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bioRxiv2025

Advancing RNAi-Based Strategies Against Downy Mildews: Insights Into dsRNA Uptake and Gene Silencing

Downy mildew (DMs) dieases are caused by destructive obligate pathogens with limited control options, posing a significant threat to global agriculture. RNA interference (RNAi) has emerged as a promising, environmentally sustainable strategy for disease management. In this study, we evaluated the efficacy of dsRNA-mediated RNAi in suppressing key biological functions in DM pathogens of Arabidopsis thaliana, pea and lettuce DM pathogens, Hyaloperonospora arabidopsidis (Hpa), Peronospora viciae f. sp. pisi (Pvp) and Bremia lactucae (Bl), respectively. We specifically targeted the cellulose synthase 3 (CesA3) and the beta tubulin (BTUB) genes. Silencing CesA3 impaired spore germination and infection across multiple species, while BTUB silencing reinforced the potential of dsRNA-mediated inhibition. Reduction in gene expression levels correlated well with the sporulation assays confirming the effectiveness of dsRNA-mediated gene silencing. We used dsRNAs that were chemically synthesized, in vitro transcribed (IVT) or produced in E. coli. We found that the length and concentration of these dsRNAs significantly affected uptake efficiency, spore germination, and sporulation, with higher concentrations enhancing inhibitory effects. Confocal microscopy using Cy-5-labelled short-synthesized dsRNA (SS-dsRNA) provided direct evidence of spore uptake, confirming the potential of SS-dsRNA for pathogen control. However, species-specific sequence variations influenced dsRNA efficacy, underscoring the importance of target sequence design. Multiplexed RNAi impacted silencing synergisticly, further reducing germination and sporulation in Hpa. Additionally, we demonstrated that SS-dsRNA-mediated gene silencing is sustained over time, with a significant reduction in gene expression level at 4, 7, 10 and 11dpi. This indicates the durability and efficacy of this approach. Taken together, these findings demonstrate the potential of dsRNA-mediated gene silencing as a precision tool for managing DM pathogens.

plant biology↗

bioRxiv2023

The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex

The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each of SR45 domains by examining their involvement in: (i) the spatial distribution of SR45, (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components, and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RNA recognition motif (RRM) domain specifically binds purine-rich RNA motifs via three residues (H101, H141, Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues likely phosphorylated by kinases from both CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies. HighlightThe contribution of the Arabidopsis SR45 splicing factor individual domains to its nuclear localization, ability to contact in planta novel protein partners and specifically bind RNA motifs was examined.

plant biology↗

bioRxiv2023

Coffee microsporogenesis and related small interfering RNAs biosynthesis have a unique pattern among eudicots suggesting a sensitivity to climate changes.

Recently, the siRNAs pathways, and especially reproductive phasiRNAs, have attracted attention in eudicots since their biological roles are still unknown and their biogenesis took different evolutionary pathways compared to monocots. In this work, we used Coffea arabica L., a recently allotetraploid formed from the hybridization of C. canephora and C. eugenioides unreduced gametes, to explore microsporogenesis and small RNAs related pathways in a eudicot crop. First, we identified the microsporogenesis stages during anther development revealing that pre-meiosis occurs in anthers of 1.5 mm inside floral buds (FBs), whereas meiosis between 1.5 and 4.2 mm FBs, and post-meiosis in FBs larger than 4.2mm. These stages coincide with the Brazilian winter, a period of FBs reduced growth which suggests temperature sensitivity. Next, we identified and quantified the expression of reproductive 21- and 24-nt phasiRNAs during coffee anther development together with their canonical and novel miRNA triggers, and characterized the DCL and AGO families. Our results showed that the pattern of reproductive phasiRNA abundance in C. arabica is unique among described eudicots and the canonical trigger car-miR2275 is involved in the processing of both 21 and 24 nt phasiRNAs. Fourteen DCL genes were identified, but DCL5, related to phasiRNA biosynthesis in monocots, was not according to its specificity for monocots. Thus, our work explored the knowledge gap about microsporogenesis and related siRNAs pathways in coffee, contributing to the control of reproductive development and to the improvement of fertility in eudicots.

plant biology↗

bioRxiv2018

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

Predicting gene regulatory networks (GRNs) from gene expression profiles has become a common approach for identifying important biological regulators. Despite the increase in the use of inference methods, existing computational approaches do not integrate RNA-sequencing data analysis, are often not automated, and are restricted to users with bioinformatics and programming backgrounds. To address these limitations, we have developed TuxNet, an integrated user-friendly platform, which, with just a few selections, allows to process raw RNA-sequencing data (using the Tuxedo pipeline) and infer GRNs from these processed data. TuxNet is implemented as a graphical user interface and, using expression data from any organism with an existing reference genome, can mine the regulations among genes either by applying a dynamic Bayesian network inference algorithm, GENIST, or a regression tree-based pipeline that uses spatiotemporal data, RTP-STAR. To illustrate the use of TuxNet while getting insight into the regulatory cascade downstream of the Arabidopsis root stem cell regulator PERIANTHIA (PAN), we obtained time course gene expression data of a PAN inducible line and inferred a GRN using GENIST. Using RTP-STAR, we then inferred the network of a PAN secondary downstream gene, ATHB13, for which we obtained wildtype and mutant expression profiles. Our case studies feature the versatility of TuxNet to infer networks using different types of gene expression data (i.e time course and steady-state data) as well as how inference networks are used to identify important regulators.\n\nSUMMARYTuxNet offers a simple interface for non-computational biologists to infer GRNs from raw RNA-seq data.

plant biology↗

bioRxiv2021

Stress Resistance Heat Shock Protein 70 (HSP70) Analysis in Sorghum (Sorghum bicolor L.) at Genome-Wide Level

Heat shock proteins (HSP70) play an important role in many biological processes. However, as typical in Sorghum bicolor, the systematic identification of the HSP70 gene is very limited, and the role of the Hsp70 gene in the evolution of Sorghum bicolor has not been described systematically a lot. To overcome the gap, Insilco analysis of HSP70 gene family was conducted.The investigation was utilizing the bioinformatics method to analyze the HSP70 gene family and it has been identified that 30 HSP70 genes from the genome sequence of Sorghum bicolor. A comprehensive analysis of these 30 identified genes undertaking the analysis of gene structure, phylogeny, and physicochemical properties, subcellular localization, and promoter region analysis. The gene structure visualization analyses revealed that 22 genes contains both 5 and 3 UTRS and one 5 and one 3 gene and 6 genes without UTR. The highest number of introns was recorded as 12 and those genes have shown that without in any intron. In the promoter region analysis, ten protein motifs are identified and characterized and 2219 cis-acting elements are identified. Among those, the promoter enhancer elements share the highest number (1411) and light-responsive elements share the next value (335). The physicochemical properties analysis revealed that 23 families have an acidic nature while four families are basic and the rests are neutral. In general, the different analyses performed disclosed their structural organization, subcellular localization, physicochemical properties, cis-acting elements, phylogenetic, and understress conditions. This study provides further information for the functional characterization of HSP70 and helps to understand the mechanisms of abiotic stress tolerance under diverse stress conditions in Sorghum bicolor.

plant biology↗

bioRxiv2023

Variability in the phytoplankton response to upwelling across an iron limitation mosaic within the California Current System

Coastal upwelling currents such as the California Current System (CCS) comprise some of the most productive biological systems on the planet. Diatoms, a distinct taxon of phytoplankton, dominate these upwelling events in part due to their rapid response to nutrient entrainment. In this region, they may also be limited by the micronutrient iron (Fe), an important trace element primarily involved in photosynthesis and nitrogen assimilation. The mechanisms behind how diatoms physiologically acclimate to the different stages of the upwelling conveyor belt cycle with respect to Fe limitation remains largely uncharacterized. Here, we explore their physiological and metatranscriptomic response to the upwelling cycle with respect to the Fe limitation mosaic that exists in the CCS. Subsurface, natural plankton assemblages that would potentially seed surface blooms were examined over wide and narrow shelf regions. The initial biomass and physiological state of the phytoplankton community had a large impact on the overall response to simulated upwelling. Following on-deck incubation under varying Fe physiological states, our results suggest that diatoms quickly dominated the blooms by "frontloading" nitrogen assimilation genes prior to upwelling. However, diatoms subjected to induced Fe limitation exhibited reductions in carbon and nitrogen uptake and decreasing biomass accumulation. Simultaneously, they exhibited a distinct gene expression response which included increased expression of Fe-starvation induced proteins and decreased expression of nitrogen assimilation and photosynthesis genes. These findings may have significant implications for upwelling events in future oceans, where changes in ocean conditions are projected to amplify the gradient of Fe limitation in coastal upwelling regions.

plant biology↗

bioRxiv2026

Spatially resolved transcriptomics of poplar reveals tissue organization across shoot-associated organs

Poplar (Populus spp.) is a model for tree biology and a platform for engineering woody biomass, biofuels, biomaterials, and bioproducts. Many relevant traits depend on tissue position, developmental stage, and cell type, yet these spatial relationships are difficult to recover from bulk or single-cell transcriptomes. Here, we generated a spatial transcriptome atlas of Populus tremula x P. alba INRA 717-1B4 across the shoot apex, axillary bud, stem, and petiole. After quality control, the atlas retained 29,687 spatial spots from 45 tissue sections and detected 58,748 genes. Histology-guided clustering and marker analysis resolved meristematic, epidermal, cortical, vascular, and organ-specific domains. Cross-organ comparisons assessed whether published markers retained tissue-associated expression across different anatomical contexts and developmental stages, while de novo analysis identified additional domain-enriched candidates. As case studies of the utility of the atlas, we examined the emergence of trichome-associated programs in the shoot apex and adaxial - abaxial expression differences in petioles. A trichome identity score based on poplar markers from the single-cell shoot atlas peaked along the inferred meristem-to-primordium trajectory, revealing spatially localized expression of trichome-associated programs during early leaf development. Petiole expression differences were concentrated in the epidermis and cortex and involved polarity-associated, auxin-responsive, and cell-wall-remodeling genes, with distinct expression profiles across leaf positions. Together, these data provide a spatial reference for investigating tissue differentiation and developmental patterning in a transformable poplar genotype.

plant biology↗

bioRxiv2025

Regenerative agriculture effects on biomass, drought resilience and 14C-photosynthate allocation in wheat drilled into ley compared to disc or ploughed arable soil

Regenerative agriculture practices including leys and no-tillage facilitate biological reassembly of soil aggregates, increasing water, carbon and nutrient storage, but how this effects crop biomass, photosynthate partitioning, and drought resilience is unclear. To address this, we took monoliths growing semi-dwarf and taller wheat genotypes from 3-year plots that were ploughed or disc cultivated, or direct-drilled into a grass-clover ley and applied 35 kg N ha-1. Half the monoliths received a spring drought, then all were watered and the wheat 14CO2 pulse-labelled at stem elongation. The ley soil had lower bulk density, stored more water, and the taller wheat genotype maintained 8-fold higher proportion of water-stable macroaggregates despite unexpectedly having the smaller root biomass. Yields on the ley soil (3.74 t ha-1) were 77% -123% higher than on ploughed and disc cultivated soils, and unaffected by genotype or drought, despite its >70% reduction in root biomass. Of the 14C initially retained in wheat, 72% was in shoots, with root allocation decreasing by 75-90% in droughted ley soil, and at harvest soil retained <1% of the 14C, with significantly lower values for taller wheat, and ley. We conclude that soil health regeneration in the ley enhanced wheat yields, but reduced photosynthate allocation to root biomass under drought. Although taller wheat maintained better macroaggregation in ley soil, this was not explained by root biomass or photosynthate allocation and unexpectedly failed to increase soil 14C sequestration. We find no evidence that ley regeneration of macroaggregation enhances soil C sequestration under wheat, despite higher yields.

plant biology↗

bioRxiv2024

The use of X-ray Computed Tomography revolutionises soil pathogen detection

Potato cyst nematodes (PCN), namely Globodera pallida, pose a significant threat to potato production worldwide. Accurately quantifying nematode population densities is crucial for effective management strategies. However, traditional detection methods are time-consuming and often imprecise. X-ray computed tomography (CT) offers high-resolution, non-destructive and three-dimensional (3D) imaging frequently used to visualise internal structures of objects, materials or biological tissues, allowing for detailed analysis of their composition, defects, and morphology. Here, we demonstrate the effectiveness of X-ray CT in detecting and quantifying PCN cysts in different soil types. The ability to achieve 3D imaging and volume quantification of PCN cysts from soils allows accurate enumeration of their egg content. To explore future potential, we propose that when integrated with AI-led quantification of X-ray CT-generated cyst counts, this method could evolve into a next-generation technology to accurately and rapidly quantify these damaging pests in agricultural soils. Combined with the potential to co-analyse other organisms within the same sample, we propose X-ray CT as a fundamental tool for comprehensive soil health assessments and sustainable pest management in agriculture. Author SummaryPotato cyst nematodes are a major threat causing significant crop losses worldwide. Traditionally, detecting this pathogen in soil is challenging, often requiring time-consuming and imprecise. Our study explores a new approach using X-ray computed tomography (CT), a powerful imaging tool that creates detailed 3D images in situ. We observed that X-ray CT can effectively detect and measure the cysts nematodes, even within different soil types. This detailed analysis allows us to determine the cyst structures and estimate the eggs contained. In the future, combining X-ray CT with artificial intelligence could make detecting and quantifying these nematodes even faster and more accurate. This method could also be expanded to study other soil organisms, making it a valuable tool for monitoring soil health and improving agricultural pest management.

plant biology↗

bioRxiv2022

Single and multi-analyte deep learning-based analysis framework for class prediction in biological images

Measurement of biological analytes, characterizing flavor in fruits, is a cumbersome, expensive and time-consuming process. Fruits with higher concentration of analytes have greater commercial or nutritional values. Here, we tested a deep learning-based framework with fruit images to predict the class (sweet or sour and high or low) of analytes using images from two types of trees in a single and multi-analyte mode. We used fruit images from kinnow (n = 3,451), an edible hybrid mandarin and neem (n = 1,045), a tree with agrochemical and pharmaceutical properties. We measured sweetness in kinnows and five secondary metabolites in neem fruits (azadirachtin or A, deacetyl-salannin or D, salannin or S, nimbin or N and nimbolide or E) using a refractometer and high-performance liquid chromatography, respectively. We trained the models for 300 epochs, before and after hyper-parameters evolution, using 300 generations with 50 epochs/generation, estimated the best models and evaluated their performance on 10% of independent images. The validation F1score and test accuracies were 0.79 and 0.77, and 82.55% and 60.8%, respectively for kinnow and neem A analyte. A multi-analyte model enhanced the neem A models prediction to high class when the D:N:Ss combined class predictions were high:low:high and to low class when D:Ns combined class predictions were low:high respectively. The test accuracy increased further to ~70% with a 10-fold cross-validation error of 0.257 across ten randomly split train:validation:test sets proving the potential of a multi-analyte model to enhance the prediction accuracy, especially when the numbers of images are limiting.

plant biology↗

bioRxiv2023

The invasive brown seaweed Rugulopteryx okamurae (Dictyotales, Ochrophyta) continues to expand: first record in Italy.

The brown seaweed Rugulopteryx okamurae (Dictyotales, Ochrophyta), native to the Pacific Ocean and widely distributed in Asia, has been recently recognized as an emblematic case of biological invasion by marine macroalgae in European waters. Since 2015 and from the Strait of Gibraltar, R. okamurae has rapidly spread towards Atlantic and Mediterranean coastal areas exhibiting an invasive behaviour with significant ecological and economic impacts. Here, we report by morphology and genetics the first observation of this species in Italy along the north-western coast of Sicily (Gulf of Palermo), as drifted material and an established population on Posidonia oceanica, representing its new eastern distribution limit in the Mediterranean Sea, previously established in Marseilles (France). Furthermore, we have performed with the current introduced distribution of the species a favorability distribution model for the Mediterranean, which shows most of the western Mediterranean, including the Balearic archipelago, Corsica and Sardinia, central Mediterranean, including Sicily, and the northern coast of Africa together with eastern Mediterranean basin, as highly favorable for R. okamurae. Arrival of the species into this new area is suggested by means of sea currents and maritime traffic, including fishing activities, hypothesis supported by some of the ranked variables that entered the favorability model, i.e, current velocity, and proximity of fishing ports. These results are a warning that the species can cover large sea distances favored by sea currents, thus also threatening the ecosystems and marine resources of the central and eastern Mediterranean, highly favorable regions for the species. We suggest coordinated actions at the European level regarding prevention, among which those that have the complicity of the fishing sector should be considered, both because it is a highly affected sector and because it potentially has a very important role in the dispersion of the species.

plant biology↗

bioRxiv2025

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

BackgroundSorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4-5 meters in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified. ResultsTo address these gaps, we reanalyzed a published RNA-seq dataset to identify genes with organ-preferential expression and to infer representative organ functions across major developmental stages. Our analysis revealed that the sorghum stem exhibits distinct temporal functional signatures, which correlate with the developmental dynamics of stem-specific genes and their associated regulatory elements. We further identified a set of genes with ubiquitous stem-specific expression across diverse sorghum genotypes, suggesting their universal importance and broad potential for genetic engineering applications. Among them, SbTALE03 and SbTALE04 emerged as stem hub transcription factors (TF). Both genes were empirically validated for their stem specificity across stages. Gene regulatory network analysis further indicated that these TFs participate in stage-specific transcriptional programs that maintain and regulate stem development. ConclusionsThis study presents a genome-wide analysis of organ-specific gene expression, functions, and regulatory networks in sorghum, with a focus on genes preferentially-expressed in stems and their promoter motifs. We identified a set of core stem-specific genes with ubiquitous expression across genotypes and developmental stages, including two experimentally validated transcription factors with potential roles in stem development. These findings offer valuable candidates for further functional characterization and genetic engineering aimed at improving sorghum stem biomass and composition.

plant biology↗

bioRxiv2021

Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation-modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice. Significance statementGenome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and positively correlation the density and breadth of H3K9ac with transcript elongation and expression. Identified numerous H3K9 acetylation-modified gene expression targets reveal a complex regulatory network and metabolism-mediated senescence network that are associated with H3K9ac during leaf aging in rice.

plant biology↗

bioRxiv2026

Large-scale phenotyping and multi-trait selection identify low-methane Napier grass (Cenchrus purpureus) accessions under contrasting environmental conditions

Abstract Napier grass (Cenchrus purpureus, NG) is an important forage in tropical and subtropical livestock systems, but the extent of naturally occurring variation in its methane (CH4) production and its potential for selecting low-CH4 emitting genotypes remains poorly characterised. This study evaluated variation in CH4 yield among NG accessions, examined the effects of season and water stress, validated contrasting CH4 phenotypes across donor cows, and identified elite accessions combining low CH4 yield with favourable digestibility. A total of 750 NG samples representing 84 accessions grown under dry and wet seasons and moderate and severe water-stress were evaluated using a high-throughput in-vitro fermentation system. To further identify forages combining low-CH4 production with acceptable digestibility, a multi-trait selection approach was applied using biologically defined thresholds for CH4 yield and in vitro organic matter digestibility (IVOMD), followed by a weighted index assigning 60% weight to CH4 yield and 40% to IVOMD. Methane yield varied widely among accessions, ranging from 0.02 to 5.07 mL/g DM and was affected by growing conditions. Methane production was generally lower during the wet season, while water stress was associated with changes in forage quality and fermentation characteristics. Low-CH4 producing accessions generally had lower IVOMD, crude protein and metabolizable energy and relatively higher fibre than high-CH4 producing accessions. Accessions initially classified as low and high-CH4 emitters based solely on CH4 yield were subsequently validated using rumen inoculum from three individual donor cows. Although the magnitude of CH4 production varied among donors, the contrast between low- and- high-CH4 accessions was generally retained, supporting the robustness of accession differences in CH4 production. Several accessions also maintained relatively low CH4 production across contrasting season and water-stress conditions, indicating that favourable CH4 phenotypes were not entirely environment dependent. A multi-trait selection identified ten elite accessions that produced 0.019-0.810 mL CH4/g DM and had 55.2-69.0% IVOMD, whereas ten poor-performing accessions produced 2.80-3.89 mL CH4/g DM and had 50.1-54.7% IVOMD. Differences in hexose fermentation and CH4 produced per unit of fermented substrate further indicated contrasting fermentation efficiency between the groups. These results demonstrate substantial variation in NG and identify accessions with low-CH4 production, favourable digestibility and relatively stable performance across growing conditions. In conclusion, incorporating CH4 yield and digestibility into forage selection could support the development of lower-emission forage cultivars for sustainable climate-smart livestock production.

plant biology↗

bioRxiv2018

Functions of farmers’ preferred tree species and their potential carbon stocks in southern Burkina Faso: implications for biocarbon initiatives

The success of terrestrial carbon sequestration projects for rural development in sub-Saharan Africa lies in the (i) involvement of local populations in the selection of woody species, which represent the biological assets they use to meet their daily needs, and (ii) information about the potential of these species to store carbon. Although the latter is a key prerequisite, there is very little information available. To help fill this gap, the present study was undertaken in four pilot villages (Kou, Dao, Vrassan and Cassou) in Ziro Province, south-central Burkina Faso. The objective was to determine carbon storage potential for top-priority woody species preferred by local smallholders. We used (i) participatory rural appraisal consisting of group discussions and key informant interviews to identify priority species and functions, and (ii) landscape assessment of carbon stocks in the preferred woody species. Results revealed over 79 priority tree and shrub species grouped into six functions, of which medicine, food and income emerge as the most important ones for the communities. For these functions, smallholders overwhelmingly listed Vitellaria paradoxa, Parkia biglobosa, Afzelia africana, Adansonia digitata, Detarium microcarpum, and Lannea microcarpa among the most important tree species. Among the preferred woody species in Cassou and Kou, the highest quantity of carbon was stored by V. paradoxa (1,460.6 {+/-}271.0 kg C ha-1 to 2,798.1{+/-}521.0 kg C ha-1) and the lowest by Grewia bicolor (1.6{+/-}1.3 kg C ha-1). The potential carbon stored by the preferred tree communities was estimated at 5,766.2 Mg C ha-1 (95% CI: 5,258.2; 6,274.2 Mg C ha-1) in Kou and 6,664.0 Mg C ha-1 (95% CI: 5,810.2; 7,517.8 Mg C ha-1) in Cassou. The findings of this study will help design data-based development of biocarbon projects, which are rare in the West African Sahel despite being considered as one of the most impactful climate change resilient strategies.

plant biology↗

bioRxiv2025

Nitrogen dynamics and yield performance of an elite bread wheat line with BNI capacity expressed in an alkaline soil

Wheat with biological nitrification inhibition (BNI) has been shown to be effective in acidic soils. BNI expressions in alkaline soil have not been documented in field studies. We present the first observation of BNI effects in alkaline soil trials (pH 8.6-8.7) of elite spring wheat that carries the Lr#N short arm from Leymus racemosus. BNI was expressed as lower soil nitrate in three trials conducted in an irrigated wheat system in northwestern Mexico. In one year, we observed 24-37% lower nitrate in soil of the translocation line compared to the control after the second ammonium-N fertilizer application. Lower nitrate was observed in the row and in the furrow. The largest difference between the control and the translocation line was approximately one month after the second ammonium-N split application (73-77% less nitrate). Potential nitrification rates were 27-32% lower in soil from the translocation line compared to the control, one week after a high ammonium-N application. Higher flag leaf nitrate concentration of the translocation line could be related to the strongly reduced soil nitrate. The translocation line took longer to reach anthesis and flowering. In two experiments, the translocation line was equivalent in terms of grain yield, whereas in one experiment it produced lower yields, with fewer grains per spike and reduced number of spikes per area. Protein content and grain N uptake of the translocation line were similar to the control. We conclude that BNI reduces nitrification with a spatially and temporally significant impact under alkaline soil and high N input conditions. This finding points to the potential major environmental benefits that could be achieved also in non-acidic soil spring wheat systems worldwide. The effect of the Lr#N short arm on yield quantity and quality in other elite lines needs further investigation.

plant biology↗

bioRxiv2023

Deciphering Drought Response Mechanisms: Transcriptomic Insights from Drought-Tolerant and Drought-Sensitive Wheat (Triticum aestivum L.) Cultivars

Drought stress poses a significant threat to wheat (Triticum aestivum L.) cultivation, necessitating an in-depth understanding of the molecular mechanisms underpinning drought response in both tolerant and sensitive varieties. In this study, 12 diverse bread wheat cultivars were evaluated for their drought stress responses, with particular emphasis on the contrasting performance of cultivars Atay 85 (sensitive), Gerek 79, and Mufitbey (tolerant). Transcriptomic analysis was performed on the root and leaf tissues of the aforementioned cultivars subjected to 4-hour and 8-hour drought stress and compared with controls. Differentially expressed genes (DEGs) were categorized based on their cellular component, molecular function, and biological function. Notably, there was greater gene expression variability in leaf tissues compared to root tissues. A noticeable trend of decreased gene expression was observed for cellular processes such as protein refolding and cellular metabolic processes like photorespiration as drought stress duration increased (8 hours) in the leaf tissues of drought-tolerant and sensitive cultivars. Metabolic processes related to gene expression were predominantly activated in response to 4-hour and 8-hour drought stress. The drought-tolerant cultivars exhibited increased expression levels of genes related to protein binding, metabolic processes, and cellular functions, indicating their ability to adapt better to drought stress compared to the drought-sensitive cultivar Atay 85. We detected more than 25 differentially expressed TFs in leaf tissues under 4-hour and 8-hour drought stress, while only 4 TFs were identified in the root tissues of sensitive cultivar. In contrast, the tolerant cultivar exhibited more than 80 different TF transcripts in both leaves and roots after 4 hours of drought stress, with this number decreasing to 18 after 8 hours of drought stress. Differentially expressed genes with a focus on metal ion binding, carbohydrate degradation, ABA-related genes, and cell wall-related genes were highlighted. Ferritin (TaFer), TaPME42 and Extensin-like protein (TaExLP), Germin-like protein (TaGLP 9-1), Metacaspase-5 (TaMC5), Arogenate Dehydratase 5 (ADT-5), Phosphoglycerate/ bisphosphoglycerate mutase (TaPGM), Serine/threonine protein phosphatase 2A (TaPP2A), GIGANTEA (TaGI), Polyadenylate-binding protein (TaRBP45B) exhibited differential expression by qRT-PCR in root and leaf tissues of tolerant and sensitive bread wheat cultivars. This study provides valuable insights into the complex molecular mechanisms associated with drought response in wheat, highlighting genes and pathways involved in drought tolerance. Understanding these mechanisms is essential for developing drought-tolerant wheat varieties, enhancing agricultural sustainability, and addressing the challenges posed by water scarcity.

plant biology↗

bioRxiv2019

Coconut inflorescence sap mediated synthesis of silver nanoparticles and its diverse antimicrobial properties

Green synthesis of nanoparticles (NPs) involves the use of diverse extracts of biological origin as substrates to synthesize nanoparticles and can overcome the hazards associated with chemical methods. Coconut inflorescence sap, which is unfermented phloem sap obtained by tapping of coconut inflorescence, is a rich source of sugars and secondary metabolites. In this study, coconut inflorescence sap was used to synthesize silver nanoparticles (AgNPs). We have initially undertaken metabolomic profiling of coconut inflorescence sap from West Coast Tall cultivar to delineate its individual components. Secondary metabolites constituted the major portion of the inflorescence sap along with sugars, lipids and, peptides. The concentration of silver nitrate, inflorescence sap and incubation temperature for synthesis of AgNPs were optimized. Incubating the reaction mixture at 40{degrees}C was found to enhance AgNP synthesis. The AgNPs synthesized were characterized using UV-Visible spectrophotometry, X-Ray Diffraction (XRD), Fourier Transform Infrared spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM). Antimicrobial property of AgNP was tested in tissue culture of arecanut (Areca catechu L.) where bacterial contamination (Bacillus pumilus) was a frequent occurrence. Significant reduction in the contamination was observed when plantlets were treated with aqueous solutions of 0.01, 0.02 and 0.03% of AgNPs for one hour. Notably, treatment with AgNPs did not affect growth and development of the arecanut plantlets. Cytotoxicity of AgNPs was quantified in HeLa cells. Viability (%) of HeLa cells declined significantly at 10 ppm concentration of AgNP and complete mortality was observed at 60 ppm. Antimicrobial properties of AgNPs synthesized from inflorescence sap were also evaluated and confirmed in human pathogenic bacteria viz., Salmonella sp., Vibrio parahaemolyticus, and Escherichia coli. The study concludes that unfermented inflorescence sap, with above neutral pH, serves as an excellent reducing agent to synthesize AgNPs from Ag+.\n\nO_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC=\"FIGDIR/small/775940v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (64K):\norg.highwire.dtl.DTLVardef@3c3f1forg.highwire.dtl.DTLVardef@1540f6borg.highwire.dtl.DTLVardef@1c069aborg.highwire.dtl.DTLVardef@159772c_HPS_FORMAT_FIGEXP M_FIG Graphical abstract\n\nC_FIG

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