Journal of Genetics and Genomics

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

Shan Jiang, Lian Wu, Luojiang Huang, Yunhai Li

2025, 52(12): 1460-1474. doi: 10.1016/j.jgg.2025.10.005

Abstract (37)

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.

Jasmonate signaling: integrating stress responses with developmental regulation in plants

Yanbing Li, Fangming Wu, Chuanyou Li

2025, 52(12): 1490-1506. doi: 10.1016/j.jgg.2025.07.007

Abstract (119)

Abstract:
Jasmonates (JAs) are essential phytohormones that coordinate plant defense and development in response to unpredictable environments. Recent advances have highlighted the SCF^COI1-JAZ-MYC2-MED25 module as a central hub for JA signaling, orchestrating transcriptional repression, derepression, activation, amplification, and feedback termination. This review summarizes current insights into the roles of JA in the regulation of biotic and abiotic stress responses and agronomic traits, including root development, regeneration, fertility, flowering, leaf senescence, and seed development, with a particular emphasis on the crosstalk between JA and a wound-induced peptide hormone, systemin, which mediates systemic wound responses. A deeper understanding of the JA regulatory mechanisms will provide valuable strategies for engineering crops with enhanced stress resilience and improved yields. We further propose JA-based strategies as a promising avenue for crop improvement.

The interplay between phosphorus nutrition and abiotic stresses in plants

Houqing Zeng, Feiyu Chen, Qiuqing Zhu, Shahid Ali, Jia Du, Yiyong Zhu, Keke Yi

2025, 52(12): 1507-1523. doi: 10.1016/j.jgg.2025.08.008

Abstract (54)

Abstract:
Phosphorus (P) is an essential macronutrient required for plant growth, development, and resilience to environmental stresses. Its availability in soil and homeostasis within plants are strongly influenced by environmental conditions, with unfavorable environments and soil factors disrupting phosphate availability, absorption, transport, and utilization. Optimizing phosphate supply can alleviate the detrimental impacts of abiotic stresses, thereby supporting growth and improving stress tolerance. Recent studies reveal that abiotic stresses modulate phosphate signaling pathways and alter the expression of phosphate-responsive genes, often affecting key regulators of P homeostasis. Strategic manipulation of phosphate transporters and their regulatory pathways offers a promising approach to enhance plant adaptation to challenging environments. This review highlights current advances in understanding the molecular mechanisms that coordinate P-responsive gene expression and homeostasis pathways under fluctuating P availability and stress conditions. It emphasizes the critical role of P nutrition in enhancing plant stress tolerance through antioxidant activation, osmolyte accumulation, membrane stabilization, and metal-phosphate complex formation. An in-depth mechanistic understanding of P-stress interactions will inform the development of P-efficient and stress-resistant crop varieties and guide more sustainable P fertilizer management in agriculture.

The mechanistic insights into fruit ripening: integrating phytohormones, transcription factors, and epigenetic modification

Chengpeng Yang, Shiyu Ying, Beibei Tang, Chuying Yu, Yikui Wang, Mengbo Wu, Mingchun Liu

2025, 52(12): 1475-1489. doi: 10.1016/j.jgg.2025.06.001

Abstract (56)

Abstract:
Fruit ripening is a complex developmental process tightly regulated by hormonal crosstalk, transcriptional networks, and epigenetic modifications, with striking divergence between climacteric and non-climacteric species. In climacteric fruits, such as tomatoes, apples, and bananas, ethylene acts as the master regulator, driving autocatalytic biosynthesis through ACS/ACO genes and activating hierarchical transcriptional cascades mediated by MADS-box (RIN), NAC (NOR), and ERF-family transcription factors. These pathways are amplified by epigenetic reprogramming, including DNA demethylation at ripening-related promoters and histone acetylation, which enhance chromatin accessibility to facilitate gene expression. Conversely, non-climacteric fruits like strawberries and grapes predominantly rely on abscisic acid (ABA) to coordinate ripening. Hormonal interplay, such as ethylene-ABA synergy in climacteric fruit systems, further fine-tunes ripening dynamics. Advances in CRISPR-based gene editing and epigenome engineering now enable precise manipulation of these pathways, offering transformative solutions to reduce postharvest losses, enhance nutritional quality, and improve climate resilience. This review integrates mechanistic insights across species, emphasizing opportunities to translate fundamental discoveries into sustainable agricultural innovations, from breeding nutrient-rich cultivars to optimizing postharvest technologies for global food security.

Enhancing quality traits in staple crops: current advances and future perspectives

Changfeng Yang, Lichun Huang, Bai-Chen Wang, Yingxin Zhong, Xiaohui Ma, Changquan Zhang, Qixin Sun, Yongrui Wu, Yingyin Yao, Qiaoquan Liu

2025, 52(12): 1438-1459. doi: 10.1016/j.jgg.2025.05.001

Abstract (24)

Abstract:
Staple crops such as rice, wheat, and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches and rational design strategies presents opportunities to develop high-yield “super-crop” varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.

Mammary stem cells: from molecular cues to orchestrated regulatory mechanisms and its implications in breast cancer

Mengna Zhang, Lingxian Zhang, Jie Liu, Jiahui Zhao, Jiayu Mei, Jiahua Zou, Yaogan Luo, Cheguo Cai

2025, 52(12): 1421-1437. doi: 10.1016/j.jgg.2025.04.007

Abstract (47)

Abstract:
Mammary stem cells (MaSCs), endowed with self-renewal and multilineage differentiation capabilities, are crucial for mammary gland development, function, and disease initiation. Recent advances in MaSCs biology research encompass molecular marker identification, regulatory pathway dissection, and microenvironmental crosstalk. This review synthesizes key progress and remaining challenges in MaSC research. Molecular profiling advances have identified key markers recently, such as Procr, Dll1, Bcl11b, and PD-L1. Central to their regulatory logic are evolutionarily conserved pathways, including Wnt, Notch, Hedgehog, and Hippo, which exhibit context-dependent thresholds to balance self-renewal and differentiation. Beyond intrinsic signaling, the dynamic interplay between MaSCs and their microenvironment, such as luminal-derived Wnt4, macrophage-mediated TNF-α signaling, and adrenergic inputs from sympathetic nerves, spatially orchestrates stem cell behavior. In addition, this review also discusses the roles of breast cancer stem cells (BCSCs) in tumorigenesis and therapeutic resistance, focusing on the molecular mechanisms underlying MaSC transformation into BCSCs. Despite progress, challenges remain: human MaSCs functional assays lack standardization, pathway inhibitors risk off-target effects, and delivery systems lack precision. Emerging tools like spatial multi-omics, organoids, and biomimetic scaffolds address these gaps. By integrating MaSCs and BCSCs biology, this review links mechanisms to breast cancer and outlines strategies to target malignancy to accelerate clinical translation.

Deep insights and clinical benefits from the comprehensive cohort of fetal skeletal dysplasia in China

Guozhuang Li, Kexin Xu, Jihao Cai, Yulin Jiang, Xiya Zhou, Yan Lv, Na Hao, Yiqing Yu, Sen Zhao, Qing Li, Lina Zhao, Zhengye Zhao, Zhihong Wu, Ying Zou, Terry Jianguo Zhang, Shuyang Zhang, Nan Wu, Qingwei Qi

2025, 52(12): 1524-1536. doi: 10.1016/j.jgg.2025.09.005

Abstract (42)

Abstract:
Fetal skeletal dysplasia (FSD) encompasses diverse clinical features and complicates prenatal diagnosis and perinatal care. In this retrospective study, we integrate prenatal deep phenotyping with exome or genome sequencing (ES/GS) to elucidate comprehensive genotype and phenotype landscapes, diagnostic outcomes, genotype-phenotype correlations, and postnatal follow-up findings and to refine genetic counseling and clinical decision-making. The study includes a cohort of 152 fetuses with FSD in China. All fetuses undergo prenatal deep phenotyping followed by ES/GS analysis. Prenatal deep phenotyping enables classification into isolated and non-isolated FSD groups and identifies previously unrecognized prenatal features associated with KBG syndrome and Segawa syndrome. Among skeletal anomalies, limb bone anomalies are the most common (72.4%). Genetic testing yields positive diagnoses in 88 fetuses (57.9%). Notably, fetuses with cranial and limb bone abnormalities demonstrate a higher diagnostic yield. Comparative analysis of prenatal and postnatal genotypes and phenotypes in individuals harboring pathogenic variants in four hotspot genes provides a deeper understanding of skeletal dysplasia phenotypes. Genetic findings from this cohort directly inform reproductive decisions in 16 subsequent pregnancies. Our findings significantly enhance genotype-phenotype correlations and contribute to improved prenatal counseling, informed clinical decision-making, and optimized perinatal care, and advance precision medicine strategies for FSD-affected families.

Harnessing lysosomal genetics: development of a risk stratification panel and unveiling of DPP7 as a biomarker for colon adenocarcinoma

Zhengdong Luo, Yanlei Wang, Shunjie Zeng, Longchen Yu, Yuxiao Zhao, Hong Wang, Yingjing Fan, Yanli Zhang, Lili Wang, Yaping Li, Zhongfang Niu, Xin Zhang, Yi Zhang

2025, 52(12): 1549-1562. doi: 10.1016/j.jgg.2025.04.009

Abstract (29)

Abstract:
Lysosomal dysfunction has been implicated in the progression of colon adenocarcinoma (COAD), yet the prognostic significance and therapeutic potential of lysosome-related genes (LRGs) remain underexplored. In this study, we construct a 6-LRG-based prognostic risk stratification model (DPP7, ADAM8, CD1B, LRP2, ATP6V1C2, and PLAAT3) by integrating LASSO and Cox regression analyses. Stratifying patients based on median risk scores, we demonstrate that high-risk patients exhibit significantly worse clinical outcomes across the TCGA cohort and five independent GEO datasets. Furthermore, this panel outperforms 136 previously published models in terms of predictive accuracy for 1-, 3-, and 5-year survival rates. Validation multiplex immunofluorescence using an in-house tissue microarray cohort confirms that the 6-LRG signature serves as an independent prognostic factor. Additionally, high-risk patients exhibit distinct immunosuppressive tumor microenvironment and aggressive malignancy characteristics. Functional depletion of DPP7 significantly inhibits tumor cell proliferation, migration, and metastasis in both in vitro and in vivo settings. Moreover, DPP7 silencing attenuates epithelial-mesenchymal transition, as evidenced by the upregulation of E-cadherin and downregulation of N-cadherin, Vimentin, and Snail. In conclusion, this study establishes an LRG-based model for COAD prognostic prediction and nominates DPP7 as a promising therapeutic target for COAD treatment.

Loss of lims1 causes aberrant cardiac remodeling and heart failure via activating gp130/Jak1/Stat3 pathway in zebrafish

Wuming Qin, Xiaobo Yang, Lu Zhang, Linghui Cao, Shi Ouyang, Dafeng Yang, Yangzhao Zhou, Anji Chen, Tao Liao, Xinyu Zhu, Yuting Liu, Wei Tang, Tongtong Ma, Yiyue Tang, Yonghe Ding, Yun Deng

2025, 52(12): 1600-1611. doi: 10.1016/j.jgg.2025.04.003

Abstract (29)

Abstract:
LIM zinc finger domain containing 1 (LIMS1), an evolutionarily conserved LIM domain adaptor protein, is implicated in diverse pathologies, including cancer and neurological disorders. However, its roles in cardiac diseases and the underlying mechanisms remain unclear. Here, we explore the functions and mechanisms of LIMS1 in cardiac remodeling and heart failure. We identify the elevated LIMS1 expression in patients with dilated cardiomyopathy and murine cardiomyocytes, suggesting that LIMS1 dysregulation contributes to cardiac pathology. Using CRISPR/Cas9 technology, we generate a zebrafish model of lims1 loss-of-function mutant, which exhibits severe cardiac chamber remodeling, systolic dysfunction, and premature mortality, demonstrating the essential role of lims1 in maintaining cardiac integrity. Transcriptomic profiling reveals the activation of the gp130/Jak1/Stat3 signaling in the lims1-deficient hearts. Strikingly, pharmacological inhibition of Stat3 or c-Fos partially rescues cardiomyopathy phenotypes. Our findings reveal the underlying mechanism of lims1 deficiency-caused heart failure through gp130/Jak1/Stat3 hyperactivation, offering insights into cardiac remodeling and potential therapeutic strategies.

Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity

Jiaxin Meng, Yan Wang, Rongkun Guo, Jianyi Liu, Kerui Jing, Jiaqi Zuo, Yanping Yuan, Fengchao Jiang, Ningguang Dong

2025, 52(12): 1612-1626. doi: 10.1016/j.jgg.2025.04.001

Abstract (49)

Abstract:
Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida “Jinruyi” (JRY) and the soft-seed, red-peel C. pinnatifida “Ruanzi” (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and has been shown to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.

Multiple nucleotide variants in genetic diagnosis: implications from 11,467 cases of hearing loss

Fandi Ai, Jiayi Zeng, Qian Zhang, Mingjun Zhong, Meilin Chen, Yu Lu, Jing Cheng, Lei Chen, Fengxiao Bu, Huijun Yuan

2025, 52(12): 1537-1548. doi: 10.1016/j.jgg.2025.03.012

Abstract (37)

Abstract:
Multiple nucleotide variants (MNVs) are frequently misannotated as separate single-nucleotide variants (SNVs) by widely utilized variant-calling pipelines, presenting substantial challenges in genetic testing and research. The role of MNVs in genetic diagnosis remains inadequately characterized, particularly within large disease cohorts. In this study, we comprehensively investigate codon-level MNVs (cMNVs) across 157 hearing loss (HL)-related genes in 11,467 HL cases and 7258 controls from the Chinese Deafness Gene Consortium (CDGC) cohort. A total of 116 cMNVs are identified, occurring in 29.07% of HL cases. Among them, 56.03% of cMNVs exhibit functional consequences distinct from constituent SNVs. Moreover, amino acid substitutions exclusive to cMNVs cause more substantial physicochemical disruptions than those associated with SNVs. Notably, 51 cMNVs show pathogenicity classifications that diverge from at least one constituent SNV, impacting genetic interpretation in 145 cases. Pathogenicity interpretation of cMNV facilitates definitive genetic diagnoses in eight HL cases that would otherwise have been subject to misdiagnoses or missed diagnoses. These findings provide critical insights into the genomic characteristics, functional impacts, and diagnostic implications of cMNVs, underscoring their clinical significance in genetic diagnosis and emphasizing the necessity for comprehensive and accurate detection and interpretation of cMNVs in genetic testing and research.

Annotation and assessment of functional variants in livestock through epigenomic data

Ruixian Ma, Renzhuo Kuang, Jingcheng Zhang, Jiahao Sun, Yueyuan Xu, Xinbo Zhou, Zheyu Han, Mingyang Hu, Daoyuan Wang, Yuhua Fu, Yong Zhang, Xinyun Li, Mengjin Zhu, Shuhong Zhao, Tao Xiang, Mengwei Shi, Yunxia Zhao

2025, 52(12): 1588-1599. doi: 10.1016/j.jgg.2025.03.013

Abstract (25)

Abstract:
Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding. However, the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods. In this study, we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions, creating a comprehensive functional annotation map of animal genomic variants. Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits, underscoring the utility of these annotations in functional variant discovery. Using our functional annotations, we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories, with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs. Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy, demonstrating their practical utility in breeding programs. To facilitate the use of our results, we develop the Integrated Functional Mutation (IFmut: http://www.ifmutants.com:8212) platform, enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently. Our study provides a robust framework for functional genomic annotations in farm animals, enhancing variant function assessment and breeding precision.

Genome-wide analysis of Q binding reveals a regulatory network that coordinates wheat grain yield and grain protein content

Jing Zhu, Qing Chen, Zhenru Guo, Yan Wang, Qingcheng Li, Yang Li, Lu Lei, Caihong Liu, Yue Li, Rui Tang, Jie Tang, Ziyi Zhang, Shijing Peng, Mi Zhang, Zhongxu Chen, Li Kong, Mei Deng, Qiang Xu, Yazhou Zhang, Qiantao Jiang, Jirui Wang, Guoyue Chen, Yunfeng Jiang, Yuming Wei, Youliang Zheng, Pengfei Qi

2025, 52(12): 1576-1587. doi: 10.1016/j.jgg.2025.02.011

Abstract (76)

Abstract:
Wheat is an important cereal crop used to produce diverse and popular food worldwide because of its high grain yield (GY) and grain protein content (GPC). However, GY and GPC are usually negatively correlated. We previously reported that favorable alleles of the wheat domestication gene Q can synchronously increase GY and GPC, but the underlying mechanisms remain largely unknown. In this study, we investigate the regulatory network involving Q associated with GY and GPC in young grains through DNA affinity purification sequencing and transcriptome sequencing analyses, electrophoretic mobility shift and dual-luciferase assays, and transgenic approaches. Three Q-binding motifs, namely TTAAGG, AAACA[A/T]A, and GTAC[T/G]A, are identified. Notably, genes related to photosynthesis or carbon and nitrogen metabolism are enriched and regulated by Q. Moreover, Q is revealed to bind directly to its own gene and the glutamine synthetase gene GSr-4D to increase expression, thereby influencing nitrogen assimilation during the grain filling stage and increasing GPC. Considered together, our findings provide molecular evidence of the positive regulatory effects of Q on wheat GY and GPC.

GLGW10 controls grain size associated with the lignin content in rice

Haolin Liu, Jinlong Ni, Yuhan Zhang, Yue Chen, Yanmin Luo, Yi Wang, Fei Shang, Yuke Yang, Rongfang Xu, Liyong Cao, Lilan Hong, Juan Xu, Yuanzhu Yang, Ming Zhou

2025, 52(12): 1563-1575. doi: 10.1016/j.jgg.2025.02.009

Abstract (42)

Abstract:
Grain size, which encompasses length, width, and thickness, is a critical agricultural trait that influences both grain yield and quality in rice. Although numerous grain size regulators have been identified, the molecular mechanisms governing grain size and the lignin content remain largely elusive. In this study, we clone and characterize GRAIN LENGTH AND GRAIN WIDTH 10 (GLGW10), a regulator of grain size in rice. Loss-of-function mutations in GLGW10 result in reduced grain size. GLGW10 encodes an evolutionarily conserved protein, the function of which has not been previously characterized in higher plants. Biochemical assays reveal that GLGW10 may interact with the transcription factor OsMYB108, which acts as a negative regulator of the lignin content. Knockout of OsMYB108 leads to longer and slender grain size, accompanied by increased lignin content, indicating that OsMYB108 negatively regulates both grain size and lignin content. Analysis of natural variations and haplotypes in GLGW10 reveals an association with grain size, suggesting an artificial selection on GLGW10 during rice domestication. In summary, our findings identify regulators of grain size and elucidate potential mechanisms linking grain size and lignin metabolism in rice, thereby providing essential insights for improving crop yields.

The HISTONE ACETYLTRANSFERASE 1 interacts with CONSTANS to promote flowering in Arabidopsis

Zhenwei Liang, Yisui Huang, Yuanhao Hao, Xin Song, Tao Zhu, Chen Liu, Chenlong Li

2025, 52(12): 1627-1637. doi: 10.1016/j.jgg.2025.01.010

Abstract (39)

Abstract:
Chromatin modifications, including histone acetylation, play essential roles in regulating flowering. The CBP/p300 family HISTONE ACETYLTRANSFERASE 1 (HAC1), which mediates histone acetylation, promotes the process of floral transition; however, the precise mechanism remains largely unclear. Specifically, how HAC1 is involved in the flowering regulatory network and which genes are the direct targets of HAC1 during flowering regulation are still unknown. In this study, we elucidate the critical function of HAC1 in promoting flowering via exerting active epigenetic markers at two key floral integrators, FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), thereby regulating their expression to trigger the flowering process. We show that HAC1 physically interacts with CONSTANS (CO) in vivo and in vitro. Chromatin immunoprecipitation results indicate that HAC1 directly binds to the FT and SOC1 loci. Loss of HAC1 impairs CO-mediated transcriptional activation of FT and SOC1 in promoting flowering. Moreover, CO mutation leads to the decreased enrichment of HAC1 at FT and SOC1, indicating that CO recruits HAC1 to FT and SOC1. Finally, HAC1, as well as CO, is required for the elevated histone acetylation level at FT and SOC1. Taken together, our finding reveals that HAC1-mediated histone acetylation boots flowering via a CO-dependent activation of FT and SOC1.

Corrigendum to “Spatiotemporal dynamics of neuron differentiation and migration in the developing human spinal cord” [J. Genet. Genom. 52 (2025) 1283–1295]

Yuan Yu, Mengjie Pan, Quanyou Cai, Ziyu Feng, Baomei Cai, Kaixuan Lin, Shangtao Cao, Mingwei Min, Lihui Lin, Yanlin Ma, Jiekai Chen

2025, 52(12): 1638-1638. doi: 10.1016/j.jgg.2025.11.004

Abstract (2)

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Current Issue 2025 Vol. 52, No. 12

Current Issue
2025 Vol. 52, No. 12