RSS 1.0Center for Desert Agriculture
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Recent Submissions
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Strigolactone biosynthesis lgs1 mutant alleles mined from the sorghum accession panel are a promising resource of resistance to witchweed (Striga) parasitism(PLANTS, PEOPLE, PLANET, Wiley, 2023-09-28) [Article]Striga is a parasitic plant that greatly limits the production of Africa's most staple cereals, including sorghum. Infection occurs when the parasite germinates in response to biomolecules emitted into the soil from the host's roots. Some sorghum genotypes harbor a mutation that makes them ineffective in stimulating Striga seed germination. This resistance is of great importance because of its possible application in Striga management. Here, additional resistant sorghum genotypes with varying levels of Striga resistance are discussed in the context of their candidacy for integration in breeding programs and their possible role in alleviating food insecurity in sub-Saharan Africa by reducing crop losses because of Striga infestation. Sorghum is a food staple for millions of people in sub-Saharan Africa, but its production is greatly diminished by Striga, a parasitic weed. An efficient and cost-effective way of managing Striga in smallholder farms in Africa is to deploy resistant varieties of sorghum. Here, we leverage genomics and the vast genetic diversity of sorghum—evolutionarily adapted to cope with Striga parasitism in Africa—to identify new Striga-resistant sorghum genotypes by exploiting a resistance mechanism hinged on communication molecules called strigolactones (SLs), exuded by hosts to trigger parasite seed germination. We achieved this by mining for mutant alleles of the LOW GERMINATION STIMULANT 1 (LGS1) that are ineffective in stimulating Striga germination from the sorghum accession panel (SAP). Our analysis identified lgs1 sorghum genotypes, which we named SAP-lgs1. SAP-lgs1 had the SL exudation profile of known lgs1 sorghum, whose hallmark is the production of the low inducer of germination, orobanchol. Laboratory and field resistance screens showed that the SAP-lgs1 genotypes also exhibited remarkable resistance against Striga. Our findings have the potential to reduce crop losses because of Striga parasitism and therefore have far-reaching implications for improving food security in Africa
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Horizon scanning the application of probiotics for wildlife(Trends in Microbiology, Elsevier BV, 2023-09-25) [Article]The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called ‘probiotics for wildlife’ is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Mapping the potential for pumped storage using existing lower reservoirs(Journal of Energy Storage, Elsevier BV, 2023-09-23) [Article]The increasing utilization of wind and solar power sources to lower CO2 emissions in the electric sector is causing a growing disparity between electricity supply and demand. Consequently, there is a heightened interest in affordable energy storage solutions to address this issue. Pumped Hydropower Storage (PHS) emerges as a promising option, capable of providing both short and long-term energy storage at a reasonable cost, while also offering the advantage of freshwater storage. To identify potential PHS locations in Brazil existing hydroelectric reservoirs as the lower reservoirs, we employed an innovative methodology that combines (i) plant-siting model that leverages high-resolution topographical and hydrological data to identify the most promising sites for further studies. (ii) An economic methodology was applied to configure PSH projects identified by the plant-siting model in terms of their installed capacity and discharge time, and to select the most attractive projects. (iii) A comprehensive analysis of the socio-environmental impacts of the projects was carried out, which enables the elimination of projects with severe impacts. Results created a ranking of 5600 mutually exclusive projects by net present value (NPV). The highest NPV is 2145 USD which refers to a PHS plant in the Doce Basin and Salto Grande dam as the lower reservoir. The upper reservoir stores 0.36 km3 of water and a 75 m high dam, the PHS has a 2 km tunnel, a 1 GW power capacity and discharge rate of 220 h. The paper shows a vast potential for weekly, monthly, and seasonal PHS with existing lower reservoirs in Brazil.
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Engineering carbon sequestration on arid lands(Trends in Plant Science, Elsevier BV, 2023-09-21) [Article]To limit the effects of global warming, arid lands, which constitute approximately one-third of terrestrial surfaces and are not utilized for agriculture, could serve as an effective method for long-term carbon (C) storage. We propose that soil–plant–microbiome engineering with oxalogenic plants and oxalotrophic microbes could facilitate C sequestration on a global scale.
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Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase(Cold Spring Harbor Laboratory, 2023-09-12) [Preprint]Septoria tritici blotch (STB), caused by the Dothideomycete fungus Zymoseptoria tritici, is of one of the most damaging diseases of bread wheat (Triticum aestivum)1 and the target of costly fungicide applications2. In line with the fungus’ apoplastic lifestyle, STB resistance genes isolated to date encode receptor-like kinases (RLKs) including a wall-associated kinase (Stb6) and a cysteine-rich kinase (Stb16q)3,4. Here, we used genome-wide association studies (GWAS) on a panel of 300 whole-genome shotgun-sequenced diverse wheat landraces (WatSeq consortium) to identify a 99 kb region containing six candidates for the Stb15 resistance gene. Mutagenesis and transgenesis confirmed a gene encoding an intronless G-type lectin RLK (LecRK) as Stb15. The characterisation of Stb15 exemplifies the unexpected diversity of RLKs conferring Z. tritici resistance in wheat.
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PNA-Pdx: Versatile Peptide Nucleic Acid-Based Detection of Nucleic Acids and SNPs(Analytical Chemistry, American Chemical Society (ACS), 2023-09-11) [Article]Monitoring diseases caused by pathogens or by mutations in DNA sequences requires accurate, rapid, and sensitive tools to detect specific nucleic acid sequences. Here, we describe a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, termed PNA-powered diagnostics (PNA-Pdx). PNA-Pdx employs PNA probes that bind specifically to a target and are then detected in lateral flow assays. This can precisely detect a specific pathogen or genotype genomic sequence. PNA probes can also be designed to invade double-stranded DNAs (dsDNAs) to produce single-stranded DNAs for precise CRISPR-Cas12b-based detection of genomic SNPs without requiring the protospacer-adjacent motif (PAM), as Cas12b requires PAM sequences only for dsDNA targets. PNA-Pdx identified target nucleic acid sequences at concentrations as low as 2 copies/μL and precisely detected the SARS-CoV-2 genome in clinical samples in 40 min. Furthermore, the specific dsDNA invasion by the PNA coupled with CRISPR-Cas12b precisely detected genomic SNPs without PAM restriction. Overall, PNA-Pdx provides a novel toolkit for nucleic acid and SNP detection as well as highlights the benefits of engineering PNA probes for detecting nucleic acids.
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Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice(Plant Physiology, Oxford University Press (OUP), 2023-09-04) [Article]Developing drought resistant rice (Oryza sativa, L.)is essential for improving field productivity, especially in rainfed areas affected by climate change. Wild relatives of rice are potential sources for drought resistant traits. Therefore, we compared root growth and drought response among 22 wild Oryza species, from which Oryza glumaepatula was selected as a promising source for further exploration. A geographically diverse panel of 69 O. glumaepatula accessions was then screened for drought stress related traits, and six of these accessions showed lower shoot dry weight reduction, greater percentage of deep roots, and lower stomatal density under drought than the drought tolerant O. sativa variety, Sahbhagi dhan. Based on whole genome resequencing of all 69 O. glumaepatula accessions and variant calling to a high-quality O. glumaepatula reference genome, we detected multiple genomic loci co-locating for shoot dry weight, root dry weight at 30-45 cm depth, and stomatal density in consecutive drought trials. Geo-referencing indicated that the potential drought donors originated in flood-prone locations, corroborating previous hypotheses about the co-existence of flood and drought tolerance within individual Oryza genomes. These findings present potential donor accessions, traits, and genomic loci from an AA genome wild relative of rice that, together with the recently developed reference genome, may be useful for further introgression of drought tolerance into Oryza sativa backgrounds.
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Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development(Cold Spring Harbor Laboratory, 2023-09-01) [Preprint]Our study aimed to identify candidate genes for flowering time regulation and photoperiod response in quinoa. We investigated the timing of photoperiod-driven floral transition and analyzed the transcriptomes of leaf and shoot apical meristems in photoperiod-sensitive and -insensitive quinoa accessions. Histology analysis of the apical meristem showed that floral transition in quinoa initiates two to three weeks after sowing. We found four groups of differentially expressed genes responding to plant development and floral transition, which were annotated in the QQ74-V2 reference genome, including (i) 222 genes differentially responding to photoperiod in leaves, (ii) 1,812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes between weeks under short-day conditions in leaves, and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, out of the thousands of candidates, two putative FT orthologues and several others have been reported as key regulators of flowering time in other species (e.g., SOC1, COL, AP1). Additionally, we used co-expression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same co-expression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.
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Silencing translation with phenolic acids(Nature Plants, Springer Science and Business Media LLC, 2023-08-28) [Article]Phenolic acids, such as salicylic acid, are part of a mechanism that helps to suppress the growth of neighbouring plants. New work shows that phenolic acids inhibit global translation by promoting the sequestration of ribosomal subunits into stress granules.
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Pathogen-induced m6A dynamics affect plant immunity(The Plant Cell, Oxford University Press (OUP), 2023-08-23) [Article]Post-transcriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine (m6A)) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term response to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.
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Groundwater-dependent ecosystems at risk - global hotspot analysis and implications(ENVIRONMENTAL RESEARCH LETTERS, IOP Publishing, 2023-08-22) [Article]Many land-based ecosystems are dependent on groundwater and could be threatened by human groundwater abstraction. One key challenge for the description of associated impacts is the initial localisation of groundwater-dependent ecosystems (GDEs). This usually requires a mixture of extensive site-specific data collection and the use of geospatial datasets and remote sensing techniques. To date, no study has succeeded in identifying different types of GDEs in parallel worldwide. The main objective of this work is to perform a global screening analysis to identify GDE potentials rather than GDE locations. In addition, potential risks to GDEs from groundwater abstraction shall be identified. We defined nine key indicators that capture GDE potentials and associated risks on a global grid of 0.5° spatial resolution. Groundwater-dependent streams, wetlands and vegetation were covered, and a GDE index was formulated incorporating the following three aspects: the extent of groundwater use per GDE type, GDE diversity and GDE presence by land cover. The results show that GDE potentials are widely distributed across the globe, but with different distribution patterns depending on the type of ecosystem. The highest overall potential for GDEs is found in tropical regions, followed by arid and temperate climates. The GDE potentials were validated against regional studies, which showed a trend of increasing matching characteristics towards higher GDE potentials, but also inconsistencies upon closer analysis. Thus, the results can be used as first-order estimates only, which would need to be explored in the context of more site-specific analyses. Identified risks to GDEs from groundwater abstraction are more geographically limited and concentrated in the US and Mexico, the Iberian Peninsula and the Maghreb, as well as Central, South and East Asia. The derived findings on GDEs and associated risks can be useful for prioritising future research and can be integrated into sustainability-related tools such as the water footprint.
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Deciphering Salt Stress Responses in Solanum pimpinellifolium through High-Throughput Phenotyping.(Cold Spring Harbor Laboratory, 2023-08-17) [Preprint]Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium, can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum. In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium diversity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.
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Low flow sensitivity to water withdrawals in Central and Southwestern Europe under 2 K global warming(ENVIRONMENTAL RESEARCH LETTERS, IOP Publishing, 2023-08-17) [Article]A sufficient freshwater supply is vital for humans, ecosystems, and economies, but anticipated climate and socio-economic change are expected to substantially alter water availability. Across Europe, about two-third of the abstracted freshwater comes from rivers and streams. Various hydrological studies address the resulting need for projections on changes in river discharge. However, those assessments rarely specifically account for the impact of various water withdrawal scenarios during low flow periods. We present here a novel, high-resolution hydrological modeling experiment using pseudo-global warming climate data to investigate the effects of changing water withdrawals under 2 K global warming. Especially in Western and Central Europe the projected impacts on low flows highly depend on the chosen water withdrawal assumption and can severely decrease under the worst case assumptions. Our results highlight the importance of accounting for future water withdrawals in low flow projections, showing that climate-focused impact assessments in near-natural catchments provide only one piece of the anticipated response and do not necessarily reflect changes in heavily managed river basins.
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Perpetual motion electric truck, transporting cargo with zero fuel costs(Journal of Energy Storage, Elsevier, 2023-08-14) [Article]The transportation sector is going through a rapid transition to electric vehicles to minimize our reliance on fossil fuels and reduce CO2 emissions. This is also happening in the cargo transport sector, with a rapid deployment of electric trucks. This paper proposes that the replacement of diesel trucks with electric trucks should first happen on routes where cargo is delivered from a location with a higher altitude to a location with a lower altitude. This way, the regenerative braking system of the truck can completely recharge the truck's battery. This paper investigates scenarios where electric trucks could operate indefinitely without grid electricity to charge their batteries. This concept was named perpetual motion electric truck (PMET). Results show that with an average road slope of 5 %, 60 km/h speed, the weight of the cargo should be at least 1.32 times the weight of the truck, PMET can be achieved. PMET is an interesting alternative to reduce electricity demand and increase the sustainability of the transport sector.
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How greenhouse horticulture in arid regions can contribute to climate-resilient and sustainable food security(Global Food Security, Elsevier BV, 2023-08-14) [Article]A potential change in climate and temperature could strongly affect weather-related crop losses. Using wastelands to grow crops in controlled greenhouse environments could improve global food security and preserve ecosystems. However, the impact of climate change on additional energy and water requirements of greenhouse-horticulture food production is still unknown. Using a greenhouse simulator for four locations (The Netherlands, Spain, Saudi Arabia and Namibia), we show that a rise in outdoor temperatures can be counterbalanced with a more intensive water-based cooling. Between 6.9% and 17.9%, more water is required in the worst-case scenario in the year 2100, while the yield quantity decreases by 3%–6% due to slightly deteriorating growth conditions within the greenhouse. Since cooling systems consume up to 90% of the total water use in desert greenhouses, saltwater cooling could play an essential role in increasing the efficiency and sustainability of greenhouse horticulture systems in arid regions. In this study, we investigate the economic and technical feasibility of such greenhouse systems on a larger scale and show the massive potential of these systems. The developed scenarios demonstrate considerable climate resilience, enabling the cultivation of fresh vegetables in arid and infertile regions both presently and in the future.
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Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast(Archives of Microbiology, Springer Science and Business Media LLC, 2023-08-14) [Article]Isoptericola sp. AK164 is a Gram-positive, aerobic bacterial genus from the family Promicromonosporaceae, isolated from the root rhizosphere of Avicennia marina. AK164 significantly enhanced the growth of the Arabidopsis thaliana plant under normal and saline conditions. These bacteria can produce ACC deaminase and several enzymes playing a role in carbohydrate hydrolyses, such as cellulose, hemicellulose, and chitin degradation, which may contribute to plant growth, salt tolerance, and stress elevation. The genome sequence AK164 has a single circular chromosome of approximately 3.57 Mbp with a GC content of 73.53%. A whole genome sequence comparison of AK164 with type strains from the same genus, using digital DNA–DNA hybridization and average nucleotide identity calculations, revealed that AK164 might potentially belong to a new species of Isoptericola. Genome data and biochemical analyses indicate that AK164 could be a potential biostimulant for improving agriculture in submerged saline land.
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Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits(Communications Biology, Springer Science and Business Media LLC, 2023-08-12) [Article]Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.
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β-Cyclocitric acid enhances drought tolerance in peach (Prunus persica) seedlings(Tree Physiology, Oxford University Press (OUP), 2023-08-10) [Article]β-Cyclocitric acid (β-CCA) is a bioactive apocarotenoid previously shown to improve drought tolerance in annual plants. However, the underlying molecular mechanism of this process remains largely elusive. Moreover, the question about the activity of β-CCA in perennial fruit crops is still open. Here, we found the treatment of β-CCA to enhance drought tolerance in peach seedlings. The application of β-CCA significantly increased the relative water content and root activity, and reduced the electrolyte leakage of peach seedlings under drought stress. Moreover, treatment with β-CCA under drought stress increased chlorophyll fluorescence, indicating a positive effect on photosynthesis, while also enhancing superoxide dismutase and peroxidase activity, and reducing ROS levels. Consistent with these alterations, transcriptome analysis revealed an up-regulation of photosynthesis and antioxidant-related genes upon the application of β-CCA under drought stress. We also detected an induction in genes related to detoxification, environmental adaptation, primary metabolism, phytohormone, phenylpropanoid, and the biosynthesis of cutin, suberine and wax, which might contribute to the induction of drought resistance. Altogether, our study reveals that β-CCA positively modulates peach drought tolerance, which is mainly mediated by enhancing photosynthesis and reducing ROS, indicating the potential of utilizing β-CCA for drought control in peach and perhaps other fruit crops.
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Climate impact on combined cycle thermoelectric power plant in hot and humid regions(Results in Engineering, Elsevier BV, 2023-08-05) [Article]Thermoelectric power plants have been designed to operate in ISO conditions, similar to the temperate climatic conditions of the northern hemisphere. Thus, some equipment used in tropical regions operated outside the ideal conditions, with high relative humidity and ambient temperature. This ends up impairing its efficiency and maximum generation. This paper presents the analysis of 2020 and 2021 hourly electric generation and climatic conditions data for 2020 from the gas based combined cycle Cuiabá Thermoelectric Power Plant, located in the state of Mato Grosso do Sul, center-west region of Brazil. The main objective is to present and discuss the correlations between meteorological conditions and power generation in the plant. Results show a strong correlation between generation and the wet bulb temperature. They also show that high wind speeds, increase thermal losses and the efficiency of the steam cycle. This paper shows that thermal electric power plants are particularly sensitive to climate conditions in hot and humid regions.
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Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.(G3 (Bethesda, Md.), Oxford University Press (OUP), 2023-08-03) [Article]African rice (Oryza glaberrima Steud.), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
