Journal of Genetics and Genomics最新文献

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.

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.

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.

Stalk lodging is a major threat to global maize production, which causes great annual yield losses. Stalk bending strength (SBS) is highly associated with resistance to stalk lodging in maize. However, the genetic basis of SBS remains largely unknown. In this study, we identify a quantitative trait locus (QTL), stiff2, corresponding to a known flowering-time gene ZmCCT, by integrating QTL mapping and association mapping. A 5-kilobase (kb) transposable element inserted in the promoter region of ZmCCT significantly reduces SBS, while upregulated expression of ZmCCT through transformation significantly enhances SBS. Gene regulatory network analysis reveals that ZmCCT may indirectly regulate a set of downstream genes, which contain nrt5 for nitrogen transport, Tu1, d8, and d9 for stalk elongation, ub2, ub3, and ch1 for stalk thickening, and myb69 and bm4 for lignin biosynthesis. These genes collectively increase stalk strength and improve lodging resistance aboveground. Additionally, stiff2 regulates not only aboveground resistance to stalk bending and breakage but also influences root system architecture, which enhances resistance to root lodging belowground. The identification of stiff2 and its downstream targets provides critical insights into the genetic control of maize lodging and offers powerful tools for breeding lodging-resistant cultivars.

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.

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.

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.

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.

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.

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.