutionarily conserved target of begomoviruses for the suppression of plant resistance to whitefly vectors. Taken together, these results demonstrate that ubiquitination inhibition by begomovirus C2 protein might be a general mechanism in begomovirus, whitefly and plant interactions.

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<![CDATA[Valuing and mapping cork and carbon across land use scenarios in a Portuguese montado landscape]]> https://www.researchpad.co/article/5c8accd7d5eed0c484990136

The ecosystem services approach can inform decision-making by accounting for both short- and long-term benefits from different land use options. Here we used the InVEST toolkit to quantify and map key ecosystem services at the largest publicly-owned agro-silvo-pastoral farmstead in Portugal–a site representative for the montado landscape. We analyzed how Provisioning (cork production) and Regulating & Maintenance (carbon storage and sequestration) services would be affected under three land use change scenarios, which were developed in collaboration with the forest manager of the study area: Cattle Intensification, Forest Improvement, and Residential Development. Results show that increasing cattle or residential development would deliver substantially lower levels of services. We find that extensive management, improvements to forest quality, and promotion of traditional livestock grazing would provide the highest levels of assessed ecosystem services, resulting in 13.5% more carbon storage (worth between $0.34-$7.79 million USD depending on carbon price) and 62.7% more cork production (total value of USD $3.5 million) than the current land use. However, a shift in economic incentives to make sustainable cork harvesting and traditional low-density grazing of smaller ruminants like sheep and goats profitable are likely needed to reward traditional land stewardship and help support this iconic Mediterranean landscape in the future.

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<![CDATA[Split green fluorescent protein as a tool to study infection with a plant pathogen, Cauliflower mosaic virus]]> https://www.researchpad.co/article/5c897773d5eed0c4847d2d2c

The split GFP technique is based on the auto-assembly of GFP when two polypeptides–GFP1-10 (residues 1–214; the detector) and GFP11 (residues 215–230; the tag)–both non-fluorescing on their own, associate spontaneously to form a fluorescent molecule. We evaluated this technique for its efficacy in contributing to the characterization of Cauliflower mosaic virus (CaMV) infection. A recombinant CaMV with GFP11 fused to the viral protein P6 (a key player in CaMV infection and major constituent of viral factory inclusions that arise during infection) was constructed and used to inoculate transgenic Arabidopsis thaliana expressing GFP1-10. The mutant virus (CaMV11P6) was infectious, aphid-transmissible and the insertion was stable over many passages. Symptoms on infected plants were delayed and milder. Viral protein accumulation, especially of recombinant 11P6, was greatly decreased, impeding its detection early in infection. Nonetheless, spread of infection from the inoculated leaf to other leaves was followed by whole plant imaging. Infected cells displayed in real time confocal laser scanning microscopy fluorescence in wild type-looking virus factories. Thus, it allowed for the first time to track a CaMV protein in vivo in the context of an authentic infection. 11P6 was immunoprecipitated with anti-GFP nanobodies, presenting a new application for the split GFP system in protein-protein interaction assays and proteomics. Taken together, split GFP can be an attractive alternative to using the entire GFP for protein tagging.

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<![CDATA[Potential role of weather, soil and plant microbial communities in rapid decline of apple trees]]> https://www.researchpad.co/article/5c89776ed5eed0c4847d2c8c

An unusual decline and collapse of young established trees known as “rapid apple decline” (RAD) has become a major concern for apple growers, particularly in the northeastern United States. This decline is characterized by stunted growth, pale yellow to reddish leaves, and tree collapse within weeks after onset of symptoms. We studied declining apple trees to identify potential involvement of abiotic and biotic stresses. We used 16S and ITS to profile bacterial and fungal communities in the soil, rhizosphere, roots, and shoots and tested for the presence of six viruses in scions and rootstocks of symptomatic and asymptomatic trees. The viruses detected were not associated with RAD symptoms. Bacterial and fungal populations were highly variable in plant tissue, soil and rhizosphere samples, with bacteroidetes, firmicutes, proteobacteria, acidobacteria, and actinobacteria the predominant bacterial classes in various samples. ‘Alphaproteobacteria-rickettsiales’, a bacterial class usually reduced in water-limiting soils, had significantly low abundance in root samples of symptomatic trees. Basidiomycota and Ascomycota fungal classes were the most common fungal classes observed, but neither showed differential enrichment between symptomatic and asymptomatic trees. Analyzing weather data showed an extremely cold winter followed by drought in 2015–2016, which likely weakened the trees to make them more susceptible to varied stresses. In addition, similar physical and nutritional soil composition from symptomatic and asymptomatic trees rules out the role of nutritional stress in RAD. Necrotic lesions and wood decay symptoms dispersing from bark or vascular cambium towards the heartwood were observed primarily below the graft union of declining apple trees, suggesting that the rootstock is the originating point of RAD. We speculate that differences in abiotic factors such as moisture levels in declining roots in combination with extreme weather profiles might cause RAD but cannot clearly rule out the involvement of other factors.

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<![CDATA[Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4]]> https://www.researchpad.co/article/5c89773ed5eed0c4847d27e7

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

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<![CDATA[Chemical profile of Lippia thymoides, evaluation of the acetylcholinesterase inhibitory activity of its essential oil, and molecular docking and molecular dynamics simulations]]> https://www.researchpad.co/article/5c8c194fd5eed0c484b4d3c7

The essential oils of the fresh and dry flowers, leaves, branches, and roots of Lippia thymoides were obtained by hydrodistillation and analyzed using gas chromatography (GC) and GC–mass spectrometry (MS). The acetylcholinesterase inhibitory activity of the essential oil of fresh leaves was investigated on silica gel plates. The interactions of the key compounds with acetylcholinesterase were simulated by molecular docking and molecular dynamics studies. In total, 75 compounds were identified, and oxygenated monoterpenes were the dominant components of all the plant parts, ranging from 19.48% to 84.99%. In the roots, the main compounds were saturated and unsaturated fatty acids, having contents varying from 39.5% to 32.17%, respectively. In the evaluation of the anticholinesterase activity, the essential oils (detection limit (DL) = 0.1 ng/spot) were found to be about ten times less active than that of physostigmine (DL = 0.01ng/spot), whereas thymol and thymol acetate presented DL values each of 0.01 ng/spot, equivalent to that of the positive control. Based on the docking and molecular dynamics studies, thymol and thymol acetate interact with the catalytic residues Ser203 and His447 of the active site of acetylcholinesterase. The binding free energies (ΔGbind) for these ligands were -18.49 and -26.88 kcal/mol, demonstrating that the ligands are able to interact with the protein and inhibit their catalytic activity.

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<![CDATA[Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.)]]> https://www.researchpad.co/article/5c897798d5eed0c4847d30f2

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat.

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<![CDATA[Modern botanical analogue of endangered Yak (Bos mutus) dung from India: Plausible linkage with extant and extinct megaherbivores]]> https://www.researchpad.co/article/5c897796d5eed0c4847d30d6

The study reports the micro- and macrobotanical remains on wild Yak dung, providing evidence for understanding the diet, habitat, and ecology of extant and extinct megaherbivores. Grasses are the primary diet of the yak as indicated by the abundance of grass pollen and phytoliths. Other associated non-arboreal and arboreal taxa namely, Cyperacaeae, Rosaceae, Chenopodiaceae, Artemisia, Prunus, and Rhododendron are also important dietary plants for their living. The observation of plant macrobotanical remains especially the vegetative part and seeds of the grasses and Cyperaceae is also in agreement with the palynodata. The documented micro- and macrobotanical data are indicative of both Alpine meadow and steppe vegetation under cold and dry climate which exactly reflected the current vegetation composition and climate in the region. The recovery of Botryococcus, Arcella, and diatom was observed in trace amounts in the palynoassemblage which would have been incorporated in the dung through the ingestion of water and are indicative of the presence of perennial water system in the region. Energy dispersive spectroscopy analysis marked that the element contained in dung samples has variation in relation to the summer and winter, which might be due to the availability of the food plants and vegetation. This generated multiproxy data serves as a strong supplementary data for modern pollen and vegetation relationships based on surface soil samples in the region. The recorded multiproxy data could also be useful to interpret the relationship between the coprolites of herbivorous fauna and the palaeodietary, the palaeoecology in the region, and to correlate with other mega herbivores in a global context.

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<![CDATA[How elevated CO2 affects our nutrition in rice, and how we can deal with it]]> https://www.researchpad.co/article/5c8823f8d5eed0c48463945d

Increased concentrations of atmospheric CO2 are predicted to reduce the content of essential elements such as protein, zinc, and iron in C3 grains and legumes, threatening the nutrition of billions of people in the next 50 years. However, this prediction has mostly been limited to grain crops, and moreover, we have little information about either the underlying mechanism or an effective intervention to mitigate these reductions. Here, we present a broader picture of the reductions in elemental content among crops grown under elevated CO2 concentration. By using a new approach, flow analysis of elements, we show that lower absorption and/or translocation to grains is a key factor underlying such elemental changes. On the basis of these findings, we propose two effective interventions—namely, growing C4 instead of C3 crops, and genetic improvements—to minimize the elemental changes in crops, and thereby avoid an impairment of human nutrition under conditions of elevated CO2.

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<![CDATA[Combining biophysical parameters, spectral indices and multivariate hyperspectral models for estimating yield and water productivity of spring wheat across different agronomic practices]]> https://www.researchpad.co/article/5c897762d5eed0c4847d2b85

Manipulating plant densities under different irrigation rates can have a significant impact on grain yield and water use efficiency by exerting positive or negative effects on ET. Whereas traditional spectral reflectance indices (SRIs) have been used to assess biophysical parameters and yield, the potential of multivariate models has little been investigated to estimate these parameters under multiple agronomic practices. Therefore, both simple indices and multivariate models (partial least square regression (PLSR) and support vector machines (SVR)) obtained from hyperspectral reflectance data were compared for their applicability for assessing the biophysical parameters in a field experiment involving different combinations of three irrigation rates (1.00, 0.75, and 0.50 ET) and five plant densities (D1: 150, D2: 250, D3: 350, D4: 450, and D5: 550 seeds m-2) in order to improve productivity and water use efficiency of wheat. Results show that the highest values for green leaf area, aboveground biomass, and grain yield were obtained from the combination of D3 or D4 with 1.00 ET, while the combination of 0.75 ET and D3 was the best treatment for achieving the highest values for water use efficiency. Wheat yield response factor (ky) was acceptable when the 0.75 ET was combined with D2, D3, or D4 or when the 0.50 ET was combined with D2 or D3, as the ky values of these combinations were less than or around one. The production function indicated that about 75% grain yield variation could be attributed to the variation in seasonal ET. Results also show that the performance of the SRIs fluctuated when regressions were analyzed for each irrigation rate or plant density specifically, or when the data of all irrigation rates or plant densities were combined. Most of the SRIs failed to assess biophysical parameters under specific irrigation rates and some specific plant densities, but performance improved substantially for combined data of irrigation rates and some specific plant densities. PLSR and SVR produced more accurate estimations of biophysical parameters than SRIs under specific irrigation rates and plant densities. In conclusion, hyperspectral data are useful for predicting and monitoring yield and water productivity of spring wheat across multiple agronomic practices.

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