农学最新文献

{"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}

{"title":"On the role of Y chromosome loss in malignancies: the driving mechanisms and potentials in precision oncology.","authors":"Jia-Zhi Su, Li-Na Zhu, Xue Chen, Xu Wang, Xi-Han Guo","doi":"10.16288/j.yczz.25-329","DOIUrl":"https://doi.org/10.16288/j.yczz.25-329","url":null,"abstract":"<p><p>Biological sex is a critical determinant influencing the incidence, progression, clinical presentation, and prognosis of human diseases. Beyond sex-specific tumors, men typically exhibit higher morbidity and mortality rates in nearly all tumors compared to women. However, the genetic mechanisms underlying the cancer sex bias are not definitive. Loss of Y chromosome (LOY), the most prevalent somatic mutation in healthy males, frequently occurs in individuals over 50 years of age. On one hand, LOY in peripheral blood immune cells is strongly associated with increased tumor susceptibility. On the other hand, LOY also frequently occurs within tumor cells themselves, leading to the loss of Y-chromosome-linked tumor suppressor genes and non-coding RNAs, thereby reshaping the tumor microenvironment through mechanisms such as metabolic reprogramming and altering tumor immunity. Strikingly, LOY is a \"contagious\" mutation, which means malignant cells with LOY cause the same mutation in tumor-infiltrating immune cells, and the synergistic interaction between two types of LOY cells accelerates tumor evolution. Given the widespread occurrence of LOY in tumors and its crucial role in malignant progression, LOY holds great promise as a biomarker for early diagnosis, classification, and staging, as well as a potential target for precision therapy. Here, we summarize the mechanisms by which LOY drives malignant progression in solid tumors from the perspectives of tumor-cell-intrinsic LOY, LOY in tumor-infiltrating immune cells, and their crosstalk. We also discuss the developmental opportunities and translational potential of LOY in precision oncology. This review aims to provide novel insights into the molecular basis of sex disparities in tumors and to identify potential molecular targets for precision prevention, diagnosis, and treatment.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"781-795"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798906","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":"Paleoproteomics reveal the genetic characteristics of Middle Pleistocene <i>Homo erectus</i> in East Asia.","authors":"Zi-Yi Zou, Hui-Yun Rao, Qiao-Mei Fu","doi":"10.16288/j.yczz.26-115","DOIUrl":"https://doi.org/10.16288/j.yczz.26-115","url":null,"abstract":"<p><p><i>Homo erectus</i> remains have been found in Africa, Eurasia, and Southeast Asia, with a fossil record dating back to 2 million years, holding a significant place in human evolution. However, due to limited molecular evidence, its genetic characteristics, diversity, and potential connections to other archaic homonins and modern humans have long remained unresolved. To address these issues, a research team led by Qiaomei Fu from the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, in collaboration with other archaeological institutions, successfully extracted ancient enamel proteins from six Middle Pleistocene <i>H. erectus</i> teeth (~0.4 Ma) from the Zhoukoudian, Hexian, and Sunjiadong sites. Further in-depth paleoproteomic analyses revealed the following breakthroughs. First, a quantitative sex determination pipeline was established based on male-specific amelogenin, Y isoform (AMELY), confirming that five of these specimens are male and one is female. Second, two genetically specific amino acid variants in ameloblastin (AMBN) were identified in all specimens from three sites. One is a newly discovered variant, AMBN-253G, which has not been found in any other archaic or modern human populations. It represents a molecular marker specific to the East Asian Middle Pleistocene <i>H. erectus</i> lineage, providing solid evidence that <i>H. erectus</i> specimens from Zhoukoudian, Hexian, and Sunjiadong sites belonged to the same evolutionary lineage. The other variant, AMBN-273V, has previously been identified in Denisovans. However, genetic analysis in this study reveals that this variant may have been introduced into Denisovans through populations related to these Middle Pleistocene <i>H. erectus</i>, and some of which subsequently contributed to certain modern human populations from Southeast Asia or Oceania. This study obtains lineage-specific molecular information from <i>Homo erectus</i> fossils for the first time, and reshapes our understanding of hominin evolution and the history of genetic admixture in East Asia.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"753-758"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798873","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":"Molecular mechanisms of chronic dietary cholesterol-driven remodeling of LDLR protein fate.","authors":"Xue Feng","doi":"10.16288/j.yczz.26-155","DOIUrl":"10.16288/j.yczz.26-155","url":null,"abstract":"<p><p>The hepatic low-density lipoprotein receptor (LDLR) mediates the clearance of circulating low-density lipoprotein (LDL) and is a key determinant of cholesterol homeostasis. However, how nutritional cues such as chronic dietary cholesterol regulate LDLR intracellular trafficking and protein turnover through specific molecular switches remains poorly understood. Dr. Alan Saltiel's team at the University of California San Diego discovered a cholesterol stress-response pathway mediated by Ral GTPases, revealing a new mechanism by which dietary cholesterol reshapes LDLR protein fate and thereby affects cholesterol homeostasis. The study found that chronic dietary cholesterol loading or sustained Ral activation reduces LDLR protein levels. Mechanistically, chronic cholesterol loading activates Ral GTPases by increasing RAS activity. Activated Ral, on the one hand, recruits the RalBP1-REPS1 endocytic complex to promote LDLR internalization and lysosomal trafficking while inhibiting LDLR recycling back to the cell surface. On the other hand, Ral activation promotes the processing and lysosomal localization of cathepsin A (CTSA) and reduces its extracellular secretion, thereby enhancing CTSA-mediated LDLR degradation. This process occurs independently of LDLR transcriptional regulation or PCSK9-mediated LDLR degradation. Inhibition of CTSA stabilizes LDLR protein and promotes LDL uptake and plasma cholesterol clearance. Human genetic analyses further indicate that key components of this pathway are associated with plasma lipid levels and cardiovascular disease risk. This study reveals a dietary cholesterol-activated Ral-CTSA-LDLR protein homeostasis pathway, providing a new mechanistic framework for understanding how nutritional stress disrupts cholesterol metabolism and identifying a potential therapeutic target distinct from existing treatment strategies for hypercholesterolemia and cardiovascular disease.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"759-763"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798885","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>PIK3CA</i> in-frame deletion-activated PI3K/AKT signaling pathway drives macrodactyly.","authors":"Jing-Heng Wu, Shan-Lin Chen, Yun-Hao Xue, Peng-Cheng Li, Meng-Meng Tian","doi":"10.16288/j.yczz.25-340","DOIUrl":"https://doi.org/10.16288/j.yczz.25-340","url":null,"abstract":"<p><p>Macrodactyly is a congenital abnormality characterized by overgrowth of single or multiple digits, frequently accompanied by pathological changes in bone, soft tissue, and nerve tissue, and is caused mostly by somatic variants. Previous studies have demonstrated that macrodactyly is predominantly caused by pathogenic variants in the <i>PIK3CA</i> gene, yet the underlying molecular mechanism remains unclear. In this study, we analyzed 13 patients clinically diagnosed with isolated macrodactyly. Through whole-exome and Sanger sequencing, we identified one pediatric patient carrying a novel mosaic <i>de novo</i> in-frame deletion mutation (c.307_312del/p.Glu103_Pro104del) in the <i>PIK3CA</i> gene, which was not detected in either parent. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, we classified this mutation as a variant of uncertain significance (PM4+PM2_Supporting+PM6_Supporting). Protein structure prediction analysis indicated that this in-frame deletion altered the protein's local conformation and surface electrostatic potential. Furthermore, the wild-type and mutant expression vectors were constructed, including the well-established pathogenic mutation c.353G>A/p.Gly118Asp in <i>PIK3CA</i> gene as a control. We transfected these vectors into HEK293T cells for functional analyses, respectively. The results showed that although this mutation did not significantly affect <i>PIK3CA</i> mRNA or protein expression levels, it promoted the phosphorylation of downstream AKT protein at both Thr308 and Ser473. Therefore, the mutation may express the localized overgrowth phenotype by activating the PI3K/AKT signaling pathway. This study not only expands the genetic variant spectrum of macrodactyly, but also further clarifies the role of the PI3K/AKT pathway in the <i>PIK3CA</i>-related overgrowth.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 8","pages":"796-806"},"PeriodicalIF":0.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798922","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":"Correction to: <i>VaWRKY65</i> contributes to cold tolerance through dual requaltion of soluble sugar accumulation and reactive oxygen species scavenging in <i>Vitis amurensis</i>.","authors":"","doi":"10.1093/hr/uhag317","DOIUrl":"https://doi.org/10.1093/hr/uhag317","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/hr/uhae367.].</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"13 7","pages":"uhag317"},"PeriodicalIF":9.5,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13421080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632760","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":"Operational model of the French livestock and poultry genetic resources management system and its implications.","authors":"Xiao-Jing Zhang, Ai-Ling Wang, Jing-Juan Zhao, Li-Min Chuan, Hui Zhang, Zhi-Hui Yan","doi":"10.16288/j.yczz.26-040","DOIUrl":"https://doi.org/10.16288/j.yczz.26-040","url":null,"abstract":"<p><p>As the largest agricultural producer in the European Union, France has established a mature and systematic livestock and poultry genetic resources management system. Based on comprehensive domestic legislation and effectively aligned with EU regulations, this system forms a governance structure characterized by clear responsibilities and multi-stakeholder collaboration. National regulatory authorities, public research institutions, industry organizations, and breeding service institutions work in a coordinated manner, with close linkages among the government, research community, and industry to ensure the conservation, dynamic monitoring, and sustainable utilization of genetic resources. For different livestock and poultry species such as ruminants, pigs, and poultry, France has developed differentiated genetic improvement pathways, supported by quality assurance and lifetime animal traceability mechanisms. This paper puts forward targeted suggestions for the conservation of livestock and poultry genetic resources in China, focusing on key areas such as forming a multi-stakeholder collaborative governance pattern, improving conservation mechanisms, promoting the layout of genetic improvement adapted to different livestock and poultry species, and ensuring quality traceability.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"48 7","pages":"659-670"},"PeriodicalIF":0.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148473138","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}