Journal of Applied Genetics最新文献

{"title":"Horse racing towards antibiotic resistance. Accompanying animals as a source of antibiotic-resistant bacteria.","authors":"Aleksandra Lepianka, Izabela Sitkiewicz","doi":"10.1007/s13353-026-01053-y","DOIUrl":"10.1007/s13353-026-01053-y","url":null,"abstract":"","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"811-820"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13534203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147772219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of intronic repeat expansions in the RFC1 gene in Polish patients with cerebellar syndrome.","authors":"Tomczuk Filip, Ziora-Jakutowicz Karolina, Dominik Natalia, Houlden Henry, Cortese Andrea, Rutkowska Karolina, Pollak Agnieszka, Ploski Rafal, Janik Piotr, Elert-Dobkowska Ewelina, Sulek Anna","doi":"10.1007/s13353-025-01000-3","DOIUrl":"10.1007/s13353-025-01000-3","url":null,"abstract":"<p><p>Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a recessively inherited neurodegenerative ataxic disorder, which has been associated with intronic biallelic repeat expansions in the RFC1 gene. Our objective was to assess retrospectively the prevalence of CANVAS in Polish population. We screened 2523 Polish patients in whom other repeat expansions were excluded. To determine the repeat expansions in the RFC1 gene in patients, we performed RFC1-flanking PCR and repeat primed PCR (RP-PCR) and to measure the size of the expansion we used Southern blotting and optical genome mapping to compare the results. We have observed the biallelic pathogenic motif/unit AAGGG expansions in 4.6% and expansions of non-pathogenic motifs AAAAG, AAAGG in 25% patients of our studied population. This is the first large-scale cohort study that confirms the relatively frequent occurrence of the CANVAS in Polish population. To increase the current diagnostics of late-onset ataxias within an unexplained molecular background, we suggest involving the RFC1 repeat expansions analysis to the routine diagnostic workflow.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"731-742"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13534201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic diversity, inbreeding, and selection signatures in duroc, landrace, and yorkshire pigs from a long-term closed breeding system.","authors":"Huangyi Tang, Henrique A Mulim, Shi-Yi Chen, Allan P Schinckel, Hongfeng-Xue, Dingjie-Qiu, Yizhan-Liu, Hinayah Rojas de Oliveira","doi":"10.1007/s13353-026-01072-9","DOIUrl":"10.1007/s13353-026-01072-9","url":null,"abstract":"<p><p>Duroc (DD), Landrace (LL), and Yorkshire (YY) are among the most widely used commercial pig breeds, having undergone intense long-term selection within closed breeding systems. This study presents a comprehensive genomic analysis of genetic diversity, inbreeding patterns, and selection signatures in DD, LL, and YY populations that have been subject to close breeding for over 15 years. Genomic and pedigree data were available for 1,088 animals (DD = 348, LL = 276, YY = 464), genotyped using the GenoBaits^® Porcine 100 K SNP panel. Principal component analysis and genetic diversity metrics revealed distinct population structures among the three breeds. Pairwise genetic differentiation supported this pattern, with DD showing the greatest divergence from LL (0.34 ± 0.24) and YY (0.33 ± 0.24), while LL and YY were more closely related (FST = 0.22 ± 0.19). Linkage disequilibrium (LD) analysis further confirmed these differences, as DD exhibited the highest average r² (0.34), followed by LL (0.28) and YY (0.25). Within-breed genetic diversity metrics, including observed heterozygosity (HO: 0.37 in DD, 0.39 in LL, 0.38 in YY), expected heterozygosity (HE: 0.36 in DD, 0.37 in LL, 0.38 in YY), and minor allele frequency (MAF: 0.27 in DD, 0.28 in LL, 0.29 in YY), indicated greater genetic variability in LL and YY compared to DD. Runs of homozygosity (ROH) analyses revealed different patterns of autozygosity, with DD exhibiting more long ROH indicative of recent inbreeding, while YY harbored a higher number of short ROH, suggestive of more ancient demographic events. ROH-based inbreeding coefficients (FROH) consistently exceeded pedigree-based estimates (FPED) across all breeds, highlighting the presence of recent or unrecorded inbreeding that pedigree data may not fully capture. According to Generation Proxy Selection Mapping (GPSM), 17, 1, and 12 significant SNPs were detected in DD, LL, and YY, respectively. Functional annotation of ROH islands and GPSM-significant loci revealed both breed-specific and overlapping QTLs related to traits such as growth, reproduction, and carcass. In general, the findings of this study contribute to a deeper understanding of the genomic consequences of long-term closed breeding and provide reference information to support consideration of breeding strategies that balance continued selection for productivity with the maintenance of genetic diversity in modern commercial pig populations.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"769-786"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13534200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148149840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ataxia and oculomotor apraxia caused by a large-scale deletion in the senataxin gene.","authors":"Joanna M Rusecka, Biruta Kierdaszuk, Iwona Stępniak, Małgorzata Rydzanicz, Piotr Stawiński, Tomasz Gambin, Damian Loska, Magdalena M Kacprzak, Magdalena Kaliszewska, Dorota Piekutowska-Abramczuk, Anna M Kamińska, Ewa Pronicka, Ewa Bartnik, Anna Kostera-Pruszczyk, Rafał Płoski, Agnieszka Sobczyńska-Tomaszewska, Katarzyna Tońska","doi":"10.1007/s13353-025-01001-2","DOIUrl":"10.1007/s13353-025-01001-2","url":null,"abstract":"<p><p>Senataxin, an RNA/DNA helicase, is a key protein providing genome stability and one of the best characterized R-loop-binding factors playing an important role in transcription and DNA repair processes. Pathogenic SETX gene variants cause autosomal recessive spinocerebellar ataxia with axonal neuropathy (AOA2, MIM #606002) and autosomal dominant juvenile amyotrophic lateral sclerosis (ALS4, MIM #602433), rare neurodegenerative disorders characterized by juvenile onset of progressive cerebellar ataxia, axonal sensorimotor peripheral neuropathy, combined upper and lower motor neuron symptoms, and increased serum alpha-fetoprotein (AFP; specific for AOA2). We report two cases of adult patients presenting with cerebellar syndrome, scanned speech, and exercise intolerance which started in the second/third decade of life and were followed by muscle weakness and impaired gait coordination. Whole exome sequencing (WES) was performed to analyze single nucleotide and copy number variants. A decreased coverage of a genomic region of around 16 kb on chromosome 9 (chr9:132,295,852-132,311,876), suggesting a deletion encompassing 5 exons of the SETX gene (exons 11-15, NM_015046.7) was observed. This homozygous SETX (9q34.13) deletion leads to a frame shift and consequently truncation of the helicase domain in the protein. Loss-of-function variants in the SETX gene are known to be pathogenic. Statistical analysis of NGS data from the Polish population identified a few heterozygous carriers, suggesting its region-specific origin.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"757-767"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13534219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening and investigating the regulatory mechanisms of oxidative stress-related biomarkers in thoracic aortic aneurysms.","authors":"Tao Liu, Pandeng Wang, Chenfan Guo, Xiangsen Liang, Baoshi Zheng","doi":"10.1007/s13353-025-00988-y","DOIUrl":"10.1007/s13353-025-00988-y","url":null,"abstract":"<p><p>Excess reactive oxygen species leading to oxidative stress has been identified as a significant factor in cardiovascular disease. However, the molecular mechanisms of oxidative stress-related genes in thoracic aortic aneurysm have not been thoroughly explored. An analysis of the GSE9106 dataset, using a geneset related to oxidative stress, revealed important links to purine metabolism pathways through functional enrichment analysis. A systematic investigation identified seven candidate genes, resulting in the identification of four potential biomarkers (IL10, SNCA, MAP1LC3A, and EPX) that show strong diagnostic promise for thoracic aortic aneurysm. These biomarkers were associated with critical pathways, including neuroactive ligand-receptor interaction and olfactory transduction. Correlation analysis also highlighted their relationships with specific immune cell types. The study not only examined biomarker-drug interactions but also performed experimental validations using qRT-PCR and immunohistochemistry. While the expression patterns of IL10 aligned with existing databases, some inconsistencies were observed in the validation of the other three biomarkers. Overall, these findings provide important insights into the diagnosis and treatment of thoracic aortic aneurysm, underscoring the significant role of oxidative stress-related biomarkers in this condition.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"631-647"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Discovery of core genes and intercellular communication role in osteosarcoma.","authors":"Fanyu Meng, Xinshe Zhou, Zhi Zhao, Lijia Pei, Weiguo Xia","doi":"10.1007/s13353-026-01058-7","DOIUrl":"10.1007/s13353-026-01058-7","url":null,"abstract":"","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"855"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147716643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are head and neck versus abdominal paragangliomas driven by different single nucleotide events?","authors":"Krzysztof Kotlarz, Katarzyna Ziemnicka, Bartłomiej Budny, Magda Mielczarek, Jakub Liu, Elżbieta Wrotkowska, Jarosław Kaznowski, Tomasz Suchocki, Jarosław Kałużny, Małgorzata Wierzbicka, Paula Dobosz, Marek Ruchała, Joanna Szyda","doi":"10.1007/s13353-025-00994-0","DOIUrl":"10.1007/s13353-025-00994-0","url":null,"abstract":"<p><p>Paragangliomas (PGLs) are a heterogeneous group of tumours of the nonepithelial neuroendocrine type, with a significant percentage being genetically determined. They can develop from cells of the parasympathetic as well as the sympathetic nervous system. Tumours located in the head and neck usually have a parasympathetic origin, whereas those in the abdomen have a sympathetic origin. The aim of this study was to determine whether the development of PGLs at both locations is associated with specific variants of genes with proven relevance for the formation of these tumours. Thirty-one patients with abdominal PGL and 16 with head and neck PGLs were analysed at 12 genes whose defects are among the most common genetic determinants of PGLs. The impact of SNPs (single nucleotide polymorphisms) on differentiation between both tumour types was assessed by fitting a decision tree and quantifying genotype effects of SNPs by the Shapley Additive Explanation metric. The study demonstrated that SNPs rs3748576 within the KIF1B gene and rs10060259 within the SDHA gene increase the probability of abdominal tumour locations, while heterozygous GA genotypes of rs2435351 located within the RET gene increase the probability of head and neck locations. The SNPs marked genes involved in the formation and functioning of the nervous system, but are located in introns, and thus themselves do not contribute to protein diversity. Still, intronic SNPs can indirectly affect the transcriptome by influencing alternative splicing, mRNA stability, or overlap with non-coding genes and other regulatory elements that affect transcription. Given this, it seems important to consider variants from non-coding regions in genetic analyses.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"661-667"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13534174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144731059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revolutionizing neonatal health: India's journey from assays to advanced genetics.","authors":"Akansha Bisht, Yasha Hasija","doi":"10.1007/s13353-025-01012-z","DOIUrl":"10.1007/s13353-025-01012-z","url":null,"abstract":"<p><p>According to UNICEF India, an estimated 67,385 neonates are born daily in India, each striving to survive the initial 28 days of life, which are pivotal in determining their future health prognosis. A significant number of these neonates succumb to inborn errors of metabolism (IEM), resulting in a spectrum of either manageable or severe clinical consequences. The evolution of techniques from basics to next-generation sequencing (NGS) and cutting-edge bioinformatics has enabled the prompt and precise identification of metabolic defects during the early stages of life. But the limited awareness, facilities, and access to the screening program necessitate the urgent need for establishing a state-of-the-art screening initiative all over India. The program holds the potential to substantially diminish infant mortality rates and alleviate the national health burden. This article delineates inborn errors of metabolism, investigates the advancements in diagnostic methodologies, outlines the NGS technique, underscores the role of computational biology, and advocates for the establishment of a centralized screening initiative in India specifically for treatable IEM. Furthermore, a few case studies have been included to showcase the notable discoveries of genes and associated disorders facilitated by NGS along with some studies highlighting the advantages of employing computational biology.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"595-615"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Somatic and germinal mosaicism of a canonical splicing variant causing limb-girdle muscular dystrophy type 1B.","authors":"Guangyu Wang, Yaru Wang, Dandan Zhao, Chuanzhu Yan, Pengfei Lin","doi":"10.1007/s13353-025-01002-1","DOIUrl":"10.1007/s13353-025-01002-1","url":null,"abstract":"<p><p>Limb-girdle muscular dystrophy type 1B is one of several muscular dystrophies caused by pathogenic variants in the LMNA gene. In this study, we investigated the clinical, pathological, and genetic findings of an LGMD1B family. Genetic sequencing identified the proband and her younger brother both carried the canonical splicing c.513 + 1G > A variant in the LMNA gene. The variant was absent in the proband's mother, and a certain percentage of the LMNA variant was identified in the venous blood, urine, and semen sample of the proband's father by pyrophosphate sequencing. Further cDNA analysis demonstrated that the canonical splicing c.513 + 1G > A variant in intron 2 induced retention of the first 45 bp of intron 2, resulting in an in-frame insertion of 15 amino acids. Our study directly confirmed the presence of somatic and germinal mosaicism in the LGMD1B family and the pathogenicity of the canonical splicing variant in the LMNA gene.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"749-755"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.","authors":"Yunyan Fei, Zhenghai Mo","doi":"10.1007/s13353-025-00996-y","DOIUrl":"10.1007/s13353-025-00996-y","url":null,"abstract":"<p><p>Improving yield potential is a critical goal for breeders; however, yield-related loci are still less understood in waxy rice, which seriously limited the precise development of high-yield cultivars. Here, we investigated six yield-related traits in a collection of 109 cultivated waxy rice accessions over two seasons and perform genome-wide association study using 1.81 million single nucleotide polymorphisms (SNPs) to elucidate the genetic basis underlying grain yield. Our analysis identified a total of 28 significant quantitative trait loci (QTLs), explaining 0.71-38.46% of phenotype variance. Of these, 17 was previously reported or contained genes known to govern the associated traits, while the remaining 11 appear to be novel alleles. Within the 28 QTLs, 379 residing genes were identified, and candidate yield-related genes in close proximity to the significant SNPs were extracted for haplotype analysis. The results showed that the genetic variations in Os09g0375700, Os09g0396300, and Os03g0609500 were highly associated with variations in thousand grain weight or panicle number. Our results dissected the possible genetic determinants of waxy rice yield and will be conducive to breed new cultivars with high yield in the future.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"561-572"},"PeriodicalIF":2.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}