Journal of Applied Genetics最新文献

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Diversity of genome size, endopolyploidy and SCoT markers in 20 Trigonella (Fabaceae) species. 20 个三叶草(豆科)物种基因组大小、内倍性和 SCoT 标记的多样性。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-12-01 Epub Date: 2024-06-26 DOI: 10.1007/s13353-024-00886-9
Monika Rewers, Agnieszka Lojko, Dorota Olszewska, Aleksandra Niklas, Iwona Jedrzejczyk
{"title":"Diversity of genome size, endopolyploidy and SCoT markers in 20 Trigonella (Fabaceae) species.","authors":"Monika Rewers, Agnieszka Lojko, Dorota Olszewska, Aleksandra Niklas, Iwona Jedrzejczyk","doi":"10.1007/s13353-024-00886-9","DOIUrl":"10.1007/s13353-024-00886-9","url":null,"abstract":"<p><p>The Trigonella species possess medicinal, nutraceutical and pharmaceutical properties due to the presence of many bioactive compounds. Its therapeutic effects are mostly valuable in medicine, cosmetics and the functional food industry. Correct genetic characterisation of plant material is needed to increase the potential of Trigonella species by breeding and conservation programs. The aim of this study was to develop a reliable marker system to support the morphological and phytochemical analysis in Trigonella taxonomic research, species identification and characterization as well as determination of the interspecific variation within this genus along with relationships between species. For this purpose, flow cytometry and SCoT molecular markers were combined. Flow cytometric analyses revealed that Trigonella species possess very small and small genomes. The range of genome sizes was from 1.10 to 5.76 pg/2C, with most species possessing very small genomes (< 2.8 pg/2C). In seeds of 14 species endopolyploid nuclei were detected. Flow cytometric analysis of genome size enabled quick identification of four out of 20 species, while combined with endopolyploidy detection in seeds, facilitated distinction of the next seven species. ScoT molecular markers helped to identify closely related species with similar genome size and cell cycle activity. Therefore, flow cytometry was proposed as the first-choice method for quick accession screening, while the more detailed genetic classification was obtained using SCoT molecular markers.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450535","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
Deciphering early responsive signature genes in rice blast disease: an integrated temporal transcriptomic study. 解密稻瘟病的早期反应特征基因:一项综合时序转录组学研究
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-12-01 Epub Date: 2024-08-24 DOI: 10.1007/s13353-024-00901-z
Ajitha Antony, Shanthi Veerappapillai, Ramanathan Karuppasamy
{"title":"Deciphering early responsive signature genes in rice blast disease: an integrated temporal transcriptomic study.","authors":"Ajitha Antony, Shanthi Veerappapillai, Ramanathan Karuppasamy","doi":"10.1007/s13353-024-00901-z","DOIUrl":"10.1007/s13353-024-00901-z","url":null,"abstract":"<p><p>Rice blast disease, caused by Magnaporthe oryzae, reigns as the top-most cereal killer, jeopardizing global food security. This necessitates the timely scouting of pathogen stress-responsive genes during the early infection stages. Thus, we integrated time-series microarray (GSE95394) and RNA-Seq (GSE131641) datasets to decipher rice transcriptome responses at 12- and 24-h post-infection (Hpi). Our analysis revealed 1580 differentially expressed genes (DEGs) overlapped between datasets. We constructed a protein-protein interaction (PPI) network for these DEGs and identified significant subnetworks using the MCODE plugin. Further analysis with CytoHubba highlighted eight plausible hub genes for pathogenesis: RPL8 (upregulated) and RPL27, OsPRPL3, RPL21, RPL9, RPS5, OsRPS9, and RPL17 (downregulated). We validated the expression levels of these hub genes in response to infection, finding that RPL8 exhibited significantly higher expression compared with other downregulated genes. Remarkably, RPL8 formed a distinct cluster in the co-expression network, whereas other hub genes were interconnected, with RPL9 playing a central role, indicating its pivotal role in coordinating gene expression during infection. Gene Ontology highlighted the enrichment of hub genes in the ribosome and protein translation processes. Prior studies suggested that plant immune defence activation diminishes the energy pool by suppressing ribosomes. Intriguingly, our study aligns with this phenomenon, as the identified ribosomal proteins (RPs) were suppressed, while RPL8 expression was activated. We anticipate that these RPs could be targeted to develop new stress-resistant rice varieties, beyond their housekeeping role. Overall, integrating transcriptomic data revealed more common DEGs, enhancing the reliability of our analysis and providing deeper insights into rice blast disease mechanisms.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046704","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
Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach. 通过综合多组学和硅学方法揭示作为头颈部鳞状细胞癌潜在生物标志物的水蒸发蛋白和染色体组家族成员的作用。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-12-01 Epub Date: 2024-02-15 DOI: 10.1007/s13353-024-00843-6
Rishabh Gurung, Mohammad Masood, Prithvi Singh, Prakash Jha, Anuradha Sinha, Swati Ajmeriya, Milin Sharma, Ravins Dohare, Mohammad Mahfuzul Haque
{"title":"Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach.","authors":"Rishabh Gurung, Mohammad Masood, Prithvi Singh, Prakash Jha, Anuradha Sinha, Swati Ajmeriya, Milin Sharma, Ravins Dohare, Mohammad Mahfuzul Haque","doi":"10.1007/s13353-024-00843-6","DOIUrl":"10.1007/s13353-024-00843-6","url":null,"abstract":"<p><p>Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with <math> <msup><mrow><mtext>CD</mtext> <mn>4</mn></mrow> <mo>+</mo></msup> </math> T cells, positively with <math> <msup><mrow><mtext>CD</mtext> <mn>8</mn></mrow> <mo>+</mo></msup> </math> T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with <math> <msup><mrow><mtext>CD</mtext> <mn>4</mn></mrow> <mo>+</mo></msup> </math> T cells, negatively with <math> <msup><mrow><mtext>CD</mtext> <mn>8</mn></mrow> <mo>+</mo></msup> </math> T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139735271","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
The role of multidisciplinary diagnostic and therapeutic model of care in Lamb-Shaffer syndrome - case report. 多学科诊断和治疗模式在羔羊沙弗综合征中的作用--病例报告。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-12-01 Epub Date: 2024-02-10 DOI: 10.1007/s13353-024-00838-3
Urszula Sajewicz-Radtke, Ariadna Łada-Maśko, Małgorzata Lipowska, Bartosz M Radtke, Beata S Lipska-Ziętkiewicz, Katarzyna Krempla-Patron
{"title":"The role of multidisciplinary diagnostic and therapeutic model of care in Lamb-Shaffer syndrome - case report.","authors":"Urszula Sajewicz-Radtke, Ariadna Łada-Maśko, Małgorzata Lipowska, Bartosz M Radtke, Beata S Lipska-Ziętkiewicz, Katarzyna Krempla-Patron","doi":"10.1007/s13353-024-00838-3","DOIUrl":"10.1007/s13353-024-00838-3","url":null,"abstract":"<p><p>This case study illustrates a multidisciplinary diagnostic and therapeutic model of care for a 7-year-old male with Lamb-Shaffer syndrome (LAMSHF). LAMSHF is an ultra-rare genetic neurodevelopmental disorder, caused by heterozygous alterations in the SOX5 gene. An integrative model of therapy of cognitive functions and speech is described. The presented approach allows the development of language competences through stimulation of basic cognitive functions, which allows the learning of the abstract rules of an inflected language. A surprising, unexpected improvement in the cognitive functioning of the child was observed (both in terms of reasoning and speech), as well as an increase in his independence. The clinically important problem of the need for continued stimulation of cognitive development, in spite of the unfavourable prognosis associated with LAMSHF, is highlighted.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716123","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
RNA-Seq transcriptome profiling of Nile rat livers reveals novel insights on the anti-diabetic mechanisms of Water-Soluble Palm Fruit Extract. 尼罗河大鼠肝脏的 RNA-Seq 转录组分析揭示了水溶性棕榈果提取物抗糖尿病机制的新见解。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-12-01 Epub Date: 2024-06-18 DOI: 10.1007/s13353-024-00880-1
Soon-Sen Leow, Jia-Shiun Khoo, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K C Hayes
{"title":"RNA-Seq transcriptome profiling of Nile rat livers reveals novel insights on the anti-diabetic mechanisms of Water-Soluble Palm Fruit Extract.","authors":"Soon-Sen Leow, Jia-Shiun Khoo, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K C Hayes","doi":"10.1007/s13353-024-00880-1","DOIUrl":"10.1007/s13353-024-00880-1","url":null,"abstract":"<p><p>Water-Soluble Palm Fruit Extract (WSPFE) has been shown to confer anti-diabetic effects in the Nile rat (NR) (Arvicanthis niloticus). Liquid and powder WSPFE both deterred diabetes onset in NRs fed a high-carbohydrate (hiCHO) diet, but the liquid form provided better protection. In this study, NRs were fed either a hiCHO diet or the same diet added with liquid or powder WSPFE. Following feeding of the diets for 8 weeks, random blood glucose levels were measured to categorize NRs as either diabetes-resistant or diabetes-susceptible, based on a cut-off value of 75 mg/dL. Livers were then obtained for Illumina HiSeq 4000 paired end RNA-sequencing (RNA-Seq) and the data were mapped to the reference genome. Consistent with physiological and biochemical parameters, the gene expression data obtained indicated that WSPFE was associated with protection against diabetes. Among hepatic genes upregulated by WSPFE versus controls, were genes related to insulin-like growth factor binding protein, leptin receptor, and processes of hepatic metabolism maintenance, while those downregulated were related to antigen binding, immunoglobulin receptor, inflammation- and cancer-related processes. WSPFE supplementation thus helped inhibit diabetes progression in NRs by increasing insulin sensitivity and reducing both the inflammatory effects of a hiCHO diet and the related DNA-damage compensatory mechanisms contributing to liver disease progression. In addition, the genetic permissiveness of susceptible NRs to develop diabetes was potentially associated with dysregulated compensatory mechanisms involving insulin signaling and oxidative stress over time. Further studies on other NR organs associated with diabetes and its complications are warranted.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419226","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
Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot. DcSto微型倒装重复转座元件的多态插入揭示了栽培胡萝卜的遗传多样性结构。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-10-28 DOI: 10.1007/s13353-024-00916-6
Santosh Hadagali, Katarzyna Stelmach-Wityk, Alicja Macko-Podgórni, Sarvamangala Cholin, Dariusz Grzebelus
{"title":"Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot.","authors":"Santosh Hadagali, Katarzyna Stelmach-Wityk, Alicja Macko-Podgórni, Sarvamangala Cholin, Dariusz Grzebelus","doi":"10.1007/s13353-024-00916-6","DOIUrl":"https://doi.org/10.1007/s13353-024-00916-6","url":null,"abstract":"<p><p>Miniature inverted-repeat transposable elements (MITEs) are a potent source of polymorphisms in plant genomes. A genotyping system, named DcS-ILP, based on polymorphic insertions of Stowaway MITEs (DcStos) localized in introns and identified in the reference genome DH1, has been developed for carrot. Here, we report an extension of the DcS-ILP genotyping system by incorporation of non-reference insertions identified in resequenced genomes representing the eastern gene pool. We genotyped 52 carrot accessions representing the eastern and western carrot gene pools with 92 markers developed previously (western DcS-ILP panel) together with 84 newly developed markers (eastern DcS-ILP panel). Overall, the DcS-ILP markers revealed a highly structured genetic diversity separating the eastern and the western carrot accessions at K = 2 and differentiating Indian breeding lines from the eastern accessions at K = 3. The eastern DcS-ILP panel proved to be more robust with respect to the eastern carrot gene pool, while it provided little information on the western accessions, as many of the DcSto insertions present in the eastern gene pool were absent in the western gene pool. As the western carrot accessions represent improved cultivars, DcSto insertional polymorphisms allowed detection of a selection-driven bottleneck at the improvement stage. Selection in the course of the improvement stage generally operated on standing variation, as the subset of DcSto insertions present in the western carrot likely originated from transposition events preceding the separation of both gene pools. However, occasional frequency shifts in the opposite direction were also revealed, possibly indicating selection for favorable variants associated with DcSto insertions.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521959","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
Experimental and in silico analysis of LINC01279 expression in tumor of patients with breast cancer. 乳腺癌患者肿瘤中 LINC01279 表达的实验和硅学分析。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-10-28 DOI: 10.1007/s13353-024-00908-6
Negar Mokhtari, Najmeh Ahmadi, Sahar Moradi, Shiva Farmani, Elham Kheyrani, Nasrin Fattahi Dolatabadi
{"title":"Experimental and in silico analysis of LINC01279 expression in tumor of patients with breast cancer.","authors":"Negar Mokhtari, Najmeh Ahmadi, Sahar Moradi, Shiva Farmani, Elham Kheyrani, Nasrin Fattahi Dolatabadi","doi":"10.1007/s13353-024-00908-6","DOIUrl":"https://doi.org/10.1007/s13353-024-00908-6","url":null,"abstract":"<p><p>Breast cancer (BC) is characterized by the increase of malignant cells in the breast. The malignant cells begin in the lining of the breast milk glands or ducts (ductal epithelium). BC is the most frequent cancer in women, but it may also occur in males. Long non-coding RNAs (lncRNA) have been demonstrated to control the development and incidence of cancer. However, some lncRNAs experience potential changes in BC, but their role has not been well studied. LINC01279 is known as a valuable biomarker in gastric cancer but has not yet been studied in BC. Changes in LINC01279 expression levels in BC samples were investigated by microarray. Q-PCR was also used to evaluate the expression of LINC01279 in the tumor and normal adjacent samples of 30 BC patients. The LINC01279 co-expressed gene module was discovered using weighted gene correlation network analysis (WGCNA) on the relevant dataset. The top ten hub genes were determined using gene ontology (GO) functional enrichments on the co-expressed gene module. The results of the bioinformatics study showed an increase in LINC01279 expression levels (log2FC = 3.228749561, adj.P.Val = 1.69E - 12) in tumor samples compared to normal marginal tissue. Q-PCR results also showed a significant increase in LINC01279 expression (P-value = 0.0005) in tumor samples. WGCNA analysis identified that the black module is the LINC01279 co-expressed module, and functional annotation analysis of black module genes enriched in significant cancer-related pathways and processes, including cell growth and/or maintenance, regulation of immune response, regulation of cell proliferation, and epithelial-to-mesenchymal transition (EMT). Regarding the real-time PCR results, the analysis of expression patterns has illuminated a distinct association between the heightened expression levels of LINC01279, and the stages of cancer progression as well as the metastatic potential of tumors. However, intriguingly, our observations have failed to reveal any statistically significant correlations between the relative expression of LINC01279 and tumor grade classification, or the presence of ER, PR, and HER2 biomarkers. The present study could provide a new perspective on the molecular regulatory. Processes associated with BC pathogenic mechanisms are linked to the LINC01279, although further research is needed on the possible role of this lncRNA in BC.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500852","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
DNA methylation dysregulation patterns in the 1p36 region instability. 1p36 区域不稳定的 DNA 甲基化失调模式。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-10-26 DOI: 10.1007/s13353-024-00913-9
Joanna Swierkowska-Janc, Michal Kabza, Malgorzata Rydzanicz, Maciej Giefing, Rafal Ploski, Lisa G Shaffer, Marzena Gajecka
{"title":"DNA methylation dysregulation patterns in the 1p36 region instability.","authors":"Joanna Swierkowska-Janc, Michal Kabza, Malgorzata Rydzanicz, Maciej Giefing, Rafal Ploski, Lisa G Shaffer, Marzena Gajecka","doi":"10.1007/s13353-024-00913-9","DOIUrl":"https://doi.org/10.1007/s13353-024-00913-9","url":null,"abstract":"<p><p>In the monosomy 1p36 deletion syndrome, the role of DNA methylation in the genomic stability of the 1p36 region remains elusive. We hypothesize that changes in the methylation pattern at the 1p36 breakpoint hotspot region influenced the chromosomal breakage leading to terminal deletions. From the monosomy 1p36 material collection, four cases with 4.0 to 5.5 Mb terminal deletions and their parents were investigated. DNA samples were assessed by targeted bisulfite sequencing (NimbleGen SeqCap Epi) to examine DNA methylation status in the 1p36 hotspot region at single-base resolution as compared to the chromosomal hotspot regions, 9p22, 18q21.1, and 22q11.2. Additionally, in in silico assessment, the mean GC content of various classes of repeats in the genome and especially in the breakpoint regions was evaluated. A complex landscape of DNA methylation in the 1p36 breakpoint hotspot region was found. Changes in DNA methylation level in the vicinity of the breakpoint in the child's DNA when compared to parents' and control DNA were observed, with a shift from 15.1 to 70.8% spanning the breakpoint region. In the main classes of evaluated repeats, higher mean GC contents in the 1p36 breakpoint region (47.06%), 22q11.2 (48.47%), and 18q21.1 (44.21%) were found, compared to the rest of the genome (40.78%). The 9p22 region showed a lower GC content (39.42%) compared to the rest of the genome. Both dysregulation of DNA methylation and high GC content were found to be specific for the 1p36 breakpoint hotspot region suggesting that methylation abnormalities could contribute to aberrations at 1p36.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500851","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
Experimental evaluation of effectiveness of genomic selection for resistance to northern corn leaf blight in maize. 玉米抗北方玉米叶枯病基因组选择有效性的实验评估。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-10-24 DOI: 10.1007/s13353-024-00911-x
H C Lohithaswa, D C Balasundara, M G Mallikarjuna, M S Sowmya, N Mallikarjuna, R S Kulkarni, Anand S Pandravada, Bhupendra S Bhatia
{"title":"Experimental evaluation of effectiveness of genomic selection for resistance to northern corn leaf blight in maize.","authors":"H C Lohithaswa, D C Balasundara, M G Mallikarjuna, M S Sowmya, N Mallikarjuna, R S Kulkarni, Anand S Pandravada, Bhupendra S Bhatia","doi":"10.1007/s13353-024-00911-x","DOIUrl":"https://doi.org/10.1007/s13353-024-00911-x","url":null,"abstract":"<p><p>Northern corn leaf blight (NLB) caused by Setosphaeria turcica (Luttrell) Leonard & Suggs is a severe foliar disease in maize. Resistance to NLB is complexly inherited and controlled by several quantitative trait loci (QTL) distributed across the genome. Phenotype and DNA marker-based selection for resistance to NLB is expected to be effective. Hence, an investigation was carried out to predict the genetic value of selection candidates for resistance to NLB and compare the accuracies of genomic prediction in two F<sub>2:3</sub> populations of two crosses (CM212 × MAI172; CM202 × SKV50) derived from contrasting parents. Linkage analysis using 297 polymorphic SNPs in population-1 and 290 polymorphic SNPs in population-2 revealed ten linkage groups spanning 3623.88 cM and 4261.92 cM with an average distance of 12.40 cM and 14.9 cM in population-1 and population-2, respectively. Location-wise and pooled data across locations identified common QTLs on linkage groups 1 and 6 in population-1 and 3 and 8 in population-2. The prediction accuracy of the QTL mapping (9.92 and 9.10 for population-1 and population-2, respectively) was based on only a few markers, which explained higher percent phenotypic variation. The prediction accuracies of the genomic estimated breeding values in the present investigation were relatively low in population-1 (0.24 to 0.26) and population-2 (0.29-0.32) compared to the expected accuracies. This could be due to fewer polymorphic markers and a small training/population size. Though the GS prediction accuracies were relatively low, they were significantly higher than QTL mapping, which promises better genetic gain per cycle. The resistant progenies from both populations were advanced to derive inbred lines and crossed with four different testers in line × tester mating design to test for their combining ability and effectiveness of genomic selection. High overall general combining ability was exhibited by 21 inbred lines. Among F<sub>1</sub>s, 48% were assigned high overall specific combining ability status. Out of the 136 single crosses, seven recorded significant positive standard heterosis over the best check for grain yield. Twenty-five inbreds with high GEBVs were crossed with four testers to obtain 100 F<sub>1</sub>s and evaluated for their response to NLB. The majority of hybrids displayed moderate to resistant reaction to NLB either in combination with susceptible or resistant testers indicating the effectiveness of selection based on high GEBVs.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500835","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
Correction to: Unraveling the genetic basis of MODY: insights from next‑generation sequencing. 更正:揭示 MODY 的遗传基础:新一代测序的启示。
IF 2 3区 生物学
Journal of Applied Genetics Pub Date : 2024-10-18 DOI: 10.1007/s13353-024-00914-8
Metin Eser, Gulam Hekimoglu, Fatma Dursun
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