Journal of Genetics and Genomics

Regulation of tillering and panicle branching in rice and wheat

Ning Zhang, Yuhao Liu, Songtao Gui, Yonghong Wang

2025, 52(7): 869-886. doi: 10.1016/j.jgg.2024.12.005

Abstract (42)

Abstract:
Branching is a critical aspect of plant architecture that significantly impacts the yield and adaptability of staple cereal crops like rice and wheat. Cereal crops develop tillers during the vegetative stage and panicle or spike branches during the reproductive stage, respectively, both of which are significantly impacted by hormones and genetic factors. Tillering and panicle branching are closely interconnected and exhibit high environmental plasticity. Here, we summarize the recent progress in genetic, hormonal, and environmental factors regulation in the branching of rice and wheat. This review not only provides a comprehensive overview of the current knowledge on branching mechanisms in rice and wheat, but also explores the prospects for future research aimed at optimizing crop architecture for enhanced productivity.

In vivo adenine base editing ameliorates Rho-associated autosomal dominant retinitis pigmentosa

Sihui Hu, Yuxi Chen, Yitong Zhou, Tianqi Cao, Simiao Liu, Chenhui Ding, Dongchun Xie, Puping Liang, Li Huang, Haiying Liu, Junjiu Huang

2025, 52(7): 887-900. doi: 10.1016/j.jgg.2024.12.012

Abstract (32)

Abstract:
Mutations in the Rhodopsin (RHO) gene are the main cause of autosomal dominant retinitis pigmentosa (adRP), 84% of which are pathogenic gain-of-function point mutations. Treatment strategies for adRP typically involve silencing or ablating the pathogenic allele, while normal RHO protein replacement has no meaningful therapeutic benefit. Here, we present an adenine base editor (ABE)-mediated therapeutic approach for adRP caused by RHO point mutations in vivo. The correctable pathogenic mutations are screened and verified, including T17M, Q344ter, and P347L. Two adRP animal models are created carrying the class 1 (Q344ter) and class 2 (T17M) mutations, and dual AAV-delivered ABE can effectively repair both mutations in vivo. The early intervention of ABE8e efficiently corrects the Q344ter mutation that causes a severe form of adRP, delays photoreceptor death, and restores retinal function and visual behavior. These results suggest that ABE is a promising alternative to treat RHO mutation-associated adRP. Our work provides an effective spacer-mediated point mutation correction therapy for dominantly inherited ocular disorders.

The lawc gene emerged de novo from conserved genomic elements and acquired a broad expression pattern in Drosophila

Roman O. Cherezov, Julia E. Vorontsova, Elena E. Kuvaeva, Angelina A. Akishina, Ekaterina L. Zavoloka, Olga B. Simonova

2025, 52(7): 901-914. doi: 10.1016/j.jgg.2024.12.014

Abstract (45)

Abstract:
It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms. De novo genes frequently emerge in proximity to existing genes, forming gene overlaps. Here, we present an analysis of the evolutionary history of a putative de novo gene, lawc, which overlaps with the conserved Trf2 gene, which encodes a general transcription factor in Drosophila melanogaster. We demonstrate that lawc emerged approximately 68 million years ago in the 5′-untranslated region (UTR) of Trf2 and displays an extensive spatiotemporal expression pattern. One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short, highly conserved regions located in Trf2 introns. This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes. The observed lawc expression pattern may be due to the overlap of lawc with the 5′-UTR of Trf2. This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.

Identification of QTL-by-environment interaction by controlling polygenic background effect

Fuping Zhao, Lixian Wang, Shizhong Xu

2025, 52(7): 915-926. doi: 10.1016/j.jgg.2025.01.003

Abstract (44)

Abstract:
The quantitative trait loci (QTL)-by-environment (Q × E) interaction effect is hard to detect because there are no effective ways to control the genomic background. In this study, we propose a linear mixed model that simultaneously analyzes data from multiple environments to detect Q × E interactions. This model incorporates two different kinship matrices derived from the genome-wide markers to control both main and interaction polygenic background effects. Simulation studies demonstrate that our approach is more powerful than the meta-analysis and inclusive composite interval mapping methods. We further analyze four agronomic traits of rice across four environments. A main effect QTL is identified for 1000-grain weight (KGW), while no QTL are found for tiller number. Additionally, a large QTL with a significant Q × E interaction is detected on chromosome 7 affecting grain number, yield, and KGW. This region harbors two important genes, PROG1 and Ghd7. Furthermore, we apply our mixed model to analyze lodging in barley across six environments. The six regions exhibiting Q × E interaction effects identified by our approach overlap with the SNPs previously identified using EM and MCMC-based Bayesian methods, further validating the robustness of our approach. Both simulation studies and empirical data analyses show that our method outperforms all other methods compared.

The testis-specific gene 1700030J22Rik is essential for sperm flagellar function and male fertility in mice

Damin Yun, Sheng Gao, Xinyao Li, Jie Shi, Lingling Wang, Tiao Bu, Xiwen Yang, Yunhao Wu, Xiaolong Wu, Fei Sun

2025, 52(7): 927-941. doi: 10.1016/j.jgg.2024.12.010

Abstract (32)

Abstract:
Spermiogenesis is an indispensable process occurring during the later stages of spermatogenesis. Despite multiple proteins being associated with spermiogenesis, the molecular mechanisms that control spermiogenesis remain poorly characterized. In this study, we show that 1700030J22Rik is exclusively expressed in testes of mice and investigate its roles in spermiogenesis using genetic and proteomic approaches. The deficiency in 1700030J22Rik in male mice results in severe subfertility, characterized by a substantial decrease in sperm concentration, motility, and abnormalities in the flagella. Furthermore, 1700030J22RIK interacts with the A-kinase-anchoring protein AKAP3, and 1700030J22Rik knockout decreases AKAP3 and AKAP4 protein levels. Additionally, the absence of 1700030J22RIK alters spermatozoal levels of the subunits of protein kinase A, leading to reduced protein phosphorylation and impaired sperm motility. This study reveals that 1700030J22Rik plays a crucial role in the organization of sperm morphology and function in mice.

Establishing a semi-homology-directed recombination method for precision gene integration in axolotls

Liqun Wang, Yan Hu, Yuanhui Qiu, Huiting Lin, Xiang Li, Sulei Fu, Yan-Yun Zeng, Maria Ghouse, Cheng Long, Yanmei Liu, Ji-Feng Fei

2025, 52(7): 942-953. doi: 10.1016/j.jgg.2025.03.001

Abstract (45)

Abstract:
The axolotl is broadly used in regenerative, developmental, and evolutionary biology research. Targeted gene knock-in is crucial for precision transgenesis, enabling disease modeling, visualization, tracking, and functional manipulation of specific cells or genes of interest (GOIs). Existing CRISPR/Cas9-mediated homology-independent method for gene knock-in often causes “scars/indels” at integration junctions. Here, we develop a CRISPR/Cas9-mediated semi-homology-directed recombination (HDR) knock-in method using a donor construct containing a single homology arm for the precise integration of GOIs. This semi-HDR approach achieves seamless single-end integration of the Cherry reporter gene and a large inducible Cre cassette into intronless genes like Sox2 and Neurod6 in axolotls, which are challenging to modify with the homology-independent method. Additionally, we integrate the inducible Cre cassette into intron-containing loci (e.g., Nkx2.2 and FoxA2) without introducing indels via semi-HDR. GOIs are properly expressed in F0 founders, with approximately 5%–10% showing precise integration confirmed by genotyping. Furthermore, using the Nkx2.2:CreER^T2 line, we fate-map spinal cord p3 neural progenitor cells, revealing that Nkx2.2⁺ cells adopt different lineages in development and regeneration, preferentially generating motoneurons over oligodendrocytes during regeneration. Overall, this semi-HDR method balances efficiency and precision in the integration of GOIs, providing a valuable tool for generating knock-in axolotls and potentially extending to other species.

Variation in the promoter of OsNPF7.1 contributes to nitrate uptake, remobilization, and grain yield in upland rice

Ming Yan, Huimin Feng, Mian Gu, Hanwei Mei, Lei Wang, Kai Xu, Shoujun Chen, Anning Zhang, Liguo Zhou, Xiaoyan Xu, Peiqing Fan, Liang Chen, Fangjun Feng, Guohua Xu, Lijun Luo, Hui Xia

2025, 52(7): 954-957. doi: 10.1016/j.jgg.2025.03.010

Abstract (35)

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Characterization of zebrafish alas2 reporter for study on erythropoiesis, blood flow, and erythroid disease

Wenjuan Zhang, Shuang Wu, Yaxin Li, Mengye Cao, Biao Cao, Dantong Li, Kai Chen, Jian Zhao, Weijun Pan

2025, 52(7): 958-961. doi: 10.1016/j.jgg.2025.03.009

Abstract (41)

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Neutrophils disrupt the intestinal barrier via IL-22/TGF-β/Mmp9 axis in the zebrafish model of inflammatory bowel disease

Peixian Huang, Yiqing Yang, Junwei Lian, Tao Yu, Gaofei Li, Yiyue Zhang

2025, 52(7): 962-965. doi: 10.1016/j.jgg.2025.04.012

Abstract (70)

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2025 Vol. 52, No. 7