Sunday Evening News 373 - Week 17 - 2024
Weekly report on genetic engineering, genome editing, biotechnology and legal regulations.
April 2024-04-22 - 2024-04-28
Press Releases -Media / Presse- und Medienberichte
Voting 2024-04-2024 on the Commission’s proposal for regulation of certain ngt-plants
ECVC: Press release - European Parliament votes on GMOs/NGTs and seeds: Repeated violations of peasants' rights
euroseds: European Parliament confirms positive Vote on New Genomic Techniques; EU Council urged to embrace plant
breeding innovation
European Parliament Confirms Positive Vote on New Genomic Techniques; EU Council Urged to Embrace Plant Breeding Innovation
Meldungen zur Abstimmung am 24.04.20024 über den Kommissionsvorschlag zur Regulierung gewisser NGT-Pflanzen
Informationsdienst Gentechnik: EU-Parlament bestätigt Lockerungspläne bei neuer Gentechnik
https://www.keine-gentechnik.de/nachricht/34932?cHash=50ce641875ccc6e55da2cacdd06fe9c5
Koch J.: Gentechnik: EU-Abgeordnete stimmen für neue Züchtungstechniken
GRAIN-Club: Offener Brief von Verbänden der deutschen Agrar-, Gartenbau- sowie Ernährungs-und
Bioökonomiewirtschaft: Landwirtschaft zukunftsfähig machen: Anwendung von neuen genomischen Techniken in
Europa zeitnah ermöglichen
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Testbiotech: NGT plants: EFSA overlooked most powerful and risky applications
https://www.testbiotech.org/en/news/ngt-plants-efsa-overlooked-most-powerful-and-risky-applications
Webinar: NGT plants - a pandora's box - Presentations
https://www.testbiotech.org/node/3232
Was ist (keine) Gentechnik?
https://www.testbiotech.org/infomaterialien/was-ist-keine-gentechnik/
USDA: APHIS Issues Regulatory Status Review Responses
https://www.aphis.usda.gov/news/program-update/aphis-issues-regulatory-status-review-responses-2
BERICHT DER KOMMISSION AN DAS EUROPÄISCHE PARLAMENT UND DEN RAT über die Ausübung der der Kommission übertragenen
Befugnis zum Erlass delegierter Rechtsakte gemäß der Richtlinie 2001/18/EG über die absichtliche Freisetzung genetisch veränderter Organismen in die Umwelt und der Verordnung (EG) Nr. 1830/2003 über die Rückverfolgbarkeit und Kennzeichnung von genetisch veränderten Organismen und über die Rückverfolgbarkeit von aus genetisch veränderten Organismen hergestellten Lebensmitteln und Futtermitteln.
https://eur-lex.europa.eu/legal-content/DE/TXT/PDF/?uri=CELEX:52024DC0170
AFBV: Intellectual property on plant varieties generally and NGT-derived varieties in particular.
https://www.biotechnologies-vegetales.com/blog/reglementation/
Only some selected press releases or media reports are listed here. The daily up-date of the press releases and
media reports are ►here: April week 17
Publications – Publikationen
Schreiber T., Prange A., Schäfer P., Iwen T., +5, Tissier A. (2024): Efficient scar-free knock-ins of several kilobases in plants
by engineered CRISPR/Cas endonucleases. Mol Plant | https://doi.org/10.1016/j.molp.2024.03.013
In plants and mammals, non-homologous end-joining is the dominant pathway to repair DNA double-strand breaks, making it challenging to generate knock-in events. In this study, we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana benthamiana. We achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation systems. In Arabidopsis thaliana, fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of transformants. In addition, we demonstrated stable and heritable knock-ins in wheat in 1% of the primary transformants. Taken together, our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.
https://www.sciencedirect.com/science/article/pii/S1674205224000868
Yan, J., Oyler-Castrillo, P., Ravisankar, P. et al. (2024): Improving prime editing with an endogenous small RNA-binding
protein. Nature 628, 639–647 | https://doi.org/10.1038/s41586-024-07259-6
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3′ ends of CRISPR–Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3′ ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3′ ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
https://www.nature.com/articles/s41586-024-07259-6
Li, B., Sun, C., Li, J. et al. (2024): Targeted genome-modification tools and their advanced applications in crop breeding.
Nat Rev Genet| https://doi.org/10.1038/s41576-024-00720-2
Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.
https://www.nature.com/articles/s41576-024-00720-2
Mmbando G.S. (2024): The Adoption of Genetically Modified Crops in Africa: the Public’s Current Perception, the
Regulatory Obstacles, and Ethical Challenges. GM CROPS & FOOD 2024, VOL. 15, NO. 1, 1–15 | https://doi.org/10.1080/21645698.2024.234540
Genetically modified (GM) crops are the most important agricultural commodities that can improve the yield of African smallholder farmers. The intricate circumstances surrounding the introduction of GM agriculture in Africa, however, underscore the importance of comprehending the moral conundrums, regulatory environments, and public sentiment that exist today. This review examines the current situation surrounding the use of GM crops in Africa, focusing on moral conundrums, regulatory frameworks, and public opinion. Only eleven of the fifty-four African countries currently cultivate GM crops due to the wide range of opinions resulting from the disparities in cultural, socioeconomic, and environmental factors. This review proposed that addressing public concerns, harmonizing regulations, and upholding ethical standards will improve the adoption of GM crops in Africa. This study offers ways to enhance the acceptability of GM crops for boosting nutrition and food security globally.
https://www.tandfonline.com/doi/full/10.1080/21645698.2024.2345401
Mat Jalaluddin, N.S., Ahmad Fuaad, A.AH. & Othman, R.Y. (2024): Regulatory landscape and public perception for gene-edited
bananas in the Southeast Asian region. Transgenic Res | https://doi.org/10.1007/s11248-024-00379-9
Banana is a premier fruit crop in many parts of the world especially Southeast Asia. The demand for banana has contributed to significant national income to primary banana producers in the SEA region such as the Philippines, Indonesia, Thailand, Vietnam, and Malaysia. However, the widely traded banana industry is plagued by numerous threats including pests and diseases, post-harvest issues and extreme climate vulnerability. To address these challenges, new breeding techniques such as gene editing have been explored for breeding programs to develop improved banana varieties. The first gene-edited non-browning banana has been deregulated in the Philippines recently, and more regulatory applications are expected to submit for approvals soon. Hence, it is timely to review the policy options for gene editing that have been adopted and discussed in the Southeast Asian countries and highlight the implications of differing regulatory approaches to gene editing for trading activities. Positive stakeholders’ perceptions and public acceptance are key factors in allowing the benefits of gene editing and thus appropriate outreach strategies are important to gain acceptance and avoid the “GMO stigma” that may be associated with gene-edited products.
https://link.springer.com/article/10.1007/s11248-024-00379-9
Salojärvi, J., Rambani, A., Yu, Z. et al. (2024): The genome and population genomics of allopolyploid Coffea arabica reveal
the diversification history of modern coffee cultivars. Nat Genet 56, 721–731 | https://doi.org/10.1038/s41588-024-01695-w
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
https://www.nature.com/articles/s41588-024-01695-w
Wu, X., Hu, Z., Zhang, Y. et al. (2024): Differential selection of yield and quality traits has shaped genomic signatures of
cowpea domestication and improvement. Nat Genet | https://doi.org/10.1038/s41588-024-01722-w
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
https://www.nature.com/articles/s41588-024-01722-w
Lu, Q., Zhao, H., Zhang, Z. et al. (2024): Genomic variation in weedy and cultivated broomcorn millet accessions uncovers
the genetic architecture of agronomic traits. Nat Genet | https://doi.org/10.1038/s41588-024-01718-6
Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.
https://www.nature.com/articles/s41588-024-01718-6
Chowdhury, S., Bansal, S., Jha, S.K. et al. (2024): Characterization and identification of sources of rust resistance in
Triticum militinae derivatives. Sci Rep 14, 9408 | https://doi.org/10.1038/s41598-024-59902-x
Triticum militinae (2n = 4X = 28, AtAtGG), belonging to the secondary gene pool of wheat, is known to carry resistance to many diseases. Though some disease resistance genes were reported from T. timopheevii, the closest wild relative of T. militinae, there are no reports from T. militinae. Twenty-one T. militinae Derivatives (TMD lines) developed at the Division of Genetics, IARI, New Delhi, were evaluated for leaf and stripe rusts at seedling and adult plant stages. Eight TMD lines (6–4, 6–5, 11–6, 12–4, 12–8, 12–12, 13–7 and 13–9) showed seedling resistance to both leaf and stripe rusts while six TMD lines (7–5, 7–6, 11–5, 13–1, 13–3 and 13–4) showed seedling resistance to leaf rust but adult plant resistance to stripe rust and three TMD lines (9–1, 9–2 and 15) showed seedling resistance to leaf rust but susceptibility to stripe rust. Three TMD lines (2–7, 2–8 and 6–1) with adult plant resistance to leaf and stripe rusts were found to carry the known gene Lr34/Yr18. Ten TMD lines (7–5, 7–6, 9–1, 9–2, 11–5, 11–6, 12–12, 12–4, 12–8, and 15) with seedling resistance to leaf rust, showing absence of known genes Lr18 and Lr50 with linked markers requires further confirmation by the test of allelism studies. As not a single stripe rust resistance gene has been reported from T. militinae or its close relative T. timpopheevii, all the 8 TMD lines (6–4, 6–5, 11–6,12–4, 12–8, 12–12, 13–7 and 13–9) identified of carrying seedling resistance to stripe rust and 3 TMD lines (13–1, 13–3 and 13–4) identified of carrying adult plant resistance to stripe rust are expected to carry unknown genes. Also, all the TMD lines were found to be cytologically stable and thus can be used in inheritance and mapping studies.
https://www.nature.com/articles/s41598-024-59902-x
Liang B. et al. (2024): Genome reannotation of the sweetpotato (Ipomoea batatas (L.) Lam.) using extensive Nanopore
and Illumina-based RNA-seq datasets, Tropical Plants | DOI: 10.48130/tp-0024-0009
Sweetpotato (Ipomoea batatas (L.) Lam.) is a globally cultivated root crop of paramount significance. The hexaploid genome, known as 'Taizhong 6', has been sequenced and serves as a crucial reference genome for sweetpotato and related species within the Convolvulaceae family. However, the current annotation of the sweetpotato genome relies primarily on ab initio predictions and, to a lesser extent, transcriptome datasets, which only predict coding sequences. Therefore, an improved annotation is highly desirable. Here, we present a comprehensive reannotation of the sweetpotato genome, leveraging 12 Nanopore full-length RNA libraries and 190 Illumina RNA-seq libraries. The improved annotation, named v1.0.a2, includes 42,751 gene models, with 97.4% complete BUSCOs. Within this comprehensive set of gene models, we have modified or added 31,771 gene models and identified 8,736 genes with alternatively spliced isoforms. We have also introduced a new gene ID nomenclature (IbXXGXXXXX) as an improvement over the previous nomenclature (gene.gXXXXX). Additionally, we have annotated and provided expression levels of miRNAs and their targets at different storage roots stages. Overall, our study contributes to an updated genome annotation for the sweetpotato genome, which will significantly facilitate gene functional studies in sweetpotato and promote genomic analyses across the Convolvulaceae family.
https://www.maxapress.com/article/doi/10.48130/tp-0024-0009
Yang S., Wang G., Niu M. et al. (2024): Impacts of AlaAT3 transgenic poplar on rhizosphere soil chemical properties,
enzyme activity, bacterial community, and metabolites under two nitrogen conditions, GM Crops & Food, 15:1, 1-15, | https://doi.org/10.1080/21645698.2024.2339568
Poplar stands as one of the primary afforestation trees globally. We successfully generated transgenic poplar trees characterized by enhanced biomass under identical nutrient conditions, through the overexpression of the pivotal nitrogen assimilation gene, pxAlaAT3. An environmental risk assessment was conducted for investigate the potential changes in rhizosphere soil associated with these overexpressing lines (OL). The results show that acid phosphatase activity was significantly altered under ammonium in OL compared to the wild-type control (WT), and a similar difference was observed for protease under nitrate. 16SrDNA sequencing indicated no significant divergence in rhizosphere soil microbial community diversity between WT and OL. Metabolomics analysis revealed that the OL caused minimal alterations in the metabolites of the rhizosphere soil, posing no potential harm to the environment. With these findings in mind, we anticipate that overexpressed plants will not adversely impact the surrounding soil environment.
https://www.tandfonline.com/doi/full/10.1080/21645698.2024.2339568
Peleke, F.F., Zumkeller, S.M., Gültas, M. et al. (2024): Deep learning the cis-regulatory code for gene expression in selected
model plants. Nat Commun 15, 3488 | https://doi.org/10.1038/s41467-024-47744-0
Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predicting gene expression profiles from gene flanking regions of the plant species Arabidopsis thaliana, Solanum lycopersicum, Sorghum bicolor, and Zea mays. With over 80% accuracy, our models enabled predictive feature selection, highlighting e.g. the significant role of UTR regions in determining gene expression levels. The models demonstrated remarkable cross-species performance, effectively identifying both conserved and species-specific regulatory sequence features and their predictive power for gene expression. We illustrated the application of our approach by revealing causal links between genetic variation and gene expression changes across fourteen tomato genomes. Lastly, our models efficiently predicted genotype-specific expression of key functional gene groups, exemplified by underscoring known phenotypic and metabolic differences between Solanum lycopersicum and its wild, drought-resistant relative, Solanum pennellii.
https://www.nature.com/articles/s41467-024-47744-0
Zhou, P., Liu, X., Liang, J. et al. (2024): GMOIT: a tool for effective screening of genetically modified crops.
BMC Plant Biol 24, 329 | https://doi.org/10.1186/s12870-024-05035-2
Background: Advancement in agricultural biotechnology has resulted in increasing numbers of commercial varieties of genetically modified (GM) crops worldwide. Though several databases on GM crops are available, these databases generally focus on collecting and providing information on transgenic crops rather than on screening strategies. To overcome this, we constructed a novel tool named, Genetically Modified Organisms Identification Tool (GMOIT), designed to integrate basic and genetic information on genetic modification events and detection methods.
Results: At present, data for each element from 118 independent genetic modification events in soybean, maize, canola, and rice were included in the database. Particularly, GMOIT allows users to customize assay ranges and thus obtain the corresponding optimized screening strategies using common elements or specific locations as the detection targets with high flexibility. Using the 118 genetic modification events currently included in GMOIT as the range and algorithm selection results, a “6 + 4” protocol (six exogenous elements and four endogenous reference genes as the detection targets) covering 108 events for the four crops was established. Plasmids pGMOIT-1 and pGMOIT-2 were constructed as positive controls or calibrators in qualitative and quantitative transgene detection.
Conclusions: Our study provides a simple, practical tool for selecting, detecting, and screening strategies for a sustainable and efficient application of genetic modification.
https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-024-05035-2
Li, W.; Zou, G.; Bao, D.; Wu, Y. (2024): Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research
Techniques, Functional Analysis, and Prospects. J. Fungi 10, 311 | https://doi.org/10.3390/jof10050311
Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry.
https://www.mdpi.com/2309-608X/10/5/311
EFSA:
EFSA: Pestizidrückstände in Lebensmitteln: aktuelle Zahlen veröffentlicht
https://www.efsa.europa.eu/de/news/pesticide-residues-food-latest-figures-released
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8753
GMO Panel (2024): Assessment of genetically modified maize MON 94804 (application GMFF-2022-10651). EFSA Journal, 22 (4),
e8714. https://doi.org/10.2903/j.efsa.2024.8714
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8714
GMO Panel (2024). Assessment of genetically modified maize MON 89034 × 1507 × NK603 for renewal authorisation under Regulation
(EC) No 1829/2003 (application GMFF-2022-3670). EFSA Journal, 22 (4), e8716. https://doi.org/10.2903/j.efsa.2024.8716
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8716