Publications – Publikationen

Sowa, S., Broothaerts, W., Burns, M., De Loose, M., Debode, F. et al. (2025): Detection of microorganisms, obtained by new

genomic techniques, in food and feed products. Publications Office of the European Union, Luxembourg, 2025,

New genomic techniques (NGTs) can be used for the targeted modification of the genome, not only of plants but also of microorganisms. Traceability of genetically modified microorganisms obtained with an NGT (NGT microorganisms) is currently a regulatory requirement under the EU GMO legislation. This report highlights the possibilities and challenges to detect NGT microorganisms (NGT-Ms) in food and feed using analytical technologies. The document builds upon the conclusions of the previously published report on the detection of plant products developed by targeted mutagenesis and cisgenesis (ENGL, 2023a) and adds issues specific for the detection of NGT-Ms.

https://data.europa.eu/doi/10.2760/1846532

https://publications.jrc.ec.europa.eu/repository/handle/JRC143597

Jiang C., Kan J., Gao G., Wu W., Yang J., Stein N. (2025): Barley2035: A decadal vision for barley research and breeding

Perspective 18, 195-218

Barley (Hordeum vulgare ssp. vulgare) is one of the oldest founder crops in human civilization and has been widely dispersed across the globe to support human society as a livestock feed and a raw material for the brewing industries. Since the early half of the 20th century, it has been used for innovative research on cytogenetics, biochemistry, and genetics, facilitated by its mode of reproduction through self-pollination and its true diploid status, which have contributed to the accumulation of numerous germplasm and mutant resources. In the era of molecular genomics and biology, a multitude of barley genes and their related regulatory mechanisms have been identified and functionally validated, providing a paradigm for equivalent studies in other Triticeae crops. This review highlights important advances on barley research over the past decade, focusing mainly on genomics and genomics-assisted germplasm exploration, genetic dissection of developmental and adaptation-related traits, and the complex dynamics of yield and quality formation. In the coming decade, the prospect of integrating these innovations in barley research and breeding shows great promise. Barley is proposed as a reference Triticeae crop for the discovery and functional validation of new genes and the dissection of their molecular mechanisms. The application of precise genome editing as well as genomic prediction and selection, further enhanced by artificial intelligence-based tools and applications, is expected to promote barley improvement to efficiently meet the evolving global demands for this important crop.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(24)00393-9

Liu, H., Zheng, M., Han, S. et al. (2025): Genome-wide identification and functional characterization of the DREB gene

family in barley (Hordeum vulgare L.) reveal its role in drought and salinity responses.BMC Genomics). https://doi.org/10.1186/s12864-025-12433-9

Background: Dehydration response element-binding (DREB) proteins are crucial for plant responses to abiotic stress, particularly in molecular responses to drought and high-salt stress. However, the understanding of the role of DREB proteins in barley, an important and widespread crop, remains limited.

Results: In this study, bioinformatics-based genome-wide analysis revealed 39 DREB genes in barley. These genes are distributed on all barley chromosomes; chr6H has the highest density, with five pairs of segmentally duplicated genes. Moreover, synteny analyses revealed a relatively conserved evolutionary process shared by some HvDREB genes in barley and four other species. Moreover, promoter analysis revealed that HvDREB genes are associated with stress-, drought-, low-temperature- and hormone-responsive cis-acting elements. MicroRNA target site prediction revealed that 14 types of miRNAs regulate 16 HvDREB genes. qRT–PCR analysis verified that upon exposure to distinct stressors, the HvDREB genes presented diverse expression trends in barley roots, stems, and leaves.

Conclusion: These findings indicate that HvDREB genes may regulate plant growth and stress tolerance. On the basis of the bioinformatics and qRT–PCR results, we hypothesized that HvDREB gene expression is closely related to salt and drought stress in barley, providing a basis for further understanding the genetic underpinnings of these key stress adaptations

https://link.springer.com/article/10.1186/s12864-025-12433-9

Sun Y., Hu L., Amas J.C., Thomas W.J.W. et al (2025): BrRCO promotes leaf lobe formation by repressing BrACP5 expression

in Brassica rapa. Horticulture Research 12 (5), uhaf084 | https://doi.org/10.1093/hr/uhaf084

Lobed leaves are advantageous for gas exchange, canopy architecture, and high-density planting; however, the genetic mechanisms of leaf lobe formation in Brassica crops remains poorly understood. Here, lob10.1, our previously identified major QTL controlling the presence/absence of leaf lobes in B. rapa (AA), was fine mapped to a confidence interval of 69.8 kb. REDUCED COMPLEXITY ORGAN (BrRCO, BraA10g032440.3c), a homeodomain leucine zipper class I (HD ZIP I) transcription factor, was predicted to be the most likely candidate gene underlying lob10.1. Null mutations of BrRCO by CRISPR/Cas9 in the lobed-leaf parent RcBr and over-expression in the counter-part near isogenic lines (NIL^RcBr) lead to entire and lobed leaves, respectively. Analysis of the gene evolution revealed that A10. RCO functions as a core gene and was generally negatively selected in B. rapa. Moreover, BrRCO function as a negative regulator by directly binding to promoters of BrACP5 and repressing its expression. The function of ACID PHOSPHATASE TYPE 5 (BrACP5) was subsequently confirmed as VIGS-BrACP5 produced entire leaves in RcBr. This study identified the core gene BrRCO to be involved in the development of leaf lobes in B. rapa and elucidated a new pathway for leaf lobe formation by the BrRCO-BrACP5 module. These findings provide a theoretical basis for the formation of leaf lobes in Brassica crops.

https://academic.oup.com/hr/article/12/5/uhaf084/8071608?login=false

Kesawat, M.S., Kherawat, B.S., Reager, M.L. et al. (2025): Genome-wide identification and expression analysis of the Small

Ubiquitin-like Modifier (SUMO) gene family in Triticum aestivum L.. BMC Genomics 26, 1098 https://doi.org/10.1186/s12864-025-12416-w

Background: Post-translational modification of proteins by SUMO is critical for a wide range of cellular and developmental processes. Although SUMO proteins have been extensively studied in animals and, to some extent, in Arabidopsis, their precise functions in other crop plants are still largely unknown.

Results: In this research, we identified 31 TaSUMO genes in genome of wheat. Phylogenetic tree unveiled that genes clustered into thirteen subfamilies. Chromosomal mapping unveiled the dispersal of 31 TaSUMO genes across 11 wheat chromosomes. The eleven pairs of duplicated gene were identified in the SUMO family. Ka/Ks ratio revealed that 8 duplicated TaSUMO genes went through purifying purification. Furthermore, it was noted that TaSUMO genes displayed significant conversation in their gene structure. In addition, analysis of promoters uncovered the presence of numerous cis-regulatory elements in the promoter region of the TaSUMO genes. The differential expression patterns were observed among TaSUMO family members across various tissues and in response to multifaceted stress conditions. Moreover, this investigation explored the miRNAs targeted to TaSUMO genes and expression profile in various tissues.

Conclusion: Thus, the results of this study establish a strong basis for further investigation of the functions of TaSUMO genes across different tissues, developmental stages, phytohormone responses, and diverse stress in wheat.

https://link.springer.com/article/10.1186/s12864-025-12416-w

Wang Y., Zhang L., Liu M, Zhou M. et al. (2025): Improved efficiency of genetic transformation for the development of elite

germplasm using CRISPR/Cas12i3 in maize. aBIOTECH, 100017 | https://doi.org/10.1016/j.abiote.2025.100017

Genetic transformation and gene-editing technologies have driven progress in molecular design breeding. Jing 724, an elite founder inbred line from the X heterotic group in maize, was previously recalcitrant to genetic transformation owing to genotype-dependent restrictions. Here, we established a stable and efficient genetic transformation system for Jing 724 using the morphogenic genes Baby boom (Bbm) and Wuschel (Wus2) and the selection marker 6-phosphomannose isomerase (PMI). Under identical Bbm/Wus2-regulation conditions, the efficiencies of callus induction, regeneration, and transformation were significantly higher (30%) with PMI (mannose) selection than with bar (bialaphos) selection. By optimizing callus induction and regeneration time, we reduced the transformation period for Jing 724 from 90 days to 60 days and increased the transformation efficiency by 20%. We then combined this transformation system with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 12i3 (Cas12i3) system to edit the Sugary1 (Su1) and Waxy (Wx) genes, thereby developing elite germplasms with common sweet, waxy, and combined sweet–waxy traits in the Jing 724 background. We obtained mutation efficiencies of 29.41% (homozygous), 41.18% (heterozygous), and 35.29% (simultaneous). Additionally, concentrations of sucrose, water-soluble polysaccharides, and starch in the endosperms of T₁ homozygous kernels were confirmed to differ significantly from those in wild-type kernels. Thus, we have established a highly efficient molecular breeding system that integrates genetic transformation, gene editing, and germplasm development.

https://www.sciencedirect.com/science/article/pii/S2662173825002243

Huang, Y., Yang, X., Guo, T. et al.(2025): Genome-wide association analysis reveals novel genetic loci involved in rice

brown spot resistance. BMC Genomics (2025). https://doi.org/10.1186/s12864-025-12403-1

Background: Rice brown spot (BS) substantially impacts both yield and grain quality of rice, while research on this disease remains relatively limited compared to some major rice diseases like rice blast and rice sheath blight.

Results:In our study, 529 rice accessions were evaluated for BS resistance during two growing seasons (October 2021 and March 2022), resulting in the identification of 93 accessions that consistently exhibited resistance (R) or high resistance (HR) to BS across both seasons. Among these, 5 accessions consistently displayed high resistance (HR) grade in both seasons. Additionally, GWAS analysis was performed on the BS resistant level gathered from 529 accessions across two distinct seasons, revealing 52 significant single-season identified QTLs, 11 co-located QTLs across two seasons, and 5 algorithm co-located QTLs. Notably, 13 of these QTLs overlapped with previous studies, including the significant BS resistance QTL, qBS11. Haplotype analysis within the candidate genes located in these essential intervals led to the identification of 5 potential candidate genes (LOC_Os03g40194, LOC_Os05g48660, LOC_Os02g08440, LOC_Os11g38000, LOC_Os08g06380) correlated with BS resistance. Moreover, the varying response of these 5 genes in ‘Huilongzao No.1’ (resistant variety) and ‘ChangQi’ (susceptible variety) was analyzed through qPCR analysis, suggesting their potential involvement in diverse BS resistance mechanisms.

Conclusion: This study provides valuable germplasm resources and identifies key candidate QTLs and genes for BS resistance research, bridging the gap in the limited identification of genetic markers associated with this disease. These findings establish a critical foundation for advancing future research into BS resistance mechanisms and breeding strategies.

https://link.springer.com/article/10.1186/s12864-025-12403-1

Gong L., Zhang L., Zhang H., Nie F. et al.(2025): Haplotype-resolved genome assembly and genome-wide association study

identifies the candidate gene closely related to sugar content and tuber yield in Solanum tuberosum Access Horticulture Research 12 (6), uhaf075 | https://doi.org/10.1093/hr/uhaf075

As an important noncereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of ‘Ningshu 15’, a tetraploid variety featured by its high starch content and drought resistance was presented. The assembled genome size was 1.653 Gb, with a contig N50 of approximately 1.4 Mb and a scaffold N50 of 61 Mb. The long terminal repeat assembly index score of the two identified haplotypes of ‘Ningshu 15’ was 11.62 and 11.94, respectively. Comparative genomic analysis revealed that positive selection occurred in gene families related to starch, sucrose, fructose and mannose metabolism, and carotenoid biosynthesis. Further genome-wide association study in 141 accessions identified a total number of 53 quantitative trait loci related to fructose, glucose, and sucrose content. Among them, a tonoplast sugar transporter encoding gene, StTST2, closely associated with glucose content was identified. Constitutive expression of StTST2 in potato and Arabidopsis increased the photosynthetic rate, chlorophyll and sugar content, biomass tuber and seed production in transgenic plants. In addition, co-immunoprecipitation assays demonstrated that StTST2 directly interacted with SUT2. Our study provides a high-quality genome assembly and new genetic locus of potato for molecular breeding.

https://academic.oup.com/hr/article/12/6/uhaf075/8109941?login=false

Huang D., Ma J., Chen X., Wang H. et al.(2025): CsWRKY17 enhances Al accumulation by promoting pectin deesterification

in tea plant. Horticulture Research 12 (7), uhaf085 | https://doi.org/10.1093/hr/

The tea plant (Camellia sinensis) is a typical crop that accumulates aluminum (Al). Although the physiological mechanisms by which this occurs are well understood, their molecular mechanisms remain elusive. Here, an integrative approach combining quantitative trait locus (QTL) mapping of controlled hybridized populations and comparative transcriptomic analysis using samples treated with different Al concentrations was applied to identify candidate genes associated with Al accumulation in tea plants. Consequently, 41 candidate genes were selected using genome functional annotation of the qAl09 locus in the region of 35 256 594–57 378 817 bp on chromosome 7. Finally, a key gene, CsWRKY17, was identified as encoding a nucleus-localized transcription factor involved in regulating Al accumulation in tea plants, given the finding of a high correlation between its expression level and Al content in leaves. Overexpression of CsWRKY17 in Arabidopsis increased pectin deesterification, sensitivity to Al stress, and Al accumulation in leaves. Expression of the pectin methylesterase gene CsPME6 was found to be highly consistent with CsWRKY17 expression under various Al concentrations. In addition, experiments using a yeast monoclonal, electrophoresis mobility shift assay and dual-luciferase reporter (DLR) system confirmed that CsWRKY17 activated CsPME6 promoter activity. Antisense oligodeoxynucleotide silencing revealed a positive association between CsPME6 expression and Al accumulation in tea shoots. In conclusion, this study suggests that CsWRKY17 promoted the process of pectin deesterification by binding to the CsPME6 promoter, thereby enhancing Al enrichment in tea plants. Our findings lay the foundation for studying the precise mechanisms through which Al enriched in tea leaves.

https://academic.oup.com/hr/article/12/7/uhaf085/8069468?login=false

EFSA

FEZ Panel (2025): Safety evaluation of the food enzyme leucyl aminopeptidase from the non-genetically modified Lichtheimia

ramosa strain AE-PER. EFSA Journal, 23(12), e9771. https://doi.org/10.2903/j.efsa.2025.9771

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9771

FEZ Panel (2025):  Safety evaluation of the food enzyme triacylglycerol lipase from the genetically modified Aspergillus oryzae

strain NZYM-PH. EFSA Journal, 23(12), e9768. https://doi.org/10.2903/j.efsa.2025.9768

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9768

FEZ Panel (2025): Safety evaluation of the food enzyme endo-1,3(4)-β-glucanase from the non-genetically modified Trichoderma

reesei strain TG-M5-337. EFSA Journal, 23(12), e9770. https://doi.org/10.2903/j.efsa.2025.9770

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9770

FEZ Panel (2025): Safety evaluation of the food enzyme prolyl oligopeptidase from the genetically modified Aspergillus niger

strain NZYM-MR. EFSA Journal, 23(12), e9769. https://doi.org/10.2903/j.efsa.2025.9769

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9769

21.12.2025

last one 2025