Journal of Applied Genetics最新文献

Reevaluating the total genotype score: a practical perspective from applied sport science. 重新评估总基因型得分：从应用体育科学的实际观点。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-10-01 DOI: 10.1007/s13353-025-01020-z

Ricardo Muller Bottura, Daniel Blasioli Dentillo

引用次数: 0

Bioinformatics and machine learning reveal novel prognostic biomarkers in head and neck squamous cell carcinoma. 生物信息学和机器学习揭示头颈部鳞状细胞癌新的预后生物标志物。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-10-01 DOI: 10.1007/s13353-025-01018-7

Amir Ali Judaki, Mohammad Shirinpoor, Masoumeh Farahani, Tahmineh Aldaghi, Afsaneh Arefi-Oskouie, Elham Nazari

{"title":"Bioinformatics and machine learning reveal novel prognostic biomarkers in head and neck squamous cell carcinoma.","authors":"Amir Ali Judaki, Mohammad Shirinpoor, Masoumeh Farahani, Tahmineh Aldaghi, Afsaneh Arefi-Oskouie, Elham Nazari","doi":"10.1007/s13353-025-01018-7","DOIUrl":"https://doi.org/10.1007/s13353-025-01018-7","url":null,"abstract":"Head and neck squamous cell carcinoma (HNSCC), the seventh most common cancer worldwide, has become more closely linked to poor lifestyle habits. Despite improvements in cancer treatment approaches, patients with stage I-II HNSCC have a 70-90% 5-year survival rate, and for patients with advanced stages III-IV, this rate falls to about 40%. This controversy is all about the heterogeneity of HNSCC. Finding diagnosis and prognosis biomarkers has the potential to make significant improvements in the life expectancy and overall health of these patients. The combination of bioinformatics and machine learning has facilitated the finding of the best markers for HNSCC. In this regard, RNA expression data were obtained to identify genes that were expressed differently (DEGs) and utilize a deep learning algorithm to identify genes that exhibited significant variability. In addition, correlations between clinical data and DEGs, the building of a Receiver Operating Characteristic (ROC) curve, and the prediction of tumor-infiltrating immune cells were analyzed. Deep learning analysis identified diagnostic and prognostic biomarkers strongly associated with carcinogenesis, such as KRT33B, KRTAP3-3, C14orf34, and ACADM. In addition, after analyzing the ROC curve, it was found that the combination of ACADM, KRT33B, and C14orf34 is the most practical combination of diagnostic markers. This combination achieved sensitivity, specificity, and Area Under the Curve (AUC) values of 0.92, 0.86, and 0.93, respectively.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145199536","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}

引用次数: 0

Interfungal antagonism between Trichoderma and Fusarium proliferatum - metabolomic and DNA-based analyses. 木霉和增肉镰刀菌的真菌间拮抗作用-代谢组学和dna分析。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-26 DOI: 10.1007/s13353-025-01014-x

Modrzewska Marta, Popowski Dominik, Błaszczyk Lidia, Stępień Łukasz, Waśkiewicz Agnieszka, Urbaniak Moniak, Bryła Marcin

{"title":"Interfungal antagonism between Trichoderma and Fusarium proliferatum - metabolomic and DNA-based analyses.","authors":"Modrzewska Marta, Popowski Dominik, Błaszczyk Lidia, Stępień Łukasz, Waśkiewicz Agnieszka, Urbaniak Moniak, Bryła Marcin","doi":"10.1007/s13353-025-01014-x","DOIUrl":"https://doi.org/10.1007/s13353-025-01014-x","url":null,"abstract":"This study evaluated the antagonistic capacity of eight Trichoderma isolates against two Fusarium proliferatum isolates that differed in their toxigenic potential. Using co-cultures on solid and liquid media, significant variability in antifungal efficacy was observed among Trichoderma species. T. atroviride and T. viridescens isolates demonstrated the highest antagonistic activity, with markedly stronger inhibition of the less toxigenic F. proliferatum isolate. Quantitative PCR analysis confirmed a reduction in Fusarium biomass, which closely correlated with decreased levels of fumonisins (FB1, FB2, FB3) and beauvericin, as determined by UHPLC-HRMS. Notably, the most effective Trichoderma isolates (AN153, AN215, AN523) consistently suppressed both fungal growth and mycotoxin biosynthesis. Although fumonisin levels were reduced in co-cultures, independent assays in FB1-supplemented liquid media indicated that Trichoderma did not directly degrade mycotoxin. The presence of selected secondary metabolites, including 6-pentyl-2H-pyrone and phenolic acids, was confirmed in co-culture extracts. These findings highlight the isolate-specific nature of Trichoderma-Fusarium interactions and emphasise the potential of selected Trichoderma isolates as biocontrol agents capable of simultaneously limiting pathogen growth and mycotoxin accumulation. Further mechanistic studies are warranted to identify the molecular basis of these antagonistic effects.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145149080","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}

引用次数: 0

Revolutionizing neonatal health: India's journey from assays to advanced genetics. 革新新生儿健康：印度从化验到先进遗传学的旅程。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-23 DOI: 10.1007/s13353-025-01012-z

Akansha Bisht, Yasha Hasija

{"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":"https://doi.org/10.1007/s13353-025-01012-z","url":null,"abstract":"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.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-23","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}

引用次数: 0

Genome-wide identification and expression profiling of the MYC gene family in Triticum monococcum L. subsp. aegilopoides with a focus on the red glume mutant. 小麦MYC基因家族的全基因组鉴定及表达谱分析以红色颖片突变体为重点的贝壳属植物。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-23 DOI: 10.1007/s13353-025-01013-y

Xin Liu, Jia Zhao, Xin Zhao, Mang Shen, Minghu Zhang, Lianquan Zhang

{"title":"Genome-wide identification and expression profiling of the MYC gene family in Triticum monococcum L. subsp. aegilopoides with a focus on the red glume mutant.","authors":"Xin Liu, Jia Zhao, Xin Zhao, Mang Shen, Minghu Zhang, Lianquan Zhang","doi":"10.1007/s13353-025-01013-y","DOIUrl":"https://doi.org/10.1007/s13353-025-01013-y","url":null,"abstract":"MYC transcription factors, belonging to the basic helix-loop-helix (bHLH) superfamily, are widely recognized for their critical involvement in controlling various aspects of plant growth, developmental processes, and responses to environmental stresses. Triticum monococcum L. subsp. aegilopoides, a wild diploid wheat species, provides valuable Genetic resources for improving stress tolerance and nutritional traits. In this study, 18 TbMYC genes were identified in T. monococcum L. subsp. aegilopoides, characterized by diverse gene structures, conserved motifs, and distinct tissue-specific expression patterns. Phylogenetic analysis grouped these genes into six groups, revealing unique structural features and motifs that suggest functional diversification. Promoter analysis uncovered numerous cis-regulatory elements linked to light response, stress adaptation, and hormonal regulation, with TbMYC8 notably enriched in ABA-responsive elements, highlighting its potential involvement in abscisic acid-mediated stress responses. Synteny analysis demonstrated conserved TbMYCs across Triticeae species, underscoring their evolutionary significance. RNA-seq analysis identified five TbMYCs significantly implicated in the anthocyanin biosynthetic pathway, particularly in regulating pigment accumulation in a red-glume mutant. These findings underscore the critical roles of TbMYCs in stress adaptation and secondary metabolism, providing valuable insights for wheat improvement and functional genomics.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124893","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}

引用次数: 0

Genome-wide identification and characterization of GATA transcription factors in Avena sativa L. and expression profiling under salinity stress. 盐胁迫下玉米叶片GATA转录因子的全基因组鉴定与表达谱分析

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-19 DOI: 10.1007/s13353-025-01007-w

Muskan Bokolia, Tanu Singh, Nandni Goyal, Avneesh Kumar, Kashmir Singh, Baljinder Singh

{"title":"Genome-wide identification and characterization of GATA transcription factors in Avena sativa L. and expression profiling under salinity stress.","authors":"Muskan Bokolia, Tanu Singh, Nandni Goyal, Avneesh Kumar, Kashmir Singh, Baljinder Singh","doi":"10.1007/s13353-025-01007-w","DOIUrl":"https://doi.org/10.1007/s13353-025-01007-w","url":null,"abstract":"GATA transcription factors are a group of type IV zinc-finger proteins that play critical roles in regulating plant growth, development, and responses to abiotic stress. These genes are characterized by a conserved DNA-binding domain with the consensus sequence (A/T)GATA(A/G) and a type IV zinc-finger motif containing the conserved sequence CX2CX18-20CX2C. In this study, 27 GATA genes (designated AsGATA) were identified in Avena sativa using the GrainGenes genome database. Comprehensive analyses were performed to examine their conserved motifs, physicochemical properties, chromosomal localization, gene structures, phylogenetic relationships, and cis-acting regulatory elements. Based on the classification of GATA family members in Arabidopsis thaliana, the AsGATA genes were categorized into four subfamilies. Gene structure analysis revealed that members of the same subfamily generally exhibited similar structural features. Subcellular localization predictions indicated that most AsGATA proteins are Likely to function in the nucleus. Chromosomal mapping demonstrated the random distribution of the 27 AsGATA genes across the 21 chromosomes of Avena sativa. Expression profiling, based on RNA-Seq data from the NCBI SRA database, identified six AsGATA genes that are responsive to salt stress. These genes represent promising candidates for functional studies and could be leveraged in breeding programs to develop salt-tolerant Avena sativa varieties.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086346","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}

引用次数: 0

Genome-wide association study bridging genomics-phenomics gap in natural plant populations. 全基因组关联研究：弥合天然植物群体基因组学-表型学差距。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-18 DOI: 10.1007/s13353-025-01010-1

Sarbani Roy, Hari Shankar Gadri, Vikas Sharma, Md Asif Chowdhary, Rohini Dwivedi, Pankaj Bhardwaj

引用次数: 0

Shifting genetic structure of Polish sea trout populations: a contemporary perspective. 波兰海鳟种群遗传结构的变化：当代视角。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-13 DOI: 10.1007/s13353-025-01006-x

Rafał Bernaś, Anna Wąs-Barcz, Tomasz Horbacz, Remigiusz Szymański, Adam M Lejk

{"title":"Shifting genetic structure of Polish sea trout populations: a contemporary perspective.","authors":"Rafał Bernaś, Anna Wąs-Barcz, Tomasz Horbacz, Remigiusz Szymański, Adam M Lejk","doi":"10.1007/s13353-025-01006-x","DOIUrl":"https://doi.org/10.1007/s13353-025-01006-x","url":null,"abstract":"The genetic structure and variability of sea trout populations in the southern Baltic Sea were shaped during the last glaciation, in parallel with the evolution of the Baltic Sea. However, human activities-particularly hydrotechnical development and the introduction of non-local genetic lines-have altered and partially reduced the original genetic diversity. In the present study, the authors describe the historical changes that have occurred and present the current level of genetic variability within Polish sea trout populations. A total of 575 sea trout from nine river populations and three hatchery broodstocks were genotyped at 13 microsatellite loci. The global FST obtained via AMOVA was moderate, at 0.041. The highest pairwise FST values were observed between the Rutki and Aquamar broodstocks and all other populations. The lowest and statistically non-significant pairwise differences were detected between the Rega and Ina river populations, as well as between the Słupia and Łupawa. Genetic structure analysis revealed geographic differentiation, identifying either four or seven distinct clusters. Additionally, neighbour-joining clustering showed that the examined populations and stocks were divided into two main subgroups: one consisting of samples related to the Vistula origin, and the other comprising clearly separated Pomeranian populations. This paper discusses the emergence of new genetic variability driven by microevolutionary processes and presents a revised approach for sea trout population management.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145064560","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}

引用次数: 0

Development and application of duplex and triplex assays for simultaneous detection of resistance genes to leaf rust, Fusarium head blight, powdery mildew, Septoria tritici blotch, eyspot, stem rust and yellow rust in wheat. 同时检测小麦叶锈病、赤霉病、白粉病、黑斑病、茎锈病和黄锈病抗性基因的双联法和三联法的建立与应用。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-13 DOI: 10.1007/s13353-025-01004-z

Roksana Bobrowska, Jakub Moskalik, Aleksandra Noweiska, Julia Spychała, Agnieszka Tomkowiak, Michał Tomasz Kwiatek

{"title":"Development and application of duplex and triplex assays for simultaneous detection of resistance genes to leaf rust, Fusarium head blight, powdery mildew, Septoria tritici blotch, eyspot, stem rust and yellow rust in wheat.","authors":"Roksana Bobrowska, Jakub Moskalik, Aleksandra Noweiska, Julia Spychała, Agnieszka Tomkowiak, Michał Tomasz Kwiatek","doi":"10.1007/s13353-025-01004-z","DOIUrl":"https://doi.org/10.1007/s13353-025-01004-z","url":null,"abstract":"Resistance breeding is a widely promoted strategy for minimizing yield losses in wheat caused by various fungal diseases, including leaf rust (Puccinia triticina; Lr genes), Fusarium head blight (Fusarium spp.; Fhb), powdery mildew (Blumeria graminis; Pm), Septoria tritici blotch (Septoria tritici; Stb), eyespot (Oculimacula spp.; Pch-previously known as Pseudocercosporella herpotrichoides), stem rust (Puccinia graminis f. sp. tritici; Sr) and yellow rust (Puccinia striiformis; Yr). Understanding the prevalence of resistance genes in currently cultivated European varieties is crucial for their effective utilization in breeding programs. In this study, we developed 11 duplex and 13 triplex PCR assays for the simultaneous identification of diverse allelic combinations of disease resistance genes. Selected assays were used to analyze 70 European wheat varieties for the presence of 15 molecular markers associated with 12 resistance genes. The analyses identified diverse resistance gene combinations. The optimized multiplex PCR methods significantly reduce cost and time of analysis, making them valuable tools for marker-assisted selection (MAS) in wheat breeding programs.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145053549","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}

引用次数: 0

Strigolactones modulate jasmonate-dependent transcriptional reprogramming during wound signalling in Arabidopsis. 拟南芥创伤信号传导过程中独角甘内酯调节茉莉酸依赖的转录重编程。

IF 1.9 3区生物学

Journal of Applied Genetics Pub Date : 2025-09-09 DOI: 10.1007/s13353-025-01005-y

Marek Marzec

{"title":"Strigolactones modulate jasmonate-dependent transcriptional reprogramming during wound signalling in Arabidopsis.","authors":"Marek Marzec","doi":"10.1007/s13353-025-01005-y","DOIUrl":"https://doi.org/10.1007/s13353-025-01005-y","url":null,"abstract":"Mechanical wounding triggers rapid transcriptional and hormonal reprogramming in plants, primarily driven by jasmonate (JA) signalling. While the role of JA, ethylene, and salicylic acid in wound responses is well characterised, the contribution of strigolactones (SLs) remains largely unexplored. Here, for the first time, it was shown that SLs modulate wound-induced transcriptional dynamics in Arabidopsis thaliana. Using transcriptome profiling of wild-type (Columbia-0) and the SL biosynthesis mutant more axillary growth3 (max3), a discrete cohort of genes whose wound induction is SL-dependent was identified. These genes include core JA biosynthetic genes and several JA-responsive transcriptional repressors, indicating that SLs potentiate early JA signalling. Promoter motif and protein-protein interaction analyses revealed that SLs regulate a transcriptional module composed of AP2/ERF, WRKY, and C2H2 zinc-finger factors, which integrate JA signalling, ROS homeostasis, and tissue regeneration. Notably, many of these factors are misregulated in max3 even prior to wounding, suggesting a primed but hypo-responsive state. Presented findings suggest a model in which SLs act upstream of the JA burst, coordinating transcriptional readiness and post-injury activation. This expands the functional scope of SLs in stress response and positions them as potential modulators of hormone crosstalk during wound responses.","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145023342","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}

引用次数: 0