Genomics最新文献

{"title":"Association between salivary microbiota and tacrolimus pharmacokinetic variability in kidney transplant","authors":"Xuyu Xiang ,&nbsp;Yi Zhu ,&nbsp;Tianyin Wang ,&nbsp;Peng Ding ,&nbsp;Ke Cheng ,&nbsp;Yingzi Ming","doi":"10.1016/j.ygeno.2024.110952","DOIUrl":"10.1016/j.ygeno.2024.110952","url":null,"abstract":"<div><div>Kidney transplantation (KT) serves as a highly effective treatment for end-stage renal disease (ESRD). Nonetheless, the administration of tacrolimus, a commonly used immunosuppressant in KT, faces challenges due to the lack of dependable biomarkers for its efficacy and the considerable variability in tacrolimus pharmacokinetics (TacIPV). In this study, 183 saliva samples from 48 KT recipients under tacrolimus therapy, alongside 9 healthy control samples, were subjected to 16S rRNA sequencing. The analysis revealed significant differences in the composition of salivary microbiota among KT recipients, patients with ESRD, and healthy controls. Moreover, trough blood concentrations (C₀) of tacrolimus were associated with alterations in microbiota composition. Notably, <em>Capnocytophage</em> consistently exhibited a negative correlation in both group-level and individual trends. Furthermore, distinct taxa were identified that effectively distinguished recipients with varying TacIPV, as demonstrated by a cross-validation random forest model (mean AUC = 0.7560), with <em>Anaerolinea</em> emerging as a prominent contributor to the classifier. These findings suggest that salivary microbiota is closely linked to tacrolimus C₀ levels and could aid clinicians in differentiating KT recipients based on TacIPV.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110952"},"PeriodicalIF":3.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of small RNAs in the spleen of MASH in a non-human primate model","authors":"Juan Zhao ,&nbsp;Yuelei Zhao ,&nbsp;Hongyu Qin ,&nbsp;Yun Ye ,&nbsp;Liwei Zhang ,&nbsp;Ruike Ding ,&nbsp;Wenbin Cao ,&nbsp;Yanru Zhang ,&nbsp;Chenjing Duan ,&nbsp;Haoze Leng ,&nbsp;Yandong Li ,&nbsp;Bo Wang ,&nbsp;Liangshuo Hu ,&nbsp;Enqi Liu ,&nbsp;Pengxiang Qu","doi":"10.1016/j.ygeno.2024.110953","DOIUrl":"10.1016/j.ygeno.2024.110953","url":null,"abstract":"<div><div>Metabolic dysfunction-associated steatotic liver disease (MASLD) and its advanced stage, metabolic dysfunction-associated steatohepatitis (MASH), are increasingly recognized as a global health issue. This study examines the role of small RNAs in the spleen of MASH using a non-human primate model. We performed high-throughput small RNA sequencing on spleen tissues from MASH-primates, revealing significant alterations in the expression of small non-coding RNAs, especially miRNAs. Notably, miR-96, miR-182, miR-183, and miR-122 showed differential expression in MASH spleens. Predictive and validation studies have identified potential target genes, such as PTX3 and NFIX, that were significantly dysregulated in spleens of MASH. These findings characterized small RNAs in spleen of MASH and offer a novel insight for further research for MASH.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110953"},"PeriodicalIF":3.4,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PLOD1 promote proliferation and migration with glycolysis via the Wnt/β-catenin pathway in THCA","authors":"Wei Cong,&nbsp;Jingfu Sun,&nbsp;Zhanyu Hao,&nbsp;Maosong Gong,&nbsp;Jianing Liu","doi":"10.1016/j.ygeno.2024.110943","DOIUrl":"10.1016/j.ygeno.2024.110943","url":null,"abstract":"<div><div>THCA (Thyroid carcinoma) is the most common endocrine malignancy in the world. The PLOD1 is highly expressed in THCA, but the mechanism is still unclear. It is found that the cell proliferation and migration were inhibited in si-PLOD1 group, and promoted with PLOD1 overexpression. MAZ is the transcription factor of PLOD1. The cell activities induced MAZ were reversed by si-PLOD1. The Glucose uptake, lactate production and ATP/ADP ratio were decreased with si-PLOD1. The glycolysis related proteins GLUT1, HK2, PFKP, PKM2, LDHA and Wnt/β-catenin pathway proteins WNT5A, cyclin D1, β-catenin were inhibited, GSK-3β is increased in si-PLOD1 group. BML-284 could reversed the si-PLOD1 effects on cell activities and Wnt/β-catenin pathway. The tumor xenografts were inhibited in si-PLOD1 group. As a potential therapeutic target, PLOD1 is regulated by MAZ in THCA. PLOD1 depletion could inhibit THCA cell proliferation and metastasis by glycolysis, which is inhibited by Wnt/β-catenin pathway in THCA.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110943"},"PeriodicalIF":3.4,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer","authors":"Hao Chen ,&nbsp;Meizi Zeng ,&nbsp;Syeda Sundas Batool ,&nbsp;Yiming Zhao ,&nbsp;Zheng Yu ,&nbsp;Jumei Zhou ,&nbsp;Ke Liu ,&nbsp;Jing Huang","doi":"10.1016/j.ygeno.2024.110951","DOIUrl":"10.1016/j.ygeno.2024.110951","url":null,"abstract":"<div><div>Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110951"},"PeriodicalIF":3.4,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142462532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration analysis of transcriptome and metabolome revealed the potential mechanism of spermatogenesis in Tibetan sheep (Ovis aries) at extreme high altitude","authors":"Miaoshu Zhang ,&nbsp;Xuejiao An ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Binpeng Xi ,&nbsp;Jianbin Liu ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110949","DOIUrl":"10.1016/j.ygeno.2024.110949","url":null,"abstract":"<div><div>Testis has an indispensable function in male reproduction of domestic animals. Numerous genes and metabolites were related to testicular development and spermatogenesis. However, little is known about the biological regulation pathways associated with fecundity in male Tibetan sheep. In this study, Testes were collected from Huoba Tibetan sheep (HB, 4614 m) and Gangba Tibetan sheep (GB, 4401 m) at extreme high altitude, and Alpine Merino sheep (AM, 2500 m, control group) at medium-high altitude, investigating the genes and metabolites levels of them. The histological analysis of testicular tissue using hematoxylin-eosin (HE) staining was performed for Tibetan sheep and Alpine Merino sheep, and the testes of them were analyzed by transcriptomics and metabolomics to explore the potential mechanism of testicular development and spermatogenesis. The statistical results showed that the cross-sectional area of testicular seminiferous tubules, diameter of seminiferous tubules, and spermatogenic epithelium thickness were significantly smaller in HB and GB than in AM (<em>P</em> &lt; 0.05). Overall, 5648 differentially expressed genes (DEGs) and 336 differential metabolites (DMs) were identified in three sheep breeds, which were significantly enriched in spermatogenesis and other related pathways. According to integrated metabolomic and transcriptomic analysis, glycolysis/gluconeogenesis, AMPK signaling pathway, and TCA cycle, were predicted to have dramatic effects on the spermatogenesis of Tibetan sheep. Several genes (including <em>Wnt2</em>, <em>Rab3a</em>, <em>Sox9</em>, <em>Hspa8</em>, and <em>Slc38a2</em>) and metabolites (including L-histidinol, Glucose, Fumaric acid, Malic acid, and Galactose) were significantly enriched in pathways related to testicular development and spermatogenesis, and might affect the reproduction of Tibetan sheep by regulating the acrosome reaction, meiotic gene expression, and the production of sex hormones. Our results provide further understanding of the key genes and metabolites involved in testicular development and spermatogenesis in Tibetan sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110949"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of genetic evolutionary differences among four Tibetan pig populations in China","authors":"Yiting Yang ,&nbsp;Mailin Gan ,&nbsp;Chengming Liu ,&nbsp;Zhongwei Xie ,&nbsp;Meng Wang ,&nbsp;Chengpeng Zhou ,&nbsp;Wenqiang Cheng ,&nbsp;Lei Chen ,&nbsp;Shunhua Zhang ,&nbsp;Ye Zhao ,&nbsp;Lili Niu ,&nbsp;Yan Wang ,&nbsp;Jingyong Wang ,&nbsp;Linyuan Shen ,&nbsp;Li Zhu","doi":"10.1016/j.ygeno.2024.110950","DOIUrl":"10.1016/j.ygeno.2024.110950","url":null,"abstract":"<div><div>Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957–0.1978). Ratio of runs of homozygosity (F_roh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336–0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110950"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis and identification of candidate bZIP transcription factors involved in anthraquinone biosynthesis in Rheum officinale Baill","authors":"Jing Tang ,&nbsp;Yi-min Li ,&nbsp;Yan Wang ,&nbsp;Feng Yan ,&nbsp;Zhao Feng ,&nbsp;Rui-hua LV ,&nbsp;Jing Gao ,&nbsp;Liang Peng ,&nbsp;Xiao-chen Hu ,&nbsp;Gang Zhang","doi":"10.1016/j.ygeno.2024.110948","DOIUrl":"10.1016/j.ygeno.2024.110948","url":null,"abstract":"<div><div>Rhubarb is a traditional medicinal plant in China, whose pharmacological effects derive mainly from its anthraquinones. However, the regulatory mechanism affecting anthraquinone biosynthesis in <em>R. officinale</em> remains poorly understood. We assembled a high-quality, full-length transcriptome using single-molecule real-time (SMRT) sequencing. 274 unigenes potentially involved in the biosynthesis of anthraquinones, including those in the shikimate, polyketide, MVA and MEP pathways, were identified based on full-length transcriptome. Differentially expressed genes (DEGs) induced by MeJA treatment and DEGs between different tissues were identified through next-generation sequencing (NGS), revealing the genes that may be involved in the biosynthesis of anthraquinones. The basic leucine zipper (bZIP) transcription factors of <em>R. officinale</em> were systematically identified. Key genes such as <em>RobZIP50</em> and <em>RobZIP53</em> were systematically identified and found to be associated with anthraquinone biosynthesis in <em>R. officinale</em> through differential expression, co-expression and protein interaction analyses. <em>RobZIP50</em> and <em>RobZIP53</em> were highly expressed in roots and rhizomes, and significantly increased after 12 h of MeJA treatment. Additionally, both RobZIP50 and RobZIP53 were localized exclusively in the nucleus, with RobZIP53 showing significant transcriptional activity. Taken together, our results suggest that RobZIP53 may play a role in regulating anthraquinone biosynthesis in <em>R. officinale</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110948"},"PeriodicalIF":3.4,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 molecular regulated mechanism of METTL3 and FTO in lipid metabolism of Hu sheep","authors":"Bowen Chen ,&nbsp;Chao Yuan ,&nbsp;Tingting Guo ,&nbsp;Jianbin Liu ,&nbsp;Bohui Yang ,&nbsp;Zengkui Lu","doi":"10.1016/j.ygeno.2024.110945","DOIUrl":"10.1016/j.ygeno.2024.110945","url":null,"abstract":"<div><h3>Background</h3><div>Balanced lipid metabolism can improve the growth performance and meat quality of livestock. The m6A methylation-related genes <em>METTL3</em> and <em>FTO</em> play important roles in animal lipid metabolism; however, the mechanism through which they regulate lipid metabolism in sheep is unclear.</div></div><div><h3>Results</h3><div>We established lipid deposition models of hepatocytes and preadipocytes in Hu sheep. In the hepatocyte lipid deposition model, the genes expression levels of <em>FABP4</em>, Accα, <em>ATGL</em> and <em>METTL3</em>, <em>METTL14</em>, and <em>FTO</em>—were significantly up-regulated after lipid deposition (<em>P</em> &lt; 0.05). Transcriptomic and metabolomic analyses showed that lipid deposition had a significant effect on MAPK, steroid biosynthesis, and glycerophospholipid metabolism pathway in hepatocytes. The m6A methylation level decreased but the difference was not significant after <em>METTL3</em> interference, and the expression levels of <em>FABP4</em> and <em>ATGL</em> increased significantly (<em>P</em> &lt; 0.05); the m6A methylation level significantly increased following <em>METTL3</em> overexpression, and <em>LPL</em> and <em>ATGL</em> expression levels significantly decreased (<em>P</em> &lt; 0.05), indicating that overexpression of <em>METTL3</em> inhibited the expression of lipid deposition-related genes in a m6A-dependent manner. The m6A methylation level was significantly increased, <em>ATGL</em> expression was significantly decreased (<em>P</em> &lt; 0.05), and <em>LPL</em>, <em>FABP4</em>, and <em>Accα</em> expression was not significantly changed following <em>FTO</em> interference (<em>P</em> &gt; 0.05); the m6A methylation level was significantly decreased after <em>FTO</em> overexpression, and <em>LPL</em>, <em>FABP4</em>, and <em>ATGL</em> expression was significantly increased (<em>P</em> &lt; 0.05), indicating that <em>FTO</em> overexpression increased the expression of lipid deposition-related genes in a m6A-dependent manner. Transcriptomic and metabolomic analyses showed that m6A methylation modification mainly regulated lipid metabolism through triglyceride metabolism, adipocytokine signaling, MAPK signaling, and fat digestion and absorption in hepatocytes. In the lipid deposition model of preadipocytes, the regulation of gene expression is the same as that in hepatocytes.</div></div><div><h3>Conclusions</h3><div><em>METTL3</em> significantly inhibited the expression of lipid deposition-related genes, whereas <em>FTO</em> overexpression promoted lipid deposition. Our study provides a theoretical basis and reference for accurately regulating animal lipid deposition by mastering <em>METTL3</em> and <em>FTO</em> genes to promote high-quality animal husbandry.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110945"},"PeriodicalIF":3.4,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Definition of regulatory elements and transcription factors controlling porcine immune cell gene expression at single cell resolution using single nucleus ATAC-seq","authors":"Pengxin Yang ,&nbsp;Ryan Corbett ,&nbsp;Lance Daharsh ,&nbsp;Juber Herrera Uribe ,&nbsp;Kristen A. Byrne ,&nbsp;Crystal L. Loving ,&nbsp;Christopher Tuggle","doi":"10.1016/j.ygeno.2024.110944","DOIUrl":"10.1016/j.ygeno.2024.110944","url":null,"abstract":"<div><div>The transcriptome of porcine peripheral blood mononuclear cells (PBMC) at single cell (sc) resolution is well described, but little is understood about the cis-regulatory mechanism behind scPBMC gene expression. Here, we profiled the open chromatin landscape of porcine PBMC that define cis-regulatory elements and mechanism contributing to the transcription using single nucleus ATAC sequencing (snATAC-seq). Approximately 22 % of the identified peaks overlapped with annotated transcription start sites (TSS). Using clustering based on open chromatin pattern similarity, we demonstrate that cell type annotations using snATAC-seq are highly concordant to that reported for sc RNA sequencing (scRNA-seq). The differentially accessible peaks (DAPs) for each cell type were characterized and the pattern of accessibility of the DAPs near cell type markers across cell types was similar to that of the average gene expression level of corresponding marker genes. Additionally, we found that peaks identified in snATAC-seq have the potential power to predict the cell type specific transcription starting site (TSS). We identified both transcription factors (TFs) whose binding motif were enriched in cell type DAPs of multiple cell types and cell type specific TFs by conducting transcription factor binding motif (TFBM) analysis. Furthermore, we identified the putative enhancer or promoter regions bound by TFs for each differentially expressed gene (DEG) with a DAP that overlapped with its TSS by generating cis-co-accessibility networks (CCAN). To predict the regulators of such DEGs, TFBM analysis was performed for each CCAN. The regulator TF-target DEG pairs predicted in this way were largely consistent with the results reported in the ENCODE Transcription Factor Targets Dataset (TFTD). This snATAC-seq approach provides insights into the regulation of chromatin accessibility landscape of porcine PBMCs and enables discovery of TFs predicted to control DEG through binding regulatory elements whose chromatin accessibility correlates with the DEG promoter region.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110944"},"PeriodicalIF":3.4,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key role of CYP17A1 in Leydig cell function and testicular development in Qianbei Ma goats.","authors":"Tang Wen, Zhang Yuan, Wang Zhong, Guo Wei, Chen Jiajing, Ji Quan, Wang Yanfei, Li Ruiyang, Xu Houqiang, Chen Xiang","doi":"10.1016/j.ygeno.2024.110937","DOIUrl":"10.1016/j.ygeno.2024.110937","url":null,"abstract":"<p><p>Reproductive traits are vital economic parameters in goat production, and boosting the reproductive capacity of breeding rams is crucial for enhancing the profitability of goat farming. Currently, research on the reproductive performance of Qianbei Ma goats mainly centers on investigating mechanisms associated with prolificacy and estrous ovulation in ewes, with limited emphasis on ram reproductive aspects. This study used scanning electron microscopy and enzyme-linked immunosorbent assay (ELISA) to profile the morphology of testis and the dynamic changes of Luteinizing Hormone (LH), Follicle-Stimulating Hormone (FSH), and Testosterone (T) in serum at different developmental stages of Qianbei Ma goats. Meanwhile, transcriptome sequencing technology was used to investigate the mRNA expression patterns in testicular tissues at different developmental stages: newborn (0 M), puberty (6 M), sexual maturity (12 M), and physical maturity (18 M). The results showed that the diameter, circumference, and area of the testicular seminiferous tubules gradually increased with age. The levels of T and LH in serum significantly increased from 0 to 6 months after birth (p < 0.05), followed by a stabilization of T levels and a significant decrease in LH levels (p < 0.05). Meanwhile, FSH shows a decreasing trend between 0 and 18 months after birth. A total of 26,437 differentially expressed genes were identified in 6 comparison groups, which involve various biological processes such as immunity, growth, metabolism, development, and reproduction, and are significantly enriched in signaling pathways related to testicular development and spermatogenesis. WGCNA analysis identified 6 regions significantly associated with testicular development and spermatogenesis, and selected 320 genes for constructing a PPI network. Ten candidate genes related to testicular development and spermatogenesis were identified, including TP53, PLK4, RPS9, PFN4, ACTB, CYP17A1, GPX4, CLDN1, AMH and DHH. Of these, the CYP17A1 gene promotes interstitial cell proliferation, and promotes T synthesis. This study provides a theoretical basis and data support for promoting efficient breeding of goats and early breeding of excellent male goats.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110937"},"PeriodicalIF":3.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}