In vitro cryopreservation of date palm caulogenic meristems

Cryopreservation is the technology of choice not only for plant genetic resource preservation but also for virus eradication and for the efficient management of large-scale micropropagation. In this chapter, we describe three cryopreservation protocols (standard vitrification, droplet vitrification, and encapsulation vitrification) for date palm highly proliferating meristems that are initiated from vitro-cultures using plant growth regulator-free MS medium. The positive impact of sucrose preculture and cold hardening treatments on survival rates is significant. Regeneration rates obtained with standard vitrification, encapsulation-vitrification, and droplet-vitrification protocols can reach 30, 40, and 70%, respectively. All regenerated plants from non-cryopreserved or cryopreserved explants don't show morphological variation by maintaining genetic integrity without adverse effect of cryogenic treatment. Cryopreservation of date palm vitro-cultures enables commercial tissue culture laboratories to move to large-scale propagation from cryopreserved cell lines producing true-to-type plants after clonal field-testing trials. When comparing the cost of cryostorage and in-field conservation of date palm cultivars, tissue cryopreservation is the most cost-effective. Moreover, many of the risks linked to field conservation like erosion due to climatic, edaphic, and phytopathologic constraints are circumvented. (Résumé d'auteur

Fertiledatepalm – a transdisciplinary collaboration project to ameliorate date palm cultivation via microbial inoculation, organic matter management and mixed cropping using nurse plants

Date palm is an important crop in Morocco, Tunisia and other drylands with a high agricultural, economic and cultural value. Harsh environmental conditions of those areas, further accelerated by climate change and the spread of root diseases, threaten date palm cultivation. To overcome limitations in productivity, high inputs of mineral fertilizers and pesticides are applied. However, these external inputs strongly affect the environment and livelihoods. The project aims at establishing an integrated microbe-assisted fertilization approach, combining the inoculation of native soil microbes, namely arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) during the different date palm growth stages, with adapted agricultural management practices using organic amendments and mixed-cropping in Morocco and Tunisia. As initial step, we established a culture collection of native microbes, isolated from date palm roots and rhizosphere composed of 24 AMF isolates including eight species from six genera, twelve bacterial endophyte isolates composed of Paenibacillus, Mycobacterium, and Achromobacter species and 34 PGPR isolates. Functional characterization of PGPRs revealed that around 50 % can solubilize phosphorus and potassium and between 9 % and 68 % have the ability to produce siderophores, hydrogen cyanid, chitinase, cellulase, amylase and protease. Consortia of microbes were formed and used for inoculations. Experiments under nursery conditions revealed that inoculation with AMF and PGPR combined with compost significantly increased growth of date palms as compared to non-amended controls enabling farmers to decrease the time prior to field transplantation. On-farm trials performed in productive date palm groves have shown that PGPR inoculation with or without mixed-cropping with sorghum as nurse plants significantly increase fruit characteristics such as fruit flesh weight as well as fruit length and diameter for up to 14 % and leaf macronutrient concentrations for up to 200 % while in addition enhancing the mycorrhizal potential of the soil. Our integrated fertilization approach is developed in a participatory approach with key stakeholders in so-called innovation platforms, working at laboratory, on-station and on-farm scale to best tackle farmers’ needs in order to facilitate adoption and implementation

The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Comparison of droplet-vitrification and D-cryoplate for cryopreservation of date palm (Phoenix dactylifera L.) polyembryonic masses

In this work we tested the efficiency of two techniques, droplet-vitrification (DV) and dehydration (D) cryo-plate, for cryopreservation of polyembryonic masses (PEMs) of two date palm varieties, Sokary and Sultany. With DV, recovery of non-precultured, cryopreserved PEMs was nil without treatment with the PVS2 vitrification solution, which contained 3.3 M glycerol + 2.4 M ethylene glycol + 0.4 M sucrose + 1.9 M dimethylsulfoxide. Following PVS2 treatments between 15 and 120 min, it was comprised between 90.9-98.6% and 85.6-88.0% for varieties Sokary and Sultany, respectively, Sucrose preculture (3 days, 0.5 M) led to 21.1% recovery of cryopreserved PEMs of variety Sokary only without PVS2 treatment, and slightly reduced recovery in all other experimental conditions with both varieties, compared with noncryopreserved PEMs. Regrowth intensity of cryopreserved PEMs was generally lower with variety Sultany compared to variety Sokary. With the D cryo-plate technique, no recovery of cryopreserved PEMs was achieved without sucrose preculture. Sucrose preculture (3 days, 0.5 M) had a positive effect on recovery of cryopreserved PEMs. For variety Sokary, the highest recovery (92.0-95.8%) was achieved for desiccation periods between 60 and 120 min. Recovery was between 67.0 and 74.6% after desiccation periods of 90-120 min for variety Sultany. With the D cryo-plate technique, regrowth intensity of cryopreserved PEMs was higher with variety Sokary compared to variety Sultany