Journal of Genetics and Genomics

ZmPRX38 is required for improving stalk strength and yield in maize

Xiaqing Wang, Tianyi Wang, et al.

doi: 10.1016/j.jgg.2025.10.009

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Abstract:
Stalk lodging is a major problem in maize production, usually causing significant yield losses due to weak stalk strength. Understanding the genetic basis of stalk strength is crucial for improving maize lodging resistance. In this study, we identify 31 quantitative trait loci (QTLs) related to maize stalk strength and clone ZmPRX38 (encoding peroxidase 38) responsible for a hotspot QTL region of stalk strength. ZmPRX38 is highly expressed in maize stalk during vegetative growth stage, and its protein is localized in the cell membrane, cytoplasm and apoplast. Knockout of ZmPRX38 decreases stalk strength and yield in maize, while overexpressing ZmPRX38 increases stalk strength and yield. ZmPRX38 in phenylpropanoid pathway is involved in the biosynthesis of guaiacyl lignin, p-hydroxy-phenyl lignin, and syringyl lignin. Additionally, we identify a favorable haplotype of ZmPRX38, which enhances stalk strength, containing 3 loci distributed in the 5’ untranslated region (UTR), exon 1, and 3’UTR of ZmPRX38, respectively. Although 91.46% of maize natural lines contain this favorable haplotype, most of the Huang-gai (HG) lines, a backbone maize germplasm, contain the unfavorable haplotypes. Therefore, targeted improvement of ZmPRX38 by editing unfavorable haplotypes may be an effective strategy for increasing maize stalk strength, thereby improving maize lodging resistance and yield.

Dual-target CRISPR-Cas12 diagnostics based on asymmetrically chemical-modified DNA probe

Xinge Wang, Yangcan Chen, et al.

doi: 10.1016/j.jgg.2025.10.007

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Abstract:
CRISPR-based nucleic acid detection technologies have revolutionized infectious disease detection and environmental monitoring by leveraging RNA–DNA complementarity to enable rapid, precise, and cost-effective detection of targets. However, achieving multitarget detection in one tube still presents challenges that necessitate further research. Here, we develop a nucleic acid detection module based on the CRISPR-Cas12i system. Importantly, we find that Cas12i and AapCas12b exhibit opposite trans-cleavage preferences for asymmetrically phosphorothioate-modified single-strand DNA probes, enabling the development of an effective dual-target nucleic acid detection platform by combining these two Cas12 nucleases in one tube. Moreover, this dual-target detection platform exhibits high specificity and sensitivity in genotyping the nucleic acid targets of human papillomavirus (HPV) 16 and HPV18, as well as Influenza A virus (FluA) and Respiratory syncytial virus. Notably, combined with loop-mediated isothermal amplification, this platform achieves high detection rates for clinical samples (18/18 FluA and 18/18 GAPDH internal reference detection rate). Taken together, these results can broaden the application of CRISPR-based Cas12 proteins for multi-target nucleic acid detection in one tube.

E75-induced Toll/NF-κB signaling cooperates with Notch and Hippo pathways to promote tumor malignancy

Xianping Wang, Yifan Guo, et al.

doi: 10.1016/j.jgg.2025.10.006

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Genetic and molecular mechanisms of phytohormone-mediated seed size control in crops

Shan Jiang, Lian Wu, et al.

doi: 10.1016/j.jgg.2025.10.005

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Abstract:
Seed size is an important agronomic trait determining crop yield. Identifying key genes involved in seed size regulation and elucidating their molecular mechanisms are of great significance for crop breeding. Recent studies in crops have uncovered numerous genes that control seed size and weight, many of which function by modulating phytohormone biosynthesis, metabolism, or signaling pathways. This review provides a comprehensive overview of the genetic and molecular mechanisms by which phytohormones regulate seed size and weight and their cross-talks in modulating seed size. We highlight the functional conservation and divergence of homologous genes that control seed size across species. A particular focus is placed on those genes that have promising potential for yield improvement. Finally, we discuss current challenges in phytohormone regulation of seed size and molecular design breeding strategies for translating this knowledge into crop improvement.

A universal cost-efficient sample labeling approach for multiplexed single cell RNA-seq based on recombinant HUH-endonuclease-agglutinin tagging

Quanyong Zhang, Maorong Li, et al.

doi: 10.1016/j.jgg.2025.10.004

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Abstract:
Recent advances in single-cell transcriptomics have revolutionized our understanding of cellular diversity and tissue heterogeneity, providing unprecedented insights into biological and medical research. However, the high per-assay cost limits broader applications of this technology. Although sample-labeling strategies enabling multiplexing have emerged, current methods suffer from either impractical complexity for barcoding or high cost for preparing the index labeling reagents. To address these challenges, here we present HEATag, a universal cell membrane labeling approach that combines Duck circovirus HUH endonuclease (DCV) with wheat germ agglutinin (WGA) to efficiently tag cell membranes with indexed single-stranded DNA (indexed ssDNA). The DCV domain enables rapid, sequence-specific conjugation of indexed ssDNA, while the WGA domain ensures robust labeling of fresh or fixed cells across diverse species. This method is compatible with both commercial platforms and custom systems, readily adaptable to various single cell omics workflows. Therefore, HUH-endonuclease-agglutinin tagging (HEATag) provides a universal, cost-effective and scalable solution for high-throughput single-cell studies, enhancing library preparation efficiency and minimizing batch effects for single-cell researchers.

To see and to know: the power of live imaging in illuminating and decoding biological complexity

Miaoling Yang, Zhuo Du

doi: 10.1016/j.jgg.2025.10.003

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Abstract:
Live imaging enables direct observation of dynamic biological processes, capturing their progression from molecular to organismal scales in space and time. Through high-resolution observation, it provides a powerful means to decode biological complexity by revealing dynamic behaviors, spatial patterns, and regulatory changes. This review illustrates the application of live imaging in investigating complex biological processes with spatiotemporal resolution and mechanistic insight. We first highlight the analytical power and integrative strategies of live imaging, and then summarize recent advances that further extend its capacities. We then focus on four complex processes—cell proliferation, lineage regulation, morphogenesis, and atlas construction—to elucidate how live imaging contributes to their decoding through representative studies. We also discuss the conceptual and practical limitations that currently constrain the full interpretive potential of live imaging, underscoring the need for deeper integration between observation, perturbation, and modeling. Looking ahead, live imaging will benefit from both technical refinement and advances in data standardization and visualization, functional quantification, multiscale integration, and the discovery of generalizable principles. Together, these directions advance a more integrative and mechanistic understanding of complex biological processes.