遗传最新文献

{"title":"Transmission history of major China-prevalent <i>Mycobacterium tuberculosis</i> sub-lineages in East Asia.","authors":"Wei Wu, Bin Yang, Zhi-Wei Zhou, Hai-Bing Yuan, Qun Sun","doi":"10.16288/j.yczz.25-345","DOIUrl":"https://doi.org/10.16288/j.yczz.25-345","url":null,"abstract":"<p><p><i>Mycobacterium tuberculosis</i> complex (MTBC) is distributed globally and has posed a severe threat to human health throughout history. In this study, we analyzed whole-genome data from the four major MTBC sub-lineages prevalent in China (L2.2, L4.2, L4.4, and L4.5) to reconstruct their transmission and expansion histories across East Asia and parts of Central Asia. We found that L2.2 has established a highly connected transmission network centered in Southern China, whereas L4.2 is characterized by cross-border transmission between Central Asia and Western China, and L4.4 and L4.5 exhibit repeated transmission events between Southeast Asia and Southern China. By reconstructing their population histories, we demonstrated that these sub-lineages have experienced multi-stage expansions since the 15th century, accompanied by a recent rapid proliferation of evolutionary clades. These findings reveal that the MTBC epidemic in East Asia may follow a pattern of long-term historical adaptation superimposed with recent concentrated outbreaks, providing potential genomic evidence to inform precise regional tuberculosis control strategies in China.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 9","pages":"921-930"},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991592","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":"A nonlinear multi-omics data integration and classification model based on pathway self-attention and graph convolutional networks.","authors":"Qiao-Sheng Zhang, Jun-Jie Xu, Zhen-Yu Sun, Zhao-Man Zhong, Jie Liu, Yan-Li Wu, Wan-Qin Li, Meng-Jie Hu, Hong-Peng Li","doi":"10.16288/j.yczz.25-275","DOIUrl":"https://doi.org/10.16288/j.yczz.25-275","url":null,"abstract":"<p><p>The abundance of omics data has significantly advanced the development of multi-omics data integration techniques. Non-linear embedding approaches for data integration have gradually become the mainstream in multi-omics research, as these approaches can substantially improve cancer analysis by enhancing the quality of the embeddings. However, current multi-omics data integration methods are typically confined to omics measurements, neglecting domain-specific prior knowledge encompassing biological pathways. In this study, we proposed a multi-omics integrated classification model, PathTransGCN, based on pathway self-attention and graph convolutional networks (GCN). The model integrated biological pathway information into multi-omics data analysis with the aim of enhancing the accuracy of cancer classification. Multi-omics data for breast cancer (BRCA), non-small cell lung cancer (NSCLC), and low-grade glioma (LGG) were obtained from The Cancer Genome Atlas (TCGA) and UCSC Xena databases. These data included gene mutations, DNA methylation, copy number variations, and gene expression, and were used to assess the model's generalizability across different cancers. First, PathTransGCN employed a pathway self-attention module to learn latent representations of samples across different pathways, thereby obtaining multi-omics integration vectors. Concurrently, a patient similarity network (PSN) was constructed using the similarity network fusion (SNF) approach. Second, the integrated vectors and the PSN were jointly fed into a GCN for end-to-end training, enabling precise classification of cancer subtypes. Through multi-omics data analysis of the BRCA dataset, PathTransGCN outperformed several popular algorithms (such as MoGCN and DeePathNet) in the five-class classification of cancer subtypes, achieving an accuracy rate of 87.6% and an F1 score of 86.4%. Moreover, the model demonstrated robust generalization capabilities across both NSCLC and LGG datasets, while effectively identifying key disease-associated biomarkers at the pathway level. Experimental results demonstrate that PathTransGCN exhibits outstanding performance in integrating omics data and delivering interpretable classification outcomes, presenting significant potential for clinical applications.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 9","pages":"931-945"},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991601","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 efficacy evaluation of the STRSeqTyper122 kit and the FASTASeq 300 second generation sequencer in kinship identification.","authors":"Zhi Chen, Yao-Sen Feng, Hui Xu, Qing-Zhen Meng, Chi Zhang, Ke-Lai Kang, Shi-Yu Tong, Zhe Zhang, Jian Ye, Le Wang","doi":"10.16288/j.yczz.25-241","DOIUrl":"https://doi.org/10.16288/j.yczz.25-241","url":null,"abstract":"<p><p>Forensic DNA technology is the method of choice for kinship identification. However, existing standard methods still have certain limitations in accurately determining the range of kinship relationships. China's independently developed second generation sequencing technology and equipment are expected to enhance the capability of forensic DNA kinship identification. In this study, we utilized the STRSeqTyper122 second generation sequencing STR typing kit and the FASTASeq 300 second generation sequencer to analyze 107 real kinship samples. The analysis included 63 autosomal STR loci, 42 Y-STR loci, 16 X-STR loci, and one gender-determining locus, Amel. The samples covered various kinship relationships, including 113 parent-child pairs, 48 full-sibling pairs, 76 uncle-nephew pairs, 66 grandparent-grandchild pairs, and 4 half-sibling pairs. Combined with simulated data, the ITO method was applied to calculate the cumulative likelihood ratio (CLR) for different levels of kinship based on the length polymorphism and sequence polymorphism of autosomal STR loci, systematically evaluating the practical application performance of this system in kinship identification. The results showed that, using log₁₀CLR values of 4 and -4 as thresholds, the system achieved 100% efficiency in identifying real parent-child and full-sibling relationships. For second degree kinship identification, the system efficiency based on simulated length polymorphism data was 55.2%, while sequence polymorphism improved it to 75.11%. For real sample data, length polymorphism based efficiency was 54.45%, and sequence polymorphism based efficiency reached 76.71%. The findings indicate that the STRSeqTyper122 kit holds significant value in first degree kinship identification. Sequence polymorphism can improve second degree kinship identification efficiency to over 75%.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 9","pages":"878-891"},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991627","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 identification and cold-stress-responsive expression analysis of the NOX gene family in <i>Cucumis melo</i>.","authors":"Xu-Dong Qian, Yu-Lu Zhong, Shu-Hui Zheng, Jia-Ning Lü, Su-Shuang Liu","doi":"10.16288/j.yczz.26-113","DOIUrl":"https://doi.org/10.16288/j.yczz.26-113","url":null,"abstract":"<p><p>NADPH oxidases (NOXs) are crucial enzymes for reactive oxygen species (ROS) generation in plants and play vital roles in growth, development, and stress responses. To elucidate the sequence characteristics of the NOX gene family and its low-temperature response patterns in melon (<i>Cucumis melo</i> L.), this study conducted genome-wide identification and expression profiling of NOX family members using bioinformatics analysis, RNA-seq transcriptome sequencing, and real-time quantitative PCR (RT-qPCR). The results revealed that eight NOX members were identified in the melon genome, distributed across six chromosomes. All members harbored conserved domains including Ferric_reductase, FAD_binding_8, NAD_binding_6, and NADPH_Ox, and the encoded proteins were generally basic and hydrophilic. Phylogenetic analysis classified the NOX proteins into five subgroups. Synteny analysis indicated the presence of only one pair of intraspecific duplicated genes in melon, which was under purifying selection. The promoter regions contained multiple hormone- and stress-responsive <i>cis</i>-acting elements, with <i>CmNOX2</i> and <i>CmNOX4</i> harboring low-temperature responsive elements. Following treatment at 4℃ for 24 h and 48 h, leaf relative electrolyte leakage (REL) increased from 28.33% to 42.67% and 52.67%, respectively; transcriptome analysis identified 5,633 and 6,882 differentially expressed genes (DEGs), respectively. Cold-responsive genes exhibited significant differential expression, with <i>SLAC1</i> and <i>CPK19</i> showing sustained upregulation. RT-qPCR results demonstrated that the expression of <i>CmNOX2</i>, <i>CmNOX5</i>, <i>CmNOX6</i>, and <i>CmNOX7</i> was significantly downregulated after low-temperature treatment, whereas <i>CmNOX4</i> expression was significantly upregulated at 48 h. Integrating promoter elements and expression characteristics, <i>CmNOX4</i> may represent an important candidate gene involved in melon low-temperature response. This study systematically characterized the structure, evolution, and expression patterns of the melon NOX gene family, identified candidate genes responsive to low temperature, and provides a reference for further investigation into the mechanisms underlying melon cold adaptation.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 9","pages":"904-920"},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991649","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":"Research and practice on shuttle breeding between Henan and Xinjiang based on elite cotton germplasm from China's mainland.","authors":"Zhong-Jie Tang, De-Yi Xie, Wei-Ping Fang, Feng-Yin Lu, Wei Zhu","doi":"10.16288/j.yczz.26-133","DOIUrl":"https://doi.org/10.16288/j.yczz.26-133","url":null,"abstract":"<p><p>To address the bottleneck of a narrow genetic base and the difficulty of concurrently improving high yield and superior fiber quality in Xinjiang cotton, which has resulted from long-term reliance on local germplasm, this study introduced excellent germplasm resources from China's mainland. A total of 16 hybrid populations were developed by crossing these mainland resources with the superior Xinjiang cultivar Xinluzhong 51. Through shuttle breeding between Henan and Xinjiang (referred to as Yu-Jiang shuttle breeding) and multi-ecological alternating selection, the yield potential and stability of the derived lines were precisely evaluated using the GGE biplot method. The results demonstrated that the Yu-Jiang shuttle breeding strategy significantly increased lint yield, with an average annual increase of 54.143 kg/hm² from 2018 to 2025 (regression equation: <i>y</i>=54.143<i>x</i>+2,440.7, <i>R</i>²=0.827), confirming its continuous improvement effect on yield. Furthermore, novel lines represented by M3 were successfully selected, exhibiting high and stable yields alongside superior fiber quality. Specifically, fiber length increased by 1.6 mm, and the micronaire grade improved from C1 to B1, achieving synchronous optimization of both yield and quality traits. Correlation analysis revealed that lint yield was significantly positively correlated with planting density, bolls per plant, and lint percentage (<i>P</i><0.05), but negatively correlated with boll weight, providing a theoretical basis for optimizing planting density and plant architecture improvement.In conclusion, utilizing mainland germplasm resources for Yu-Jiang shuttle breeding effectively broadens the genetic base of Xinjiang cotton and enhances environmental adaptability. This approach represents an effective technical pathway for overcoming regional breeding bottlenecks and concurrently improving lint yield and fiber quality.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 9","pages":"892-903"},"PeriodicalIF":0.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991623","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 impact of sequencing depth and DP filtering on genotyping accuracy of SNP based on next-generation sequencing.","authors":"Jin-Kun Yan, Wen-Chuan Zhou, Hua-Ming Xue, Yuan Xia, Liang Xu, Zhe-Peng Wang","doi":"10.16288/j.yczz.26-069","DOIUrl":"https://doi.org/10.16288/j.yczz.26-069","url":null,"abstract":"<p><p>Next-generation sequencing (NGS) is the primary method for SNP genotyping in a large-scale population. However, it still faces a challenge to balance the paradox between SNP genotyping accuracy and sequencing cost in populations characterized by high heterozygosity and low genomic linkage disequilibrium. Although sequencing depth and depth of coverage (DP) are critical parameters influencing SNP genotyping accuracy, comprehensive investigation on genotyping consistency of SNP among different sequencing depths and impact of DP on SNP genotyping accuracy of low-depth sequencing is of absence. In this study, we utilized Lueyang Black-boned chickens (<i>n</i>=11) to evaluate genotyping consistency of SNP at 5× and 10× sequencing depths via two strategies: (1) comparison of SNP genotyping results between 5× and 10×; (2) comparison of genotyping accuracies of 5× and 10× by employing Sanger-genotyping results of 162 SNP at the <i>SLCO1B3</i> locus as the criteria. Furthermore, we investigated the effect of DP filtering on genotyping consistency between 5× and 10× by increasing DP from 0 to 5. We studied the association of genotyping results of NGS with GC contents and repeat sequences for each chromosome. The results show that the ratio of genotyping consistency is 78.07% between 5× and 10×. The ratio is 78.40% between 5× and Sanger sequencing, and increased to 87.17% for 10×. Almost all (99.18%) of inconsistent results happen in heterozygotes, of which 5×AB-10×AA/BB is mainly present in 14 microchromosomes with lengths less than 10 Mb. The 5×AB-10×AA/BB subset of inconsistent results is significantly associated with repeat sequences and GC contents. The ratio of consistent loci increases from 78.07% to 87.33% with the increasing of DP from 0 to 5. However, calling rates of SNP dramatically reduces from 100% to 35.07%. The ratio of missing loci decreases from 13.16% to 4.08%. DP filtering has no significant effect on the ratio of inconsistent loci. The results indicate that challenge of the NGS-based SNP genotyping approach focuses on genotyping of heterozygotes. Sequencing depth and sequence features of chromosomes affect genotyping accuracy. To physically increase sequencing depth improves the genotyping accuracy of SNP, whereas to algorithmically raise DP has a negligible effect. Increasing DP can significantly improve the genotyping consistency between low- and high-depth sequencing. The improving effect quickly decays with the increasing of DP, whereas calling rates of SNP dramatically reduce.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"817-827"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798853","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":"Genomic diversity and selection pressure analyses of low-virulence <i>Yersinia pestis</i> lineages.","authors":"Jia-Yi Zhang, Yi-Hua Jia, Kai Mu, Meng-Nan Cui, Hai-Feng Pan, Yu-Jun Cui, Ya-Rong Wu","doi":"10.16288/j.yczz.25-318","DOIUrl":"https://doi.org/10.16288/j.yczz.25-318","url":null,"abstract":"<p><p><i>Yersinia pestis</i>, the causative agent of plague, is a highly virulent pathogen that has caused three historical pandemics and currently persists in multiple active natural foci worldwide, posing a serious threat to human health and public safety<i>.</i> Distinct phylogenetic lineages of <i>Y. pestis</i> exhibit differences in virulence, among which the Microtus biovar within the 0.PE4 lineage is nearly avirulent to large mammals. Comparative genomics between low-virulence and highly virulent populations is therefore key to elucidating the evolutionary basis of virulence. However, comprehensive population-genomic analysis of the low-virulence lineage remains limited, particularly those integrating multiple types of genomic variations. In this study, we analyzed 169 low-virulence strains and 215 representative high-virulence strains collected from long-term national surveillance data in China and public databases. Phylogenetic and spatiotemporal analyses revealed geographic clustering within the low-virulence 0.PE4 lineage. The 0.PE4.3 subclade circulating in China and Mongolia was further subdivided into three regionally associated tertiary lineages, with two more finely resolved quaternary lineages identified specifically in Inner Mongolia. Comparative genomic analyses with representative high-virulence genomes identified mutations fixed in the most recent common ancestor (MRCA) of the low-virulence population and its subclades. Among these, 81 single nucleotide polymorphisms (SNPs), 19 insertion and deletions (Indels), and 5 large fragment losses are shared by all low-virulence strains, defining the genomic features of their MRCA. Together with selection pressure analysis, we identified five genes (<i>ail</i>, <i>rovA</i>, <i>tssH</i>, <i>cdiA</i>, and <i>alr</i>) under strong positive selection, which are involved in virulence, metabolism, and adaptation. Collectively, this study reconstructs the phylogenetic topology of the global low-virulence <i>Y. pestis</i> population and identifies key genomic variations that occurred during its evolutionary process, providing valuable insights for fine-scale tracing and identifying potential molecular targets for elucidating virulence mechanisms.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"828-841"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798860","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 genetic structure and genetic diversity in Diannan small-ear pig.","authors":"Zhang Li, Qun Lan, Ming Li, Sheng-Ju Lian, Jia-Wen Liu, Heng Zhao, Hai-Ming Ma, Hong-Jiang Wei, Yu-Long Yin, Mei Liu","doi":"10.16288/j.yczz.26-112","DOIUrl":"https://doi.org/10.16288/j.yczz.26-112","url":null,"abstract":"<p><p>The Diannan small-ear pig, an indigenous breed in Yunnan of China, has significant conservation and utilization value due to its unique economic traits. To investigate the population genetic diversity and structure of this breed, this study applied Illumina Porcine 50K SNP chip to detect genome-wide SNPs in 424 Diannan small-ear pigs. Using PLINK software, a total of 29,468 SNPs were detected. The results showed that the average polymorphism information content (PIC) was 0.21, the minor allele frequency (MAF) was 0.18, and the average expected heterozygosity (<i>H_e</i>) was 0.24, indicating a moderately low level of genetic diversity in the Diannan small-ear pigs population. Subsequently, the phylogenetic tree was constructed using MEGA X software, showing that the Diannan small-ear pigs could be divided into eight linages. Computed with Plink software, the distance matrix was built from pairwise identity by state (IBS) proportions. The results revealed that the average IBS proportion across all individual pairs was 0.23. Analysis of genetic relationships within the population with GCTA software revealed that most Diannan small-ear pigs exhibited moderate genetic proximity. Additionally, a total of 5,301 runs of homozygosity (ROH) segments were identified. 59.54% of those ROHs ranged from 0 to 5 Mb in length. The average inbreeding coefficient based on ROH was 0.006, indicating a low level of inbreeding in the Diannan small-ear pigs population. This study provides a worthwhile genetic foundation for the future conservation and utilization of Diannan small-ear pigs. These findings indicated that the Diannan small-ear pig conservation farm could introduce other more gene flows from other subpopulations to promote population genetic diversity based on preserving their unique and desirable traits, and integrate modern biotechnology for breeding organisms like genomic selection to promote its potential for the discovery and utilization of the merit phenotype-related genes, contributing to the long-term scientific protection and sustainable development and utilization of this valuable genetic resource.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"807-816"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798931","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":"Mechanosensitive ion channels in embryonic development: advances in the regulation of mitochondrial function.","authors":"Wei-Ying Zhang, Xin Ning, Bo-Yu Luo, Kai Wei, Yue Teng, Wei Shang","doi":"10.16288/j.yczz.25-343","DOIUrl":"https://doi.org/10.16288/j.yczz.25-343","url":null,"abstract":"<p><p>Mechanical forces are persistent and dynamic physical cues during embryonic development and reproduction. Through mechanosensitive ion channels (MSCs), these forces are converted into intracellular signals-primarily mediated by Ca²⁺ flux, that regulate cell migration, lineage specification, and morphogenesis. In parallel, mitochondria serve as central hubs of energy metabolism and signal integration, and their metabolic state, redox homeostasis, and dynamic remodeling critically influence early developmental competence. Increasing evidence suggests that MSC-mediated Ca²⁺ signaling not only activates canonical signaling pathways but also functionally couples to mitochondrial activity, establishing a regulatory axis that links mechanical inputs to metabolic responses. This review focuses on the \"MSC-mitochondrial function- embryonic developmental fate\" axis. We systematically summarize the molecular characteristics and activation mechanisms of MSCs and discuss their roles in embryonic development and reproductive processes. Furtherly, we examine how MSC-dependent Ca²⁺ signaling modulates mitochondrial metabolic reprogramming, reactive oxygen species (ROS) homeostasis, and fusion-fission dynamics, and consider the potential implications of this coupling in key developmental events including blastocoel formation, lineage specification, and organogenesis. We also discuss the current limitations and technical challenges in the field, together with future research directions and potential translational implications. By integrating mechanotransduction with mitochondrial metabolic regulation in the developmental context, this framework provides insights into how mechanical and metabolic signals coordinately shape embryonic cell fate and morphogenesis, and offers a theoretical basis for elucidating the mechanisms underlying developmental abnormalities and reproductive disorders, as well as exploring potential intervention strategies.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"764-780"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798855","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":"A teaching case on mapping nematode mutations based on whole-genome sequencing.","authors":"Yong-Bin Li","doi":"10.16288/j.yczz.26-078","DOIUrl":"https://doi.org/10.16288/j.yczz.26-078","url":null,"abstract":"<p><p>With advances in high-throughput sequencing technologies, whole-genome sequencing-based mutation mapping (mapping-by-sequencing) has become an important approach in modern genetic studies. However, in undergraduate life science courses, students have relatively few opportunities to engage with authentic sequencing data analysis workflows, and systematic teaching resources related to sequencing data analysis remain limited, particularly in conventional genetics teaching. Based on the Galaxy platform and the MiModD tool, this study reorganized the mutation mapping analysis workflow for instructional purposes and developed a case that can be applied in functional genomics and bioinformatics courses and integrated into genetics teaching. Using the published whole-genome sequencing data from the <i>Caenorhabditis elegans</i> mutant <i>ot266</i> as a case, students are guided through the complete analytical workflow, including sequencing data quality control, read alignment, variant calling, allele frequency-based mapping, and candidate mutation identification. This teaching design provides a feasible teaching case for undergraduate bioinformatics or functional genomics education and can serve as a useful supplement to genetics teaching.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"842-852"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798890","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}