农学最新文献

{"title":"Gapless genome assembly and population genomics highlights diversity of mango germplasms.","authors":"Cuixian Zhang, Huaifeng Yi, Xiuxu Ye, Jingxiao Fu, Dehong Xie, Tianqi Bai, Xinyue Gong, Zhangguang Ni, Xinping Luo, Yusuf Chong Yu Lok, Qiong Luo, Peng Wang","doi":"10.1093/hr/uhaf007","DOIUrl":"10.1093/hr/uhaf007","url":null,"abstract":"","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"12 4","pages":"uhaf007"},"PeriodicalIF":7.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of PANoptosis-related lncRNAs in hepatocellular carcinoma based on bioinformatics and construction of a prognostic model.","authors":"Rui He, Xiu-Juan Zheng, Ning-Ning Wang, Xu-Ying Li, Ming-Qi Li, Shi-Jing Nian, Ke-Wei Wang","doi":"10.16288/j.yczz.24-208","DOIUrl":"https://doi.org/10.16288/j.yczz.24-208","url":null,"abstract":"<p><p>PANoptosis, a novel form of pro-inflammatory programmed cell death, plays a role in the progression of various cancers. However, its mechanisms in hepatocellular carcinoma (HCC) remain unclear. Recent studies have highlighted the critical role of long non-coding RNAs (lncRNAs) in the development and progression of multiple cancers. In this study, we retrieve HCC datasets from the TCGA and GEO databases. We identify PANoptosis-related lncRNAs through correlation analysis based on HCC datasets and previous research. Consistent clustering analysis reveals two distinct subtypes of HCC patients: Cluster 1 and Cluster 2. Compared with the Cluster 2 subtype, Cluster 1 shows a better prognosis and higher levels of immune infiltration. We then perform a Lasso-Cox regression analysis of PANoptosis-related lncRNAs to construct a risk assessment model for predicting the prognosis of HCC patients. Kaplan-Meier analysis indicates that patients in the low-risk group have higher survival rates, while ROC (receiver operating characteristic curve) and calibration curves demonstrate the model's good predictive performance. These findings provide deeper insights into the critical role of PANoptosis-related lncRNAs in developing HCC, offering potential biomarkers and therapeutic targets for future HCC treatment.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"456-475"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144032445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of <i>Drosophila melanogaster</i> RNA m⁶A modification pathway factors.","authors":"Shu-Yang Gao, Hou-Guang Lu, Yan-Hua Wang, Dong Yan","doi":"10.16288/j.yczz.24-341","DOIUrl":"https://doi.org/10.16288/j.yczz.24-341","url":null,"abstract":"<p><p><i>N</i>⁶-methyladenosine (m⁶A), one of the most prevalent mRNA modifications, plays crucial roles during animal and plant development and in various physiological and pathological processes. Previous studies have characterized m⁶A methyltransferase complexes, demethylases, and m⁶A-binding proteins, but as a relatively new epitranscriptomic pathway, it is likely that new m⁶A components remain to be discovered. To explore the effects of m⁶A modification on tissues and organs, the m⁶A reader <i>Ythdc1</i> was overexpressed in <i>Drosophila melanogaster</i> eye imaginal discs. Our results showed that overexpression of <i>Ythdc1</i> leads to ectopic expression of Sxl in males, the rough eye in both males and females, and the activation of JNK signaling and apoptotic pathway. In order to screen m⁶A modifiers using the rough eye phenotype, a stable <i>Drosophila</i> strain overexpressing <i>Ythdc1</i> was further constructed. By screening of more than 1,500 RNAi lines, several repressors and enhancers that may be involved in m⁶A modification were successfully identified. These genes are less studied in m⁶A pathway, and therefore we further verified them and conducted preliminary mechanistic analyses on them. In summary, this study identified multiple potential factors of the m⁶A modification pathway, expanded our understanding of the m⁶A modification network, and provided ideas and directions for exploring new regulatory mechanisms of this important pathway.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"476-488"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the research hotspots and trends in genetic education reform.","authors":"Yan Guo, Da-Jin Zhang, Dong-Li Zhu, Shan-Shan Dong, Tie-Lin Yang","doi":"10.16288/j.yczz.24-292","DOIUrl":"https://doi.org/10.16288/j.yczz.24-292","url":null,"abstract":"<p><p>Genetics, as a core discipline of life sciences, has broad applications in medicine, agriculture, and environmental protection. With the rapid development in biotechnology, genetic education is facing new challenges and demands. Traditional teaching models have gradually revealed limitations in cultivating students' innovative abilities, practical skills, and comprehensive qualities. To enhance the quality and effectiveness of genetic education, promoting educational reform has become a focal point for educators and researchers. This study employs bibliometric methods to comprehensively review and analyze 690 relevant publications on genetic education reform from 1986 to 2023, encompassing both domestic and international contexts. The analysis covers multiple dimensions, including the time distribution of publications, research topics, major research institutions and authors, and keyword co-occurrence. Results indicate a steady annual growth in research on genetic education reform. Keyword analysis reveals prominent themes such as \"educational reform\", \"experimental education\" and \"medical genetics\", focusing on innovative teaching methods and improving educational outcomes. High-output institutions are primarily found in the fields of agriculture and life sciences, particularly within agricultural universities and the life sciences of comprehensive universities. Here, we summarize the current state and development trends in genetic education reform, providing a scientific basis and reference for future research. This study will promote the innovative development of genetic education and cultivate more high-quality talents with innovative spirit and practical abilities.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"399-408"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hematopoietic mosaic loss of Y chromosome: from population cohorts to pathogenic mechanisms.","authors":"Li-Na Zhu, Xu Wang, Xi-Han Guo","doi":"10.16288/j.yczz.24-211","DOIUrl":"https://doi.org/10.16288/j.yczz.24-211","url":null,"abstract":"<p><p>Mosaic loss of Y Chromosome (mLOY) refers to genetic mosaicism in males where some somatic cells have lost the Y chromosome (ChrY) while other cells remain their ChrY. mLOY is primarily found in the blood, not only because blood cells are easily accessible, but also because hematopoietic stem cells with LOY mutation gain competitive advantages, therefore producing a large number of LOY-positive blood cells via clonal hematopoiesis. Due to the specific structures, human ChrY is prone to be missegregated during mitosis, and driving by the germline variants, environmental insults and aging microenvironments, mLOY becomes the most commonly acquired age-related mutation in male genomes. Population-based cohort studies have shown that men with a certain degree of mLOY is associated with significantly reduced life expectancy and increased risks of cancer, Alzheimer's disease, cardiovascular diseases and among others. Recent studies using mouse models have further demonstrated that mLOY is a driving factor of leukemia and cardiovascular diseases. These findings suggest that mLOY not only provides a common genetic explanation for the occurrence of many chronic diseases in men, but also provides a new kernel for studying sex differences in human lifespan and disease risk. Here, we briefly summarize the findings from the population-based cohort studies on clonal hematopoiesis driven by LOY. Subsequently we sort out the risk factors of mLOY, methods for detecting mLOY and developing mLOY mouse models, and the potential mechanisms of mLOY in promoting a myriad of chronic diseases. Finally, we provide our own forward-looking perspectives for the future challenges and opportunities in mLOY. The findings from this review provide references for studying the biological role of Y chromosome and sex difference of chronic diseases.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"409-427"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144032056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of structure and function of phage community occurring in the abnormal fermentation of vinegar mash through virome sequencing.","authors":"Jia-Wen Ma, Xin-le Liang","doi":"10.16288/j.yczz.24-226","DOIUrl":"https://doi.org/10.16288/j.yczz.24-226","url":null,"abstract":"<p><p>In order to investigate the cues, which cause abnormal fermentation during the traditional Zhejiang rosy rice vinegar production, here, the Illumina Novaseq sequencing platform is adopted to decipher the abnormal phage community organization, structure, and related function annotation. The results show that the dominant viral families from the abnormal and the normal fermentation vinegar mash are inconsistency on known taxonomic identification information. Population network analysis and PCA (principal component analysis) indicate that the composition and structure of phage communities differ significantly between abnormal and normal fermentation vinegar mash. Only 3.29% VCs (viral clusters) simultaneously contain vOTUs (viral operational taxonomic units) from both fermentation situation. The abnormal phageome displays high network heterogeneity and dominant phage species at the genus level. Accompanied by the widespread distribution of phage-derived hydrolases that target bacterial cell wall, the lower proportion of lysogenic phages contributes to the phages of abnormal fermentation vinegar mash more inclined to lyse the hosts. Furthermore, the predicted bacterial host community coupling with the aberrant phage community is quite different from that in the normal vinegar fermentation. In conclusion, the abnormal structure and function of the phage community constitutes one of the primary reasons for the failure of traditional rosy vinegar fermentation. Phageome research has opened up a new approach for analyzing the causes of abnormal fermentation in traditional fermented foods as well as for regulating and transforming microbial communities.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"489-498"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application and research of genomic optical mapping technology in disease diagnosis.","authors":"Jing Quan, Yan-Qun Xiao, Da-Ru Lu, Yun Bao","doi":"10.16288/j.yczz.24-192","DOIUrl":"https://doi.org/10.16288/j.yczz.24-192","url":null,"abstract":"<p><p>In the continuous progression of genomic research, an increasing number of investigations have revealed that structural variations (SVs) hold a vital role in human evolution and the pathogenesis of diseases. Consequently, SVs have attracted extensive attention within the realm of clinical research.In recent years, optical genome mapping (OGM), which represents a high-resolution, ultra-long-read, automated, non-sequencing genomic detection technique, has exhibited remarkable advantages in the exploration of structural variations. When compared with karyotyping, fluorescence <i>in situ</i> hybridization (FISH), chromosomal microarray analysis (CMA), and high-throughput sequencing technologies, OGM is capable of detecting structural and numerical aberrations throughout the entire genome in a single assay. These encompass aneuploidy, insertions, deletions, duplications, inversions, balanced translocations, and complex structural variations. With a detection resolution reaching as high as 500 bp, OGM is alternatively designated as the next-generation cytogenetic technology due to its high-resolution and long-fragment analysis capabilities. This endows it with substantial practical value in the detection of genomic structural variations. In this review, we comprehensively summarize the application of OGM methods in the detection of disease-related SVs, with the intention of providing valuable references and profound insights for SVs research, especially in the domain of disease diagnosis.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"47 4","pages":"428-436"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Mildew resistance locus O</i> (<i>MLO</i>)-edited petunia shows reduced seed germination, seed set, seed vigor, and growth.","authors":"Aung Htay Naing, Jova Riza Campol, Hay Mon Aung, Hyunhee Kang, Su Bin Cho, Yun-Jae Ahn, Junping Xu, Mi Young Chung, Chang Kil Kim","doi":"10.1007/s42994-024-00187-z","DOIUrl":"https://doi.org/10.1007/s42994-024-00187-z","url":null,"abstract":"<p><p>In this study, we evaluated the impact of editing the powdery mildew-susceptible gene <i>MLO1</i> in <i>Petunia hybrida</i> cv. 'Mirage Rose' using CRISPR/Cas9. We evaluated plant growth, seed physiology, pollen viability and germination, and gibberellin (GA)-associated gene expression. The <i>mlo1</i> mutants exhibited delayed seed germination, reduced plant growth, delayed flowering, and lower seed set and weight compared to wild type (WT). While pollen viability and germination were not significantly affected in the <i>mlo1-14</i> mutant, both were notably reduced in the <i>mlo1-25</i> mutant. Expression analysis revealed significantly higher levels of GA biosynthesis and receptor genes in the mutants, suggesting alterations in the GA signaling pathways. Application of exogenous GA₃ effectively mitigated growth inhibition in the mutants, aligning their growth parameters with those of WT. Our findings underscore the complex role of <i>MLO1</i> in regulating plant growth and development, likely through modulation of the GA signaling pathways. This study highlights the trade-offs associated with <i>MLO1</i> editing for powdery mildew resistance, including impacts on plant growth and reproductive success, and demonstrates the potential of GA₃ application in counteracting these effects. Collectively, this study suggests that the growth penalty and impaired seed physiology caused by the <i>mlo1</i> mutation must be considered when attempting to edit <i>MLO1</i> for powdery mildew toleration in ornamental plants, as these drawbacks can severely impact the plants' utility in the floricultural industry.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42994-024-00187-z.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"263-273"},"PeriodicalIF":4.6,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant graph-based pangenomics: techniques, applications, and challenges.","authors":"Ze-Zhen Du, Jia-Bao He, Wen-Biao Jiao","doi":"10.1007/s42994-025-00206-7","DOIUrl":"10.1007/s42994-025-00206-7","url":null,"abstract":"<p><p>Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies in plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating the molecular breeding of crops. Conventional methods for genomic analysis typically rely on small variants, such as SNPs and indels, and use single linear reference genomes, which introduces biases and reduces performance in highly divergent genomic regions. By integrating the population level of sequences, pangenomes, particularly graph pangenomes, offer a promising solution to these challenges. To date, numerous algorithms have been developed for constructing pangenome graphs, aligning reads to these graphs, and performing variant genotyping based on these graphs. As demonstrated in various plant pangenomic studies, these advancements allow for the detection of previously hidden variants, especially structural variants, thereby enhancing applications such as genetic mapping of agronomically important genes. However, noteworthy challenges remain to be overcome in applying pangenome graph approaches to plants. Addressing these issues will require the development of more sophisticated algorithms tailored specifically to plants. Such improvements will contribute to the scalability of this approach, facilitating the production of super-pangenomes, in which hundreds or even thousands of de novo-assembled genomes from one species or genus can be integrated. This, in turn, will promote broader pan-omic studies, further advancing our understanding of genetic diversity and driving innovations in crop breeding.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"361-376"},"PeriodicalIF":4.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient data filtering with multiple group conditions: a command tool for bioinformatics data analysis.","authors":"Wenpeng Deng, Jianye Chang, Alun Li, He Xie, Jue Ruan","doi":"10.1007/s42994-025-00207-6","DOIUrl":"https://doi.org/10.1007/s42994-025-00207-6","url":null,"abstract":"<p><p>Bioinformatics analysis often requires the filtering of multi-datasets, based on frequency or frequency of occurrence, for decisions on retention or deletion. Existing tools for this purpose often present a challenge with complex installation, which necessitate custom coding, thereby impeding efficient data processing activities. To address this issue, Filterx, a user-friendly command line tool that written in C language, was developed that supports multi-condition filtering, based on frequency or occurrence. This tool enables users to complete the data processing tasks through a simple command line, greatly reducing both workload and data processing time. In addition, future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"274-277"},"PeriodicalIF":4.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}