Frontiers in Genetics最新文献

{"title":"Genome-wide association study of cocoon-producing traits in four Henan silkworm strains revealed new candidate genes.","authors":"Xingya Song, Yingxian Lyu, Yuqiao Zhang, Wenjia Ding, Yongzhen Huang, Shang Yang","doi":"10.3389/fgene.2025.1580806","DOIUrl":"10.3389/fgene.2025.1580806","url":null,"abstract":"<p><strong>Background: </strong>The silkworm (<i>Bombyx mori</i>), has been farmed in China for over 5,000 years, and holds significant economic value. Recent genomic advances have deepened our understanding of silk production mechanisms, enabling the development of improved silkworm breeds. Further research is needed to identify effective molecular markers linked to silk production traits, as this will enhance genetic improvement efforts.</p><p><strong>Results: </strong>In the genome-wide association analysis study, we identified 40 significant single nucleotide polymorphisms (SNPs) and 28 candidate genes which were related to cocoon shell weight, cocoon width and whole cocoon weight in four silkworm strains in Henan. Through linkage imbalance block analysis, we found that the <i>KWMTBOMO02490</i> (ATPase inhibitor-like protein) and <i>KWMTBOMO12678</i> (OTU domain-containing protein 7B) were strongly selected. By using online databases, we found that the <i>KWMTBOMO02490</i> gene was highly expressed in the posterior silk glands and may play an important role in the process of silk production.</p><p><strong>Conclusion: </strong>The candidate genes in this study may affect the production and health traits of silkworms, and may provide an important reference for silkworm breeding.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1580806"},"PeriodicalIF":2.8,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484134","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, spermatozoa, hormonal, and genetic evaluation of rare mosaic klinefelter syndrome patients in southern China.","authors":"Derong Li, Yuqing Lai, Yujuan Liao, Jinjie Pan, Yudi Luo, Yunning Liang, Bowen Luo, Lingling Zhu, Guosheng Deng, Xiang Li, Keng Feng, Feifei Lei, Liuping Lan","doi":"10.3389/fgene.2025.1573292","DOIUrl":"10.3389/fgene.2025.1573292","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Klinefelter syndrome (KS) is the most common genetic cause of male infertility in humans. Mosaic KS is a subtype of KS. Due to its low prevalence, the lack of typical clinical signs, and the limited professional awareness of the syndrome, many cases of mosaic KS remain undiagnosed.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Objective: &lt;/strong&gt;To investigate the prevalence of rare mosaic KS, karyotype characteristics, reproductive hormone levels, and sperm quality in southern China, and to enrich our knowledge of patients with mosaic KS.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;The chromosome results of 8,110 cases of infertile male patients attending the Reproductive Center of Yulin Maternal and Child Health Hospital from January 2018 to July 2024 were retrospectively analyzed. Semen, sex hormone tests, and Y chromosome microdeletions were analyzed in fourteen selected patients with a diagnosis of mosaic KS.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Among the 8,110 male infertility patients, a total of 0.703% (57/8,110) were diagnosed with KS. Of these, 0.530% (43/8,110) had the typical non-mosaic chromosomal karyotype of 47, XXY, while 0.172% (14/8,110) demonstrated mosaicism. Non-mosaic KS accounted for 75.44% (43/57), whereas mosaic KS accounted for 24.56% (14/57). Among the fourteen patients diagnosed with mosaic KS, the predominant chromosomal karyotype was 47,XXY/46,XY, observed in eleven patients, accounting for 78.57% of the cases. Additionally, one patient exhibited a chromosomal karyotype of 47,XXY [29]/46,XX [78]. Another patient had 47,XXY [92]/48,XXXY [3]/46,XY [5], and a third patient presented with 47,XXY [87]/46,XX [3]/46,XY [2]. The semen analysis of individuals with mosaic KS revealed two cases of azoospermia, one case of cryptozoospermia, one case of severe oligospermia, one case of oligospermia, and ten cases of normal sperm. The results of the sex hormone analysis revealed abnormal increases in serum follicle-stimulating hormone (FSH) levels in four patients diagnosed with mosaic KS. Additionally, two patients with mosaic KS exhibited higher luteinizing hormone (LH) and testosterone (TT) levels compared to the normal range, while four patients had lower estradiol (E2) levels than the normal range. Among the fourteen patients with mosaic KS, four couples underwent assisted reproductive technology at our hospital for fertility assistance. Of these four couples, two successfully gave birth to a healthy child.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The prevalence of mosaic KS among male infertility patients in southern China is 0.172% (14/8,110), with the predominant chromosomal karyotype being 47,XXY/46,XY, accounting for 78.57% (11/14) of the cases. Patients with mosaic KS may present with various sperm conditions, including azoospermia, cryptozoospermia, severe oligozoospermia, oligozoospermia, and normal sperm. There is a notable correlation between sperm count and the number of abnormal cell karyotypes in these patients; specifically, a higher","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1573292"},"PeriodicalIF":2.8,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484135","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":"Bioinformatics analysis identifies ZBTB16 as a potential immune biomarker for lung cancer and pan-cancer.","authors":"Danfei Shi, Yunxiang Cai, Di Zhu, Xinmin Li, Yong Li","doi":"10.3389/fgene.2025.1541732","DOIUrl":"10.3389/fgene.2025.1541732","url":null,"abstract":"<p><strong>Objective: </strong>Lung cancer (LC) is a deadly cancer and a challenging public health problem worldwide. The aim of this study is to use bioinformatics to analyze the potential of ZBTB16 as an immune biomarker in lung cancer and various other cancers.</p><p><strong>Methods: </strong>Overlapping differentially expressed genes (DEGs) in LC were selected from GSE3268, GSE 1987, GSE31547 and GSE18842 gene expression data sets. We conducted a comprehensive bioinformatics analysis of these differentially expressed genes, aiming to explore their enrichment functions and pathways, relative expression levels, interaction networks, and weighted gene co expression network (WGCNA) module analysis. Then, the potential role of ZBTB16 in the occurrence and progression of lung cancer was verified, and immune invasion analysis, pan-cancer analysis and mRNA-miRNA link analysis were performed.</p><p><strong>Results: </strong>There were 16 genes with increased expression and 100 genes with decreased expression. Among them, KEGG analysis showed that these DEGs were significantly involved in complement and coagulation cascades, as well as related pathways such as proximal tubular bicarbonate recovery. Previous studies have shown that ZBTB16 plays an important role in various systemic tumors, but its function in lung cancer has not been revealed. WGCNA analysis shows that ZBTB16 is significant in lung cancer. Therefore, we will focus our attention on ZBTB16. Then, TCGA database, Human Protein Atlas database, and whole blood qPCR testing were used to verify the differential expression of ZBTB16 in lung cancer, and immune invasion analysis of ZBTB16 in lung cancer, pan cancer analysis of ZBTB16, and mRNA miRNA linkage analysis of ZBTB16 were performed.</p><p><strong>Conclusion: </strong>Three validation methods and pan cancer analysis all showed that the expression of ZBTB16 was reduced in lung cancer and various cancers, which may be a key gene for the occurrence and development of lung cancer and various cancers.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1541732"},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474970","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":"Improving the therapeutic efficacy of gene therapy for duchenne muscular dystrophy (DMD) by evaluating and managing inflammation.","authors":"Kadalraja Raghavan, Nobunao Ikewaki, Senthilkumar Preethy, Samuel J K Abraham","doi":"10.3389/fgene.2025.1569289","DOIUrl":"10.3389/fgene.2025.1569289","url":null,"abstract":"<p><p>Duchenne muscular dystrophy (DMD): is a rare, life-limiting genetic disorder for which no curative treatment currently exists. While various gene therapy approaches, some approved and others still under clinical investigation have been explored, they have not consistently produced the desired outcome and, in some cases, have been associated with serious adverse effects, including mortality. A critical factor we wish to highlight is the hostile inflammatory environment inherent to skeletal muscles' pathology in DMD, which may be further aggravated by gene therapy, either due to the viral vector used or the gene component itself. Therefore, a comparative and detailed evaluation of inflammatory biomarkers between control and treatment arms in such clinical trials is essential to determine whether therapeutic benefits are being compromised by inflammation. Based on the implications of such hostile environment on the therapeutic outcome, adding a safer and efficacious management strategy to mitigate the inflammation during gene therapies is considered indispensable. Therefore, we recommend further research on adjuvant anti-inflammatory approaches to ensure safety and improvement of the therapeutic outcome of gene therapies for DMD.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1569289"},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474983","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":"Exploring inbreeding depression in Brazilian Angus cattle population using pedigree and genomic data.","authors":"Henrique A Mulim, Gabriel S Campos, Fernando Flores Cardoso, Hinayah Rojas de Oliveira","doi":"10.3389/fgene.2025.1613820","DOIUrl":"10.3389/fgene.2025.1613820","url":null,"abstract":"<p><strong>Introduction: </strong>Inbreeding depression refers to the decline in performance caused by increased levels of inbreeding, which results from mating individuals with common ancestors. This study aimed to estimate inbreeding coefficients based on both pedigree and genomic information using six different metrics and evaluate, the inbreeding depression on different traits officially evaluated by the Brazilian Angus Association.</p><p><strong>Material and methods: </strong>A total of 13,777 genotyped animals, imputed to a density of 78,837 SNPs, and 530,327 animals in the pedigree file, extending up to 17 generations, were used in the analysis. The inbreeding metrics evaluated included: pedigree-based inbreeding (F_PED), genomic relationship matrix-based inbreeding (F_GRM), observed vs. expected homozygosity (F_HOM1), genotyped homozygosity (F_HOM2), correlation between uniting gametes (F_UNI), and runs of homozygosity (F_ROH). Traits related to growth, conformation, meat quality, reproduction, resistance to ectoparasites, and heat stress were analyzed.</p><p><strong>Results: </strong>The results revealed a range of inbreeding coefficients, with inbreeding estimated using ROHs showing the highest values (0.13). The impact of inbreeding on various traits was predominantly negative, with significant inbreeding depression observed for traits such as hair coat. Some traits, such as intramuscular fat and birth weight, had positive associations with inbreeding, indicating a complex trait-specific relationship. Shorter ROH segments (<2 Mb) generally had smaller or beneficial effects compared to longer ROH segments (>16 Mb).</p><p><strong>Discussion: </strong>These findings underscore the complexity of inbreeding depression and highlight the importance of considering both the extent and historical depth of inbreeding when evaluating its effects on various traits. Overall, this research provides valuable insights into the genetic basis of inbreeding depression in the Brazilian Angus population and demonstrates the usefulness of genomic data in understanding and mitigating the impacts of inbreeding in livestock populations.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1613820"},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474981","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":"Retraction: Comprehensive circular RNA expression profile of lung adenocarcinoma with bone metastasis: identification of potential biomarkers.","authors":"","doi":"10.3389/fgene.2025.1637633","DOIUrl":"https://doi.org/10.3389/fgene.2025.1637633","url":null,"abstract":"<p><p>[This retracts the article DOI: 10.3389/fgene.2022.961668.].</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1637633"},"PeriodicalIF":2.8,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474985","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":"Genome-wide identification and characterisation of Toll-like receptors in Chinese spiny frog (<i>Quasipaa spinosa</i>).","authors":"Zehong Li, Zihan Gao, Dexin Mo, Zifeng Zhu, Jingqi Zhang, Mujin Liu, Han Xiao, Meng Zhou, Teng Gao, Rishen Liang","doi":"10.3389/fgene.2025.1569669","DOIUrl":"10.3389/fgene.2025.1569669","url":null,"abstract":"<p><strong>Introduction: </strong>Toll-like receptors (<i>TLR</i>s) are pattern recognition receptors essential for immune defense against pathogens, activating the host's immune response by recognizing conserved pathogen structures. The Chinese spiny frog (<i>Quasipaa spinosa</i>), an amphibian native to southern China and northern Vietnam, has been severely impacted by recent infectious disease outbreaks caused by bacterial, viral, and parasitic infections, which threaten the sustainable development of the <i>Q. spinosa</i> farming industry. However, the roles of <i>Q. spinosa</i> <i>TLRs</i> (<i>QsTLRs</i>) in combating these exogenous pathogens have not yet been explored.</p><p><strong>Methods: </strong>In the study, using the whole genome data of <i>Q. spinosa</i>, bioinformatics tools were employed to identify and analyze the <i>TLR</i> gene family. The bacteria <i>Elizabethkingia miricola</i>, a common pathogen, which causes the cataract disease and can lead to serious death of the frog. Here, we selected the bacteria to conduct the challenge experiment in order to characterize the immune responses of the <i>TLR</i> genes of <i>Q. spinosa</i> against bacterial infection.</p><p><strong>Results: </strong>The analysis identified 17 members of the <i>TLR</i> gene family in <i>Q. spinosa</i>. Phylogenetic analysis revealed that <i>QsTLRs</i> can be classified into seven subfamilies: <i>TLR1</i>, <i>TLR3</i>, <i>TLR4</i>, <i>TLR5</i>, <i>TLR7</i>, <i>TLR11</i>, and <i>TLR13</i>. Conserved synteny analysis indicated that <i>Q. spinosa</i> is more closely related to <i>Rana temporaria</i> than to <i>Xenopus laevis</i>. Protein structure prediction and motif analysis demonstrated that all <i>QsTLRs</i> are relatively conserved in both structure and function. mRNA expression levels of <i>QsTLRs</i> in spleen tissues were measured following stimulation with <i>Elizabethkingia miricola</i>, which revealing that 15 <i>QsTLR</i> genes exhibited up-regulation at various time points post-stimulation.</p><p><strong>Discussion: </strong>These findings provide a comprehensive understanding of the <i>QsTLR</i> gene family and lay the groundwork for future studies exploring the functional evolution of the amphibian <i>TLR</i> gene family.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1569669"},"PeriodicalIF":2.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474982","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":"Polymorphous corneal dystrophy subtype 3 and keratoconus aggravation after corneal refractive surgery in a three-generation family carrying both <i>ZEB1</i> and <i>ZNF469</i> pathogenic variant.","authors":"Qinghong Lin, Xuejun Wang, Xiaoliao Peng, Xiaosong Han, Xiaoyu Zhang, Ling Sun, Yan Wang, Shengtao Liu, Xingtao Zhou","doi":"10.3389/fgene.2025.1603019","DOIUrl":"10.3389/fgene.2025.1603019","url":null,"abstract":"<p><strong>Background: </strong>This study reports a three-generation Chinese family with polymorphous corneal dystrophy subtype 3 (PPCD3) and keratoconus (KC) aggravation induced by corneal refractive surgery, specifically small incision lenticule extraction (SMILE), in the context of genetic variations.</p><p><strong>Methods: </strong>The history of illnesses and blood samples of all family members were collected. One hundred healthy individuals served as normal controls. We conducted whole exome sequencing on genomic DNA and sanger sequencing to verify the variants between all controls and family members.</p><p><strong>Results: </strong>Three family members were previously diagnosed with subclinical keratoconus (III1 and III2 preoperatively, and II2). Both the proband (III1) and her younger brother (III2) underwent SMILE to correct refractive errors. One year later, visual acuity of III1 decreased significantly with KC aggravation and corneal opacification. The KC of III2 progressed significantly 6 months after surgery. Both were subsequently diagnosed with PPCD3. We detected both Zinc finger E-box-binding homeobox 1 (ZEB1) gene and zinc finger protein 469 (ZNF469) gene pathogenic variant in the proband and another two patients in this family, including a heterozygous missense variation c.13C>G (p.P5A, rs753301298) in the <i>ZEB1</i> gene, and a heterozygous non-frameshift variant c. 3093_3104del (p.D1035_K1038del) in the <i>ZNF469</i> gene. The variants including c.13C>G in <i>ZEB1</i> and c.3093_3104del in <i>ZNF469</i> were speculated to be pathogenic or a variant of uncertain significance by online prediction software.</p><p><strong>Conclusion: </strong>This study demonstrated the importance of a thorough ocular examination, especially the cornea, and a gene screening before SMILE.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1603019"},"PeriodicalIF":2.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474984","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":"Unveiling pathogenesis of pelvic organ prolapse through transcriptomic and bioinformatic analyses in uterosacral ligament tissues of postmenopausal women.","authors":"BingJie Rui, GuangHai Rui, YanFeng Yang","doi":"10.3389/fgene.2025.1588278","DOIUrl":"10.3389/fgene.2025.1588278","url":null,"abstract":"<p><strong>Background: </strong>Pelvic organ prolapse (POP) is a common gynecological disorder arising from an imbalance in the synthesis and degradation of pelvic supportive tissues. Alterations in key molecules and genetic mutations affecting extracellular matrix (ECM) remodeling have been implicated in its development. This study aimed to profile coding and noncoding RNAs (ncRNAs) in uterosacral ligament tissues of postmenopausal women to elucidate POP's molecular mechanisms.</p><p><strong>Methods: </strong>We enrolled five POP patients and three normal controls. Uterosacral ligament tissue samples were collected and analyzed using high-throughput transcriptome sequencing to profile messenger RNAs (mRNAs), micro RNAs (miRNAs), circular RNAs (circRNAs), and long noncoding RNAs (lncRNAs). Differential expression was determined using the criteria of |log₂ (fold change)|>1 and an adjusted p-value (padj) < 0.05. Bioinformatics analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, were performed to assess the functional roles of the differentially expressed genes. Competing endogenous RNA (ceRNA) networks were constructed to explore interactions among lncRNAs, miRNAs, and mRNAs. Real-time quantitative polymerase chain reaction (qPCR) validated selected targets.</p><p><strong>Results: </strong>We identified 60 mRNAs, 146 miRNAs, 29 lncRNAs, and 176 circRNAs with significant differential expression in POP tissues. Functional enrichment analyses revealed that these transcripts are primarily involved in cellular senescence, inflammation, ECM regulation, and cytoskeletal organization. Several signaling pathways were enriched, including those mediated by mitogen-activated protein kinase (MAPK), Extracellular Signal-Regulated Kinase 1/2(Erk1/2), Ras-related proteins (Rap1), Forkhead Box O (FOXO), and other oncogene homologs. Analysis of ceRNA networks uncovered interactions among lncRNAs, miRNAs, and mRNAs. Notably, lncRNA FLJ20021 was significantly downregulated in POP tissues and correlated with altered expression of collagenⅢ (COL III), CollagenⅠ (COL I), and Matrix Metalloproteinase-9 (MMP9).</p><p><strong>Conclusion: </strong>Our findings demonstrate significant alterations in both coding and ncRNAs expression in POP tissues, suggesting that dysregulation of multiple pathways contributes to its pathogenesis. In particular, ECM remodeling and reduced FLJ20021 expression may play key roles in tissue degeneration, offering potential targets for future therapeutic intervention.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1588278"},"PeriodicalIF":2.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474986","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-based genetic parameters and genome-wide association studies for productive and reproductive traits in Beef-on-Dairy crossbreds.","authors":"R H Ahmed, C Schmidtmann, J Mugambe, G Thaller","doi":"10.3389/fgene.2025.1530310","DOIUrl":"10.3389/fgene.2025.1530310","url":null,"abstract":"<p><strong>Background: </strong>Beef on Dairy (BoD) calves are born from the crossing of dairy cows with beef breeds. The genetic architecture of these calves differs significantly from the parent breeds due to heterosis and other dominance effects. Identification of the genomic regions associated with traits in BoD calves and the inheritance pattern of these regions can assist in the selection process. We conducted a genome-wide association study (GWAS) for Belgian blue and Angus crossbreds born from a Holstein dam, incorporating additive and dominance effects to identify genomic regions associated with birth weight, calving difficulty, and gestation length. Additionally, a haplotype-based GWAS was performed to compare the effectiveness of these two different methodologies and to identify the parental origin of the haplotypes based on similar allelic patterns between crossbred and parental breeds.</p><p><strong>Results: </strong>The heritability estimates for birth weight, calving difficulty, and gestation length were 0.29 (±0.03), 0.36 (±0.04), and 0.09 (±0.03), respectively. Using SNP-based GWAS for birth weight, a genomic region containing the <i>GABRG1</i> gene on BTA 6 was identified. In addition, the haplotype-based analysis identified three more genes (<i>CSER1</i>, <i>FAM13A</i>, and <i>LCORL</i>) associated with birth weight. Incorporating dominance effects into the GWAS model led to the identification of an additional gene, <i>SPP1</i>, related to birth weight. For calving difficulty, SNP-based GWAS in Angus crossbreds revealed a genomic region containing the <i>KCNIP4</i> gene. Most of the haplotypes associated with these traits originated from the three parental breeds, but six unique haplotypes for Angus and Belgian blue were identified.</p><p><strong>Conclusion: </strong>Based on this study, Haplotype GWAS was found to have superior statistical power in the identification of associated genomic regions in BoD crossbreds. However, for traits such as calving difficulty, SNP-based GWAS proved to be more effective. Both approaches are essential for the identification of genomic regions associated with traits of interest in BoD calves.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1530310"},"PeriodicalIF":2.8,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12177717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332979","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}