Publications – Publikationen

Sekerci Keles, P., Esen, Y. (2026): Genome editing and food safety: bridging the validation gap. npj Sci Food |

https://doi.org/10.1038/s41538-026-00843-2

Genome editing is increasingly positioned as a tool for improving food safety and nutritional quality, yet its real-world impact depends on outcomes that extend far beyond molecular precision. This review synthesizes evidence on how genome edits translate through phenotypes, food matrices, processing, microbial ecology, and dietary exposure, revealing a persistent validation gap between early-stage technical metrics and food-safety–relevant endpoints. We argue for an exposure-anchored, multi-layered validation framework incorporating omics, post-harvest behavior, and post-market monitoring. Closing this gap is essential for aligning genome editing innovations with measurable improvements in food system safety and consumer protection.

https://www.nature.com/articles/s41538-026-00843-2

Peer L,A. (2026): The epigenetic set-point: metabolic and redox gating of developmental transitions in plants.

New Phytologist | https://doi.org/10.1111/nph.71184

Plants survive fluctuating environments by converting transient stress signals into stable developmental decisions; however, the biophysical logic that filters environmental ‘noise’ from true ‘signals’ remains elusive. I propose the epigenetic set-point paradigm, in which chromatin acts as a biophysical integrator that couples metabolic and redox inputs to establish developmental thresholds. I delineate the molecular hardware, writers that nucleate chromatin states, readers that compact chromatin, and erasers that reset marks, which convert analog environmental cues into digital, bistable switches at master regulatory loci, such as FLOWERING LOCUS C and VERNALIZATION 1. I present a testable model showing how redox gating of histone erasers mediated by nitric oxide and reactive oxygen species and metabolic gating of chromatin writers mediated by Target of Rapamycin signaling and acetyl–CoA availability collectively modulate developmental transition probabilities. This integration generates a spectrum of memory stabilities, from the Digital Set-Point of vernalization to Metastable Set-Point underlying thermomemory and rare transgenerational inheritance. Finally, I translate this framework into an epibreeding roadmap, proposing the use of single-cell epigenomic approaches for predictive phenology and tunable epigenetic engineering to design crops with ‘rheostat-like’ resilience. Together, this synthesis positions the epigenetic set-point as a dynamic, programmable logic governing plant adaptation to climate change.

https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.71184

Zhang, X., Lan, L., Yang, Y. et al. (2026): Pangenomic analyses of rose uncover widespread structure variation and

empower genomics-directed breeding. Nat Genet | https://doi.org/10.1038/s41588-026-02569-z

Roses are economically important ornamental plants, with widespread applications in the cut flowers, garden and cosmetics industries. The genomic evolution and diversity of the subgenus Rosa remain understudied, limiting exploitation of its diversity in breeding. Here we assembled genomes of 23 accessions, comprising 51 haplotypes that capture the subgenus’s high genetic diversity. Extensive introgression across accessions from different sections highlights crossbreeding potential. Pangenome analysis revealed 1,801,537 structural variations, providing insights into the genetic basis and key regulators controlling key traits such as continuous flowering, petal number and discoloration. A key finding was the identification of a CCD4 homolog as the main regulator of petal discoloration. Additional subgenomic analysis of the allopolyploid Rosa gallica and the triploid Rosa hybrida ‘La France’, two important breeding materials of modern roses, revealed their hybrid origins. Overall, this study advances understanding of rose genomics and provides valuable resources for future breeding and trait improvement.

https://www.nature.com/articles/s41588-026-02569-z

Bian, J., Zhang, Y., Ding, S. et al. (2026): Telomere-to-telomere genome assemblies and population resequencing of diploid

and allotetraploid peanut varieties. Nat Genet | https://doi.org/10.1038/s41588-026-02577-z

Peanut (Arachis hypogaea L.) is a globally significant leguminous oil crop. Here we present telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties, resulting in high-quality reference genomes, showing that the complex activities of transposable elements, chromosomal rearrangements and centromere expansions within subgenomes collectively contribute to the asymmetrical evolution of the tetraploid genome, and unique structural variants in the four tetraploid peanut varieties provide clear evidence of domestication. Population analyses of 521 peanut accessions revealed asymmetric selection events between subgenomes during breeding, and genome-wide association studies identified candidate genes linked to oil content, seed size and weight, kernel dehydration rate, and arachidic acid content. In addition, transcriptomic and metabolomic analyses revealed enhanced activity in lipidomic and anthocyanin biosynthetic pathways during seed development. These comprehensive findings provide insights into genome organization, evolutionary dynamics and phenotypic differentiation across peanut varieties that could inform future peanut breeding and improvement strategies.

https://www.nature.com/articles/s41588-026-02577-z

Nagamine A. et al, CRISPR/Cas9-mediated knockout of DFR alters pigmentation and shifts flavonoid accumulation in red

leaf lettuce without detectable growth penalties, Frontiers in Genome Editing | DOI: 10.3389/fgeed.2026.1755922

Red leaf lettuce (Lactuca sativa L. cv. ‘Red Fire’) is a preferred crop in plant factories with artificial light (PFALs) due to its short cultivation cycle and high anthocyanin content, which increases both its nutritional value and visual appeal. However, anthocyanins strongly influence leaf coloration and antioxidant profiles, and their levels are highly responsive to the light environment. Therefore, targeted editing of flavonoid biosynthesis may provide a breeding strategy to diversify pigment composition and associated functional traits under PFAL conditions. In this study, we used CRISPR/Cas9 to knock out DFR (dihydroflavonol 4-reductase), a key enzyme in the anthocyanin pathway. Genome-edited lines were generated via a dual-guide RNA system, resulting in a successfully edited red leaf genotype. The DFR-knockout lines displayed a complete loss of red pigmentation and a visibly distinct green phenotype. Metabolite profiling revealed a significant decrease in anthocyanin levels, accompanied by an increase in total flavonoid levels in some lines. Growth traits, including shoot dry weight and leaf number, were not significantly affected, suggesting that DFR knockout does not compromise growth under PFAL conditions. These findings highlight DFR as a promising target for creating pigment-altered lettuce lines for controlled-environment cultivation, including PFAL systems.

https://www.frontiersin.org/journals/genome-editing/articles/10.3389/fgeed.2026.1755922/full

Quan Y., Wang L., Li X., Huang L. et al. (2026): Commercial planting of genetically modified maize lowers pest damage,

yield loss and pesticide usage in Northeast China Pest Manag Sci  | https://doi.org/10.1002/ps.70796

BACKGROUND: Lepidopteran herbivores and weeds greatly constrain the productivity of maize globally. Genetically modified (GM) maize lines expressing insecticidal cry genes and herbicide-tolerant epsps genes are widely adopted in the continental America, but their uptake is restricted in many parts of the other countries. Northeast China, which is the largest maize planting area of the country, GM maize with both Bt insecticidal and herbicide tolerance genes was commercially released in 2021 and its cultivation reached 250 000 ha in 2023. Here, we investigated the performance of GM maize in terms of pest damage, yield loss and pesticide usage, amongst other metrics, to assess the safety and benefits.

RESULT: We show how GM maize achieved >99% control of the locally prevailing lepidopteran pests and permitted 97% herbicidal weed control over a 3-year period. As compared to non-GM maize, GM maize yields increased by 4.6–10.1%, mycotoxin contamination levels were reduced by 91.7–95.6% and farmers' net income (under subsidized seed prices) rose by US$276–332 ha−1. Both insecticide and herbicide application frequencies in GM maize decreased significantly.

CONCLUSION: Our work underlines how GM maize curbs pesticide use intensity, upholds food security and allays food safety concerns. When tactically paired with biological control and the agroecological components of integrated pest management, GM maize could provide durable crop protection and shrink the environmental footprint of agriculture in China.

https://scijournals.onlinelibrary.wiley.com/doi/10.1002/ps.70796

González-Delgado, A., Bonillo-Lopez, L., Johnson, M.S. et al. (2026). Genome editing of phylogenetically distinct bacteria

using cross-species retron-mediated recombineering. Nat Biotechnol | https://doi.org/10.1038/s41587-026-03076-6

Advanced genome editing technologies have enabled rapid, flexible rewriting of the Escherichia coli genome, but most have not been tested in other bacterial species. Recombitrons—a genome editing tool created by pairing modified, donor-producing bacterial retrons with single-stranded binding and annealing proteins—have increased the efficiency of recombineering to install flexible, precise edits in the prokaryotic chromosome. Here, to extend their utility outside of E. coli, we surveyed the portability and versatility of retron-mediated recombineering across three different bacterial phyla (Proteobacteria, Bacillota and Actinomycetota) and a total of 15 different species. We found that retron recombineering is variable across the species tested but functional in all of them, reaching editing efficiencies >20% in six of them, >40% in three and >90% in two. Efficiencies in the remaining nine species ranged from 0.015% to 7.4%. We also tested the extension of the recombitron architecture, operon and strain modifications in a subset of hosts in which species-specific modifications were required to increase editing rates.

https://www.nature.com/articles/s41587-026-03076-6

Zhang H., Liu L., Wang D., Yang X. et al. (2026): CRISPR-Cas gene editing technology in biomanufacturing to enhance

stress tolerance of microbial strains FEMS Microbiology Letters, 373, fnag030 | https://doi.org/10.1093/femsle/fnag030

In response to the loss of microbial efficiency caused by environmental stress in biomanufacturing, CRISPR-Cas gene editing technology has become a core tool for enhancing stress tolerance by accurately targeting genomic loci. This article systematically reviews the progress of its application. By optimizing engineered nucleases, gRNA design, and innovative delivery strategies, this technology successfully regulates key pathways in oxidative stress responses. It integrates functional genome screening with dynamic regulation to examine the networks of multi-gene collaborative tolerance. In the construction of high-stress-tolerant industrial chassis cells, the stress survival rate (>90% in Bacillus subtilis under thermal stress) and product synthesis ability (such as cellulose producing ethanol up to 4.5 g/l) of strains such as Escherichia coli and Corynebacterium glutamicum were significantly improved. Current challenges focus on delivery efficiency, off-target risks, and complex regulatory bottlenecks. In the future, the development of new editing tools and intelligent circuits will promote their industrial application in sustainable biomanufacturing.

https://academic.oup.com/femsle/article-abstract/doi/10.1093/femsle/fnag030/8539736?redirectedFrom=fulltext