遗传最新文献

{"title":"High-throughput identification methods of genomic functional variation in post-GWAS era and their application in agricultural animals.","authors":"Xin-Yi Yin, Shou-Zhi Wang","doi":"10.16288/j.yczz.25-319","DOIUrl":"10.16288/j.yczz.25-319","url":null,"abstract":"<p><p>Genome-wide association study (GWAS) has identified a large number of genetic variations that are significantly associated with human diseases and animal and plant economic traits. However, the majority of these variants are located in non-coding regions of the genome, which makes it challenging to accurately pinpoint functional variants of biological significance from a vast number of candidate loci. In the post-GWAS era, high-throughput analytical approaches, such as high-throughput reporter gene analysis, CRISPR/Cas9-based gene editing technologies, and epigenetic analyses, have become powerful tools for systematically uncovering functional variants in the genome. These methods not only enable efficient identification of functional variants but also help elucidate the mechanisms through which they regulate gene expression, thereby clarifying the molecular basis underlying trait formation or disease pathogenesis. In this review, we systematically summarize current high-throughput strategies for identifying functional genomic variants, highlight their applications and recent advances in major agricultural animal species, and outline future research directions, with the aim of providing a reference for subsequent studies in related fields.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"451-470"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964839","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":"Genotype imputation improves SNP density and genetic analysis accuracy in slash pine.","authors":"Yu-Xuan Jiang, Li-Ming Bian, Shi-Liang Zhou, Charles Chen, Yousry A El-Kassaby, Zhi-Qiang Chen, Harry X Wu","doi":"10.16288/j.yczz.25-335","DOIUrl":"10.16288/j.yczz.25-335","url":null,"abstract":"<p><p>Slash pine (<i>Pinus elliottii</i>) possesses an exceptionally large, repeat-rich genome, and existing low-density SNP arrays provide limited marker coverage and resolution of linkage patterns. To increase marker density for population-based genetic analyses and improve the accuracy of genomic relationship matrix (GRM) estimation, we constructed a reference panel from about 10× whole-genome resequencing of 50 maternal parents and performed genome-wide imputation for 51K SNP-array genotypes of 715 half-sib progeny. Imputation accuracy at array loci was quantified using chromosome-local masking experiments, whereas reference-panel-expanded loci not represented on the array were evaluated for concordance and filtered via external validation using progeny resequencing data. Masking-based concordance remained stable at 95.5%, and after threshold-based filtering of expanded loci, we generated a high-density genotype matrix for all 715 individuals comprising 120,650,180 SNPs. Comparative local linkage disequilibrium (LD) heatmaps indicated more continuous LD signals and clearer block structures after densification; for the Chr4 10.22-10.33 Mb interval, the proportion of high-LD SNP pairs increased from 14.5% to 27.6%. The GRM derived from the densified dataset was highly consistent with the array-based GRM in off-diagonal elements (Pearson's <i>r</i>≈0.984). Distance-stratified analyses further showed higher concordance for GRMs constructed from imputed loci within 500 kb of array markers, with concordance decreasing progressively in more distant windows, suggesting limited incremental benefit from long-range imputed loci. Collectively, the reference panel-driven imputation, validation, and integration framework established here provides a high-density genotypic resource for genome-wide association studies and genomic selection in slash pine and other conifer species.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"506-521"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964818","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":"Genetic polymorphism and mutation analysis of 81 autosomal STR loci in the Northern Han Chinese population.","authors":"Hang He, Jin-Pei Zhang, Chu-Chu Zhang, Cheng-Tao Jiang, Wei-Wei Shui, Shi-Cheng Hao, Yi-Wen Lai, Lei Miao, Qiu-Juan Wang, Xiao-Seng Guo, Li Yuan","doi":"10.16288/j.yczz.25-172","DOIUrl":"10.16288/j.yczz.25-172","url":null,"abstract":"<p><p>Examining a greater number of short tandem repeats (STRs) is essential for cases involving mutations, consanguinity, and complex kinship testing. However, previous population studies were mostly limited to fewer than 40 STRs. Therefore, this study investigated the genetic polymorphism, linkage disequilibrium, and mutation rates of 81 autosomal STR loci in the Han Chinese population of northern China. We confirmed the core repeat structure of STR loci, and focused on evaluating the forensic application value of the Category C and 21 additional STR loci not included in the standard \"Forensic science-Data structures of selected loci from the DNA database\" (GB/T 41009-2021). Blood samples from 400 unrelated healthy Northern Han Chinese individuals and parent-child blood samples from 157 families were detected using GSTAR ^TM25, GSTAR ^TM31FS, and GSTAR ^TM29HS kits. Genetic analysis was performed on genotyping data of 81 autosomal STR loci. The core sequence structures of newly added 15 STR loci were confirmed by sequencing the allelic ladder. After applying Bonferroni correction, all 81 autosomal STR loci conformed to Hardy-Weinberg equilibrium. The observed heterozygosity ranged from 0.4375 to 0.9075, discrimination power from 0.6332 to 0.9845 (lowest at LPL), polymorphism information content from 0.3938 to 0.9092, probability of exclusion for trios from 0.1384 to 0.8108, and for duos from 0.0955 to 0.7069. Significantly, linkage disequilibrium was observed between D5S2500 and D5S2800 loci. When excluding the D5S2800 locus, the cumulative discrimination power (CDP) of remaining 80 autosomal STR loci was 1-2.293×10^-89, cumulative probability of exclusion (CPE) of trios was 1-5.074×10^-31, and cumulative exclusion probability of duos was 1-1.400×10^-19. A total of 13 mutations were observed across 508 meiotic events in 157 families at 10 STR loci. The mutation rates for D5S818, D11S2368 and D18S51 were 0.004, while those of D6S1043, D7S1517, D11S4463, D13S325, D14S1434, D20S482 and D20S85 were 0.002. In conclusion, the 81 genetic loci, including Category C and newly added STRs, exhibit good or moderate polymorphism and are suitable for individual identification, paternity testing, and kinship identification. Given the linkage disequilibrium between the D5S2500 and D5S2800, if simultaneous on the capillary electrophoresis platform, it is recommended to use only the test results from the D5S2500 locus for statistical analysis. This data generated provide allele frequency and mutation rate for a large number of STRs, along with the clarified core sequences, thus offering an important data foundation for DNA evidence evaluation.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"483-505"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964820","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":"Activation mechanism of the wheat CC_G10-NLR immune receptor.","authors":"Guang-Hao Guo, Zhi-Yong Liu","doi":"10.16288/j.yczz.26-082","DOIUrl":"10.16288/j.yczz.26-082","url":null,"abstract":"<p><p>Plants rely on nucleotide-binding, leucine-rich repeat (NLR) receptors to recognize effector proteins, activating immune responses. In recent years, researchers have elucidated the structures of various plant NLR resistosomes. However, the activation mechanism of the evolutionarily ancient and widely distributed CC_G10-NLR phylogenetic clade has remained elusive. To investigate this scientific question, the research group led by Zhiyong Liu from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, in collaboration with multiple research groups, identified the wheat spontaneous immunity gene <i>wheat autoimmunity 3</i> (<i>WAI3</i>), which encodes a CC_G10-NLR protein. Cryo-electron microscopy (cryo-EM) analysis reveals that that activated WAI3 assembles into a distinctive octameric resistosome, which triggers sustained calcium influx. The homologous CC_G10-NLR protein RPS2 in <i>Arabidopsis</i> was also shown to form an octamer and induce calcium influx, indicating that this mechanism is conserved in both monocot and dicot plants. Furthermore, the WAI3 resistosome exhibits a unique conformation of the coiled-coil (CC) domain, which may be associated with the absence of the EDVID (Glu-Asp-Val-Ile-Asp) motif in the CC domain of CC_G10-NLRs. This study reveals a novel mechanism of resistosome assembly and immune signal transduction in plant CC_G10-NLR proteins, broadening the understanding of the diversity and plasticity of plant immune receptors.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"447-450"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964787","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":"Diagnosis and treatment analysis of a case of idiopathic hypogonadotropic hypogonadism caused by <i>NSMF</i> gene mutation.","authors":"Shu-Yi Peng, Kai Wang, Shu-Qi Wang, Ming-Jin Zhang, Pei Sheng, Xiao-Fei An","doi":"10.16288/j.yczz.25-187","DOIUrl":"10.16288/j.yczz.25-187","url":null,"abstract":"<p><p>Idiopathic hypogonadotropic hypogonadism (IHH) is a rare endocrine disorder characterized by deficiency or dysfunction of endogenous gonadotropin-releasing hormone (GnRH), leading primarily to hypogonadism. Based on the presence or absence of olfactory dysfunction, IHH is classified into Kallmann syndrome (KS) and normosmic IHH (nIHH). In this study, we reported a 15-year-old male with nIHH, presenting with delayed puberty, hypogonadotropic hypogonadism and normal olfaction. High-throughput gene sequencing identified a novel <i>NSMF</i>:c.79C>G (p.Arg27Gly) variant which has not been reported in the previous literature. By summarizing the patient's clinical characteristics and analyzing new <i>NSMF</i> gene variant, this study enriches the mutation spectrum of <i>NSMF</i> gene and provides clinical data and genetic resources for the diagnosis and treatment of IHH.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"535-543"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964796","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":"Exploration and practice of artificial intelligence-assisted genetics experiment teaching.","authors":"Xue-Ying Zhao, Yi-Ming Guan, Guang-Qi A, Da-Ru Lu, Yan Pi","doi":"10.16288/j.yczz.25-347","DOIUrl":"10.16288/j.yczz.25-347","url":null,"abstract":"<p><p>With the rapid advancement of artificial intelligence (AI) technology, exploring how to integrate AI with traditional genetic experiment courses has become a key focus of current teaching reform. Based on the conventional teaching system of genetic experiments, this study introduced an innovative student-led module focused on AI-assisted experimental design, thereby establishing a model for the deep integration of AI and genetic experiment teaching. Practice results demonstrate that this integrated model not only significantly improves teaching efficiency and quality, but also effectively breaks down the disciplinary barriers inherent in traditional teaching. It provides students with a cross-disciplinary perspective for innovative thinking, stimulates their learning interest and independent creativity, and further enhances their practical ability and scientific literacy in using AI tools to explore complex scientific problems. In addition, the multi-dimensional evaluation system constructed based on AI technology realizes the automated collection and precise analysis of student learning behavior data, which further improves the comprehensive quality evaluation mechanism for students. This study offers a practical approach to the digital reform of experimental teaching in universities and holds significant theoretical and practical value for advancing experimental teaching innovation and cultivating high-quality innovative talents in the digital era.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"544-554"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964770","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":"Prediction method for transcription factor binding sites integrating channel and spatial attention mechanisms.","authors":"Ji-Hua Feng, Zhong-Xing Chen, Qi-Lin Kang, Long-Fei Li, Jia-Hui Yang, Yu-Ting Zhang","doi":"10.16288/j.yczz.25-184","DOIUrl":"10.16288/j.yczz.25-184","url":null,"abstract":"<p><p>Accurate identification of transcription factor binding sites (TFBSs) at single-nucleotide resolution remains a central challenge in deciphering gene expression regulatory networks. To improve the performance of existing computational models for predicting TFBSs across different cell types, we presented a deep learning model integrating channel and spatial attention mechanisms. In this study, we trained and tested the model using a comprehensive dataset that included ChIP-seq data from 51 groups, involving 10 core transcription factors (e.g., CTCF, EGR1, FOXA1) across 13 human cell lines (e.g., A549, GM12878, H1-hESC), and DNase-seq data from 13 datasets. The results demonstrated that this model exhibited superior performance across 23 TF-cell type combinations, achieving a mean area under the receiver operating characteristic curve (AUROC) of 0.986, with 91% of samples yielding an AUROC above 0.970. Additionally, the mean area under the precision-recall curve (AUPRC) reached 0.169, over 1,000-fold higher than the random baseline 0.000156. When compared to state-of-the-art models in the field, such as FactorNet, Leopard, and DeepGRN, our model outperformed them in terms of AUROC on nine shared TF-cell type datasets. Visualization analyses further confirmed that our model enabled accurate identification of cell-type-specific TFBSs. This study provides an efficient computational framework for precise cross-cell-type TFBS prediction, thereby facilitating in-depth investigations into gene expression regulatory mechanisms and the molecular pathogenesis of related diseases.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 5","pages":"522-534"},"PeriodicalIF":0.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147964788","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":"Genome-wide association study of body size traits in dairy goats integrating structural variants.","authors":"Yan-Shuai Feng, Jia-Xin Li, Jiong-Yao Zhao, Jia-le Cao, Xing-Quan Wang, Xiaoting Yao, Ji-Aqi Fu, Xi-Hong Wang","doi":"10.16288/j.yczz.25-293","DOIUrl":"10.16288/j.yczz.25-293","url":null,"abstract":"<p><p>Body size traits serve as crucial phenotypic indicators of body conformation and growth, showing a close correlation with production performance. To elucidate the genetic basis of these traits and identify potential molecular markers in Saanen dairy goats, we analyzed low-coverage whole-genome sequencing (lcWGS) data from 635 individuals. Following genotype imputation based on an in-house goat reference panel, we obtained 14 million single-nucleotide polymorphisms (SNPs) and 45 thousand structural variants (SVs). Genetic parameters were estimated using SNP data. Subsequently, single-trait (ST) and multi-trait genome-wide association studies (MT-GWAS) were conducted using both SNP and SV datasets. Results indicated that body height, body length, and rump height possess moderate heritability, with positive genetic and phenotypic correlations observed among these traits. ST-GWAS identified 56 significant SNPs and 3 significant SVs, mapping to 30 candidate genes, including <i>TNFSF11</i>, <i>HDAC4</i>, and <i>MURC</i>. Furthermore, MT-GWAS detected 2 significant SNPs and 2 significant SVs missed by ST-GWAS, identifying 4 additional candidate genes (<i>S100A11</i>, <i>LOC108635595</i>, <i>GALNTL6</i>, and <i>FSIP2</i>). Notably, overlapping association signals for body length and rump height were observed near <i>NRXN3</i> on chromosome 10, with colocalization analysis supporting the existence of a shared causal variant in this region. KEGG enrichment analysis indicated that candidate genes were primarily enriched in fatty acid biosynthesis and related metabolic pathways. In conclusion, this study shows that integrating structural variants into MT-GWAS can reveal association signals beyond those captured by SNPs, providing a theoretical basis for marker-assisted selection and precision breeding for body conformation.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 4","pages":"393-406"},"PeriodicalIF":0.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700096","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":"Applications and research advances of the ancient plant DNA technology.","authors":"Yu-Tian Yang, Cai-Hui Wang, Zhi-Kun Ma, Qing-Qing Li, Ming Zhang","doi":"10.16288/j.yczz.25-259","DOIUrl":"10.16288/j.yczz.25-259","url":null,"abstract":"<p><p>Ancient DNA technology directly retrieves genetic information from preserved biological materials, thereby offering significant advantages for elucidating species origins and evolution. In recent years, ancient DNA studies have yielded significant advances in our understanding of human evolution and the origins and dispersal of animals. With the rapid development of ancient DNA extraction, library construction, and sequencing techniques, ancient DNA technology is increasingly contributing to plant research and is gradually developing into a standardized and systematic research area. These studies have not only deepened our understanding of the origins, dispersal routes, and evolutionary history of crop domestication, but have also provided novel perspectives for interpreting the interactive evolution among humans, plants, and the environment. In this review, we introduce the workflow of ancient plant DNA research and review the progress of ancient plant DNA technology in the fields of crop domestication, plant diseases, environmental reconstruction, and utilization of plant resources to provide a reference for the in-depth development of this field.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 4","pages":"377-392"},"PeriodicalIF":0.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700070","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":"The mechanism of <i>synpo</i> in intracerebral hemorrhage using a zebrafish model.","authors":"Pei-Dong Ouyang, Jia-Lan Tang, Cheng-Chao Wu, Xiao-Yu Li, Shan-Shan Ke, Jing-Jing Zhang","doi":"10.16288/j.yczz.25-281","DOIUrl":"10.16288/j.yczz.25-281","url":null,"abstract":"<p><p>Intracerebral Hemorrhage (ICH) is a stroke subtype with high mortality, and its core pathological mechanism involves the disruption of cerebrovascular homeostasis. Genetic factors play a crucial role in ICH pathogenesis, underscoring the importance of identifying core regulatory factors and delineating the associated pathological network. Here, through genome-wide association study (GWAS), we identified synaptopodin (<i>SYNPO</i>) as a genetic susceptibility gene for ICH. SYNPO is an evolutionarily conserved actin-binding protein previously shown to be highly expressed in cerebrovascular endothelial cells, where it regulates the actin cytoskeleton to maintain endothelial junction stability. However, its functional role in ICH remains unclear. To investigate this, we conducted a <i>synpo</i> mutant zebrafish line using CRISPR/Cas9. Following epinephrine challenge, <i>synpo</i> mutant larvae displayed significantly elevated cerebrovascular leakage compared with wild-type controls, and adult mutants showed a markedly higher incidence of ICH. Transcriptomic profiling revealed significant downregulation of the key adhesion gene <i>cdh2</i> in mutant brains. Subsequent rescue experiments confirmed that <i>cdh2</i> mRNA supplementation effectively ameliorated the cerebrovascular leakage. In summary, our study unveils a pathway in which <i>synpo</i> maintains cerebrovascular homeostasis by positively regulating <i>cdh2</i>, demonstrating that the <i>synpo-cdh2</i> axis serves as a key regulatory pathway in ICH. These findings provide insights into the genetic mechanisms underlying ICH and highlight potential therapeutic targets.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 4","pages":"407-420"},"PeriodicalIF":0.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700073","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}