Genes最新文献

{"title":"The Potential of Transgenic Hybrid Aspen Plants with a Recombinant <i>Lac</i> Gene from the Fungus <i>Trametes hirsuta</i> to Degrade Trichlorophenol.","authors":"Elena O Vidyagina, Natalia M Subbotina, Eugenia N Belova, Yulia A Kovalitskaya, Vyacheslav A Evdokimov, Vladimir A Belyi, Alexey P Kochetov, Alexey K Surin, Konstantin V Krutovsky, Konstantin A Shestibratov","doi":"10.3390/genes16030298","DOIUrl":"10.3390/genes16030298","url":null,"abstract":"<p><p><b>Objective:</b> Laccases are known to be able to degrade phenolic compounds to simpler components. The main objective of our study was to analyze this property in transgenic aspen plants carrying the laccase gene <i>Lac</i> from <i>Trametes hirsuta</i> which can be potentially used in soil phytoremediation. <b>Methods:</b> We created transgenic aspen plants carrying the laccase gene <i>Lac</i> from <i>Trametes hirsute</i> using the agrobacterial transformation of stem explants with the pBI-Lac vector containing the <i>Lac</i> gene from the white rot fungus <i>T. hirsuta</i> 072 (NCBI GenBank accession number KP027478). Transgenic plants were micropropagated and cultivated in vitro in lines. The degradation of 2,4,6-trichlorophenol (2,4,6-TCP) by plant roots was analyzed by mass-spectrometry with electron ionization using a gas chromatograph. <b>Results:</b> Although plants have their own laccases, those of fungal origin are more effective. All transgenic plants that expressed the recombinant gene degraded 2,4,6-TCP more effectively than non-transformed plants in the control (the degradation efficiency ranged 92 to 98% versus 82% in non-transformed control). Line 47Lac8 demonstrated a 16% higher efficiency than the non-transformed plants in the control. There was also an inverse relationship between the viability of a transgenic line and its level of expression of the recombinant gene. Thus, line 47Lac4 was not viable under native conditions, probably due to lignin synthesis disruptions during the initiation of secondary tissues. This is confirmed by changes in the expression of native genes of lignin biosynthesis. The rest of the transgenic lines did not differ significantly from control in wood growth and biochemistry. The transgenic plant roots were shown to preserve the ability to express the <i>Lac</i> gene ex vitro. <b>Conclusions:</b> Three transgenic lines (47Lac5, 47Lac8, and 47Lac23) with the <i>Lac</i> gene can be recommended for use in soil phytoremediation.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728742","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":"Functional Genomics of Legumes in Bulgaria-Advances and Future Perspectives.","authors":"Miglena Revalska, Mariana Radkova, Miroslava Zhiponova, Valya Vassileva, Anelia Iantcheva","doi":"10.3390/genes16030296","DOIUrl":"10.3390/genes16030296","url":null,"abstract":"<p><p>Members of the Leguminosae family are important crops that provide food, animal feed and vegetable oils. Legumes make a substantial contribution to sustainable agriculture and the nitrogen cycle through their unique ability to fix atmospheric nitrogen in agricultural ecosystems. Over the past three decades, <i>Medicago truncatula</i> and <i>Lotus japonicus</i> have emerged as model plants for genomic and physiological research in legumes. The advancement of innovative molecular and genetic tools, particularly insertional mutagenesis using the retrotransposon <i>Tnt1</i>, has facilitated the development of extensive mutant collections and enabled precise gene tagging in plants for the identification of key symbiotic and developmental genes. Building on these resources, twelve years ago, our research team initiated the establishment of a platform for functional genomic studies of legumes in Bulgaria. In the framework of this initiative, we conducted systematic sequencing of selected mutant lines and identified genes involved in plant growth and development for detailed functional characterization. This review summarizes our findings on the functions of selected genes involved in the growth and development of the model species, discusses the molecular mechanisms underlying important developmental processes and examines the potential for the translation of this fundamental knowledge to improve commercially important legume crops in Bulgaria and globally.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729681","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":"miR395e from <i>Manihot esculenta</i> Decreases Expression of PD-L1 in Renal Cancer: A Preliminary Study.","authors":"Joanna Bogusławska, Aizhan Rakhmetullina, Małgorzata Grzanka, Alex Białas, Beata Rybicka, Joanna Życka-Krzesińska, Tomasz Molcan, Piotr Zielenkiewicz, Leszek Pączek, Agnieszka Piekiełko-Witkowska","doi":"10.3390/genes16030293","DOIUrl":"10.3390/genes16030293","url":null,"abstract":"<p><p><b>Background/Objectives</b>: microRNAs are small non-coding RNAs that regulate gene expression by inducing mRNA degradation or inhibiting translation. A growing body of evidence suggests that miRNAs may be utilized as anti-cancer therapeutics by targeting expression of key genes involved in cancerous transformation and progression. Renal cell cancer (RCC) is the most common kidney malignancy. The most efficient RCC treatments involve blockers of immune checkpoints, including antibodies targeting PD-L1 (Programmed Death Ligand 1). Interestingly, recent studies revealed the cross-kingdom horizontal transfer of plant miRNAs into mammalian cells, contributing to the modulation of gene expression by food ingestion. Here, we hypothesized that PD-L1 expression may be modulated by miRNAs originating from edible plants. <b>Methods</b>: To verify this hypothesis, we performed bioinformatic analysis to identify mes-miR395e from <i>Manihot esculenta</i> (cassava) as a promising candidate miRNA that could target PD-L1. To verify PD-L1 regulation mediated by the predicted plant miRNA, synthetic mes-miR395 mimics were transfected into cell lines derived from RCC tumors, followed by evaluation of PD-L1 expression using qPCR and Western blot. <b>Results</b>: Transfection of mes-miR395e mimics into RCC-derived cell lines confirmed that this miRNA decreases expression of PD-L1 in RCC cells at both mRNA and protein levels. <b>Conclusions</b>: This preliminary study shows the promise of plant miRNA as potential adjuvants supporting RCC treatment.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729695","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":"Synergistic Regulation at Physiological, Transcriptional, and Metabolic Levels in <i>Dendrobium huoshanense</i> Plants Under Combined Drought and High-Temperature Stress.","authors":"Xingen Zhang, Guohui Li, Peipei Wei, Binbin Du, Shifan Liu, Jun Dai","doi":"10.3390/genes16030287","DOIUrl":"10.3390/genes16030287","url":null,"abstract":"<p><p><b>Background:</b> With global warming and climate change, the occurrence of abiotic stresses has become increasingly prevalent. Drought often occurs with high temperatures, especially in arid and semi-arid regions. However, the molecular mechanisms of plants responding to combined drought and high-temperature stress remains unclear. <b>Results:</b> Through integrative physiological, transcriptomic, and metabolomic analyses, we systematically investigated the adaptive mechanisms of <i>Dendrobium huoshanense</i> under combined drought and high-temperature stress. Our findings revealed that combined drought and high-temperature stress led to significant reductions in photosynthetic efficiency and increased oxidative damage in <i>Dendrobium huoshanense</i>, with high-temperature stress being the primary contributor to these adverse effects. The joint analysis shows that three core pathways-signal transduction, lipid metabolism, and secondary metabolite biosynthesis-were identified as critical for antioxidant defense and stress adaptation. <b>Conclusions:</b> These findings not only deepen our understanding of plant responses to combined drought and high-temperature stress but also provide new directions for future research on the cultivation and resistance improvement of <i>Dendrobium huoshanense</i>.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729739","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":"The Origin of Amerindians: A Case Study of Secluded Colombian Chimila, Wiwa, and Wayúu Ethnic Groups and Their Trans-Pacific Gene Flow.","authors":"Antonio Arnaiz-Villena, Tomás Lledo, Carlos Silvera-Redondo, Ignacio Juarez, Christian Vaquero-Yuste, José Manuel Martin-Villa, Fabio Suarez-Trujillo","doi":"10.3390/genes16030286","DOIUrl":"10.3390/genes16030286","url":null,"abstract":"<p><strong>Background/objectives: </strong>The Human Leukocyte Antigen (HLA) system is composed of a set of genes that codify glycoproteins presenting antigenic proteins to clonotypic T cell receptors in order to start the immune response. Class I and Class II classical loci exhibit high allelic diversity; some of them (or their specific combinations that form haplotypes) are quasi-specific or highly frequent in certain populations and thus are useful for population genetic studies. In this study, an HLA genetic comparison of Chimila, Wayúu, Wiwa, and Barranquilla Colombian nonrelated healthy individuals was carried out together with other populations from all over the world to trace their genetic origin, obtain a virtual transplantation list, and inform future epidemiology studies.</p><p><strong>Methods: </strong>HLA-A, -B, -DRB1, and -DQB1 alleles were sequenced using the PCR-SSOP-Luminex method to analyze the HLA genetic profile of each individual. The data obtained were subsequently processed with standard software to obtain HLA alleles, haplotype frequencies, and genetic distances compared with data from global populations to generate relatedness dendrograms and carry out a correspondence analysis.</p><p><strong>Results: </strong>The results obtained place the Chimila, Wayúu, and Wiwa populations phylogenetically close to the other North and South Amerindian populations included in this study. Amerindians are genetically separated from the rest of the world's populations. Chimila, Wayúu, and Wiwa present unique extended HLA haplotypes and specific alleles, such as HLA-B*48 or HLA-A*24:01, shared with Oceanian populations.</p><p><strong>Conclusions: </strong>These genetic results and anthropological data support prehistorical trans-Pacific (bidirectional) contacts that contributed to the settlement of America and also suggest that the effects of ancient European gene flow cannot be discarded.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728492","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":"Association of +67 G/A and -426 T/C Polymorphism in Eotaxin (CCL11) Gene with Psoriasis Phenotypes.","authors":"Vladimír Vašků, Adam Fiala, Anna Vašků","doi":"10.3390/genes16030288","DOIUrl":"10.3390/genes16030288","url":null,"abstract":"<p><p><b>Background/Objectives</b>: Several gene targets were identified for psoriasis. Some are currently being explored as potential therapeutic targets, including CCL11. Our task was to prove a possible association of single-nucleotide polymorphisms +67 G/A and -426 T/C in the eotaxin gene (CCL11, 17q 21.3) with the development and clinical aspects of psoriasis as an immune-based dermatological disease and evaluate its relationship to potential comorbidities. <b>Material and Methods</b>: In total, 460 patients with psoriasis were included in the case-control and genotype-phenotype study together with 167 control persons of similar age and sex distributions without a personal and/or family history of chronic disease of the skin. Two eotaxin gene polymorphisms were detected from isolated DNA via standard PCR, restriction analysis methods, and horizontal electrophoresis. <b>Results</b>: No significant case-control differences in the frequency of the CCL11 genotype in both polymorphisms were observed. In polymorphism +67 G/A, a significant increase in the AA genotype in patients with psoriasis guttata compared to plaque psoriasis was found (<i>p</i> = 0.006). A significant association of the A allele in psoriatic patients with a personal history of allergy was found (<i>p</i> = 0.02). The A alle was also significantly associated with a family history of psoriasis (<i>p</i> = 0.00008). In men, a higher risk of a delayed start of psoriasis (later than 40 years) associated with the T allele of -426 T/C polymorphism (<i>p</i> = 0.0007) was found. When double genotypes of both polymorphisms were evaluated, we observed significant differences in double genotype distribution between men with and without a family history of allergy (Pdg = 0.0005) and between those with and without affected siblings (Pdg = 0.03). In women with psoriasis, a higher risk of the TT genotype of -426 T/C polymorphism in patients with a personal history of diabetes (<i>p</i> = 0.001) as well as in patients with both a personal history of cardiovascular disease and diabetes (<i>p</i> = 0.00005) was proved. When double genotypes of both polymorphisms were evaluated, the significance of double genotype difference between those with and without personal history of diabetes was very high (Pdg = 0.0002). Similarly, the significance of the double genotype difference between those with and without personal history of cardiovascular diseases and diabetes was very high (Pdg = 0.000001). <b>Conclusions</b>: CCL11 is considered one of the basic chemokines responsible for the origin and development of immune-based reactions. Based on our results, we suggest that the +67 G/A CCL11 polymorphism should be considered as a gene modulator of psoriasis in specific subgroups of patients.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729646","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":"Inherited Dyslipidemic Splenomegaly: A Genetic Macrophage Storage Disorder Caused by Disruptive Apolipoprotein E (<i>APOE</i>) Variants.","authors":"Elise A Ferreira, Machteld M Oud, Saskia N van der Crabben, Miranda Versloot, Susan M I Goorden, Clara D M van Karnebeek, Jeffrey Kroon, Mirjam Langeveld","doi":"10.3390/genes16030289","DOIUrl":"10.3390/genes16030289","url":null,"abstract":"<p><strong>Background: </strong>Persistent splenomegaly, often an incidental finding, can originate from a number of inherited metabolic disorders (IMDs). Variants of <i>APOE</i> are primarily known as risk factors in terms of cardiovascular disease; however, severe dysfunction of APOE can result in a disease phenotype with considerable overlap with lysosomal storage disorders (LSDs), including splenomegaly and gross elevation of N-palmitoyl-O-phosphocholine-serine (PPCS).</p><p><strong>Methods: </strong>A case study (deep phenotyping, genetic and FACS analysis) and literature study was conducted.</p><p><strong>Results: </strong>The index patient, with a family history of early-onset cardiovascular disease, presented with splenic infarctions in a grossly enlarged spleen. The identified genetic cause was homozygosity for two <i>APOE</i> variants (c.604C>T, p.(Arg202Cys) and c.512G>A, p.(Gly171Asp); ε1/ε1), resulting in a macrophage storage phenotype resembling an LSD that was also present in the brother of the index patient. A FACS analysis of the circulating monocytes showed increased lipid content and the expression of activation markers (CD11b, CCR2, CD36). This activated state enhances lipoprotein intake, which eventually converts these monocytes/macrophages into foam cells, accumulating in tissues (e.g., spleen and vascular wall). A literature search identified seven individuals with splenomegaly caused by <i>APOE</i> variants (deletion of leucine at position 167). The combined data from all patients identified male gender, splenectomy and obesity as potential modifiers determining the severity of the phenotype (i.e., degree of triglyceride increase in plasma and/or spleen size). Symptoms are (partially) reversible by lipid-lowering medication and energy restricted diets and splenectomy is contra-indicated.</p><p><strong>Conclusions: </strong>Inherited dyslipidemic splenomegaly caused by disruptive <i>APOE</i> variants should be included in the differential diagnoses of unexplained splenomegaly with abnormal lipid profiles. A plasma lipid profile consistent with dysbetalipoproteinemia is a diagnostic biomarker for this IMD.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729702","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":"In Vitro Gene Expression Profiling of Quantum Molecular Resonance Effects on Human Endometrium Models: A Preliminary Study.","authors":"Angela Grassi, Maria Santa Rocca, Marco Noventa, Gianantonio Pozzato, Alessandro Pozzato, Marco Scioscia, Alessandra Andrisani, Giovanni Pontrelli, Carlo Foresta, Luca De Toni","doi":"10.3390/genes16030290","DOIUrl":"10.3390/genes16030290","url":null,"abstract":"<p><strong>Objectives: </strong>The identification of methods to improve the endometrial receptivity (ER) is increasingly of interest. The effect of the electromagnetic field associated with Quantum Molecular Resonance (QMR) on ER was investigated here.</p><p><strong>Methods: </strong>Ishikawa cells were used to evaluate the effects of QMR both on the expression of a group of genes involved in ER, i.e., <i>HOXA10</i>, <i>HOXA11</i>, <i>LIF</i>, <i>ITGB3</i>, and <i>ITGAV</i>, and on cell toxicity. Endometrial samples were obtained from six patients during routine diagnostic procedures, four of which were subsequently used to assess the transcriptional response to QMR through microarray.</p><p><strong>Results: </strong>Compared to unexposed controls, a single exposure of Ishikawa cells to QMR for 20 min was associated with a significant and power-dependent up-regulation of all the selected ER-related genes up to 8 power units (PU). Repeated exposure to QMR, up to three consecutive days, showed a significant up-regulation of all the selected genes at power values of 4 PU, from day two onwards. Negligible cytotoxicity was observed. Gene set enrichment analysis, on microarray data of endometrial biopsies stimulated for three consecutive days at 4 PU, showed a significant enrichment of specific gene sets, related to the proteasome system, the cell adhesion, the glucocorticoid receptor, and cell cycle pathways.</p><p><strong>Conclusions: </strong>Our results suggest a possible favorable impact of QMR on ER.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729679","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":"Targeting Optimal Bone Regions: Correlations Between Bone Density and DNA Quality in Small Skeletal Elements.","authors":"Živa Miriam Geršak, Vladka Salapura, Eva Podovšovnik, Irena Zupanič-Pajnič","doi":"10.3390/genes16030291","DOIUrl":"10.3390/genes16030291","url":null,"abstract":"<p><p><b>Background</b>: Identifying the optimal bone regions for DNA analysis is critical, as DNA preservation and quality vary significantly across bone types and structures and is defined as intra-bone variability. This study aimed to evaluate the correlation between computed tomography (CT)-measured bone density and DNA preservation in small skeletal elements to identify optimal regions for DNA analysis. <b>Methods:</b> 137 bones from six skeletal elements excavated from a single burial site were analysed using Dual-Source CT (DSCT) to map compact and cancellous regions. DNA was extracted using a demineralisation method and quantified via real-time PCR to assess DNA quantity and degradation. <b>Results:</b> Among 461 bone regions analysed (137 bones; patellae, calcaneus, talus, the navicular bones, the cuboid bone, and the medial cuneiform bone), a significant difference in DNA quantity was observed only in the calcaneus, where the sulcus contained more DNA than the body. No significant differences in the degradation index were detected among bone segments or skeletal elements. Correlations between CT-measured bone density and DNA quantity or degradation index were region-specific. Higher bone density correlated positively with DNA quantity in compact regions of the calcaneus and talus. Regarding degradation, a positive correlation (higher bone density → higher degradation) was observed in the patella's anterior surface, while a negative correlation (higher bone density → lower degradation) was found in the talus's sulcus, the opposite side of the talar sulcus, the posterior calcaneal articular facet, and the cuboid's tuberosity. No significant correlations were found in other bone segments. <b>Conclusions:</b> Our study identified small skeletal elements, particularly the patella and the navicular bone, as promising sources for DNA analysis. While bone density correlated with DNA preservation in some cases, the relationship was inconsistent. Our findings support the use of small bones in forensic and archaeological research and warrant further investigation.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729741","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":"Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses.","authors":"Yaru Wang, Chi Tang, Pengfei Xue, Na Yang, Xiaoyuan Sun, Khizat Serik, Tolegen Assanbayer, Malika Shamekova, Zhassulan Kozhanov, Zagipa Sapakhova, Jurakulov Kobil Khurramovich, Xiaoling Zhou, Iskhan Kairat, Gemingguli Muhatai","doi":"10.3390/genes16030294","DOIUrl":"10.3390/genes16030294","url":null,"abstract":"<p><p><b>Background/Objectives:</b> The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. <b>Materials and Methods:</b> A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite markers. Genetic diversity parameters (e.g., allele number, heterozygosity, F-statistics) were calculated using GeneAIEX (v.6.503) and Fstat software (v.2.9.4). Parentage analysis was conducted using Cervus software. Bayesian clustering analysis was performed using STRUCTURE software (v.2.3.4), and a phylogenetic tree was constructed based on Nei's genetic distance to reveal the population genetic structure. <b>Results:</b> A total of 191 alleles were detected, with an average allele number of 11.969, observed heterozygosity of 0.481, and expected heterozygosity of 0.787. Parentage testing showed a cumulative exclusion probability (CEP) of 0.9652999 when one parent's genotype was known and 0.9996999 when both parents' genotypes were known, achieving an accuracy of 99%. Genetic differentiation analysis revealed moderate genetic divergence among populations (FST = 0.128) and moderate inbreeding levels (FIS = 0.396). Bayesian clustering analysis (K = 4) indicated that the Yanqi horse population could be divided into four genetic clusters, reflecting the impact of geographical isolation on genetic structure. <b>Conclusions:</b> The Yanqi horse conservation population exhibits moderate genetic diversity, high accuracy in parentage identification, and moderate genetic differentiation and inbreeding. The findings provide a scientific basis for the conservation and sustainable utilization of Yanqi horse genetic resources. Future efforts should focus on strengthening conservation measures, optimizing breeding strategies, and further investigating the genetic background using genomic technologies to ensure the sustainable development of the Yanqi horse population.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729673","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}