BMC Genomics最新文献

{"title":"Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice.","authors":"Tianhu Li, Zhen Yang, Yang Ang, Yingying Zhao, Yanan Zhang, Zhengbo Liu, Hao Sun, Yinping Chang, Mingyu Du, Xianping Cheng, Jinghan Sun, Erbao Liu","doi":"10.1186/s12864-025-11487-z","DOIUrl":"10.1186/s12864-025-11487-z","url":null,"abstract":"<p><strong>Background: </strong>In hybrid rice seed production, rice varieties with a small flag leaf angle (FLA) experience obstacles to cross-pollination at the early heading stage, and farmers usually need to remove flag leaves to achieve artificial pollination. Therefore, the cultivation of rice varieties with large FLAs can not only save a substantial amount of labour in the leaf-cutting process during artificial pollination but also accelerate the mechanization of hybrid rice seed production.</p><p><strong>Results: </strong>In this study, 431 rice accessions were included in a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) and the superior haplotypes for rice FLA in 2022 and 2023. The aim of the study was to identify new QTLs and provide germplasm resources for the genetic improvement of rice FLA. The population exhibited rich phenotypic variation in FLA in both years. The FLA GWAS was performed with more than 3 million single-nucleotide polymorphisms (SNPs), and eight QTLs associated with FLA were detected; of these, six QTLs located on rice chromosomes 1, 2, 8 and 9 were novel and detected in both years. In addition, these QTLs were analysed by haplotype analysis and functional annotation, and FLA2 and FLA9, which encode xyloglucan fucosyltransferase and cytokinin-O-glucosyltransferase 2, respectively, were identified as candidate genes for FLA regulation in rice. Quantitative real-time polymerase chain reaction (qRT‒PCR) results validated FLA2 and FLA9 as candidate genes. The results of this study showed that the elite alleles of FLA2 and FLA9 can increase FLA in rice. Excellent parents for FLA improvement were predicted through pyramiding breeding.</p><p><strong>Conclusions: </strong>A total of six new QTLs and two candidate genes (FLA2 and FLA9) were identified by a GWAS of 431 rice accessions over two years. The elite alleles and excellent parents predicted in our study can provide important information for the functional analysis of rice FLA-related genes and improvement through pyramiding breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"280"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676642","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":"Seminal plasma proteomics of asymptomatic COVID-19 patients reveals disruption of male reproductive function.","authors":"Jialyu Huang, Yufang Su, Jiawei Wang, Zheng Fang, Yiwei Zhang, Hong Chen, Xinxia Wan, Yuanhuan Xiong, Ning Song, Houyang Chen, Xingwu Wu","doi":"10.1186/s12864-025-11473-5","DOIUrl":"10.1186/s12864-025-11473-5","url":null,"abstract":"<p><strong>Background: </strong>A considerable proportion of males suffer from asymptomatic SARS-CoV-2 infection, while the effect on reproductive function and underlying pathomechanisms remain unclear.</p><p><strong>Results: </strong>The total sperm count decreased evidently after asymptomatic infection, yet all semen samples were tested to be SARS-CoV-2 RNA negative. Through label‑free quantitative proteomic profiling, a total of 733 proteins were further identified in seminal plasma from 11 COVID-19 patients and seven uninfected controls. Of the 37 differentially expressed proteins, 23 were upregulated and 14 were downregulated in the COVID-19 group compared with control. Functional annotations in Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome showed that these proteins were highly enriched in infection, inflammation, and immunity-related pathways as well as spermatogenesis-associated biological process. Four proteins were significantly correlated with one or more semen parameters in Spearman's coefficient analysis, and seven were filtered as potential hub proteins from the interaction network by MCODE and Cytohubba algorithms. Furthermore, we verified the proteomic results by Western blot analysis of three representative proteins (ITLN1, GSTM2, and PSAP) in the validation cohort.</p><p><strong>Conclusions: </strong>In summary, our study showed that acute asymptomatic COVID-19 could alter the seminal plasma protein profile without direct testicular infection and consequently lead to impaired semen quality. These novel findings should enlighten the physicians about the adverse effects of SARS-CoV-2 infection on male fertility, and provide valuable resources for reproductive biologists to further decipher the molecular functions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"281"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676566","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 rumen microbiome and its metabolome together with the host metabolome regulate the growth performance of crossbred cattle.","authors":"Wei Zhao, Lina Ma, Lin Xue, Qiufei Jiang, Yuan Feng, Suwan Wang, Jinli Tian, Xiaohua Tian, Yaling Gu, Juan Zhang","doi":"10.1186/s12864-025-11465-5","DOIUrl":"10.1186/s12864-025-11465-5","url":null,"abstract":"<p><strong>Background: </strong>Although it has been demonstrated that gastrointestinal microorganisms greatly influence livestock performance, the effect of gastrointestinal microorganisms on the growth performance of crossbred cattle remains unclear. Due to their superior production characteristics, understanding the impact of gastrointestinal microorganisms on the growth performance of crossbred beef cattle is of significant importance for improving farming efficiency.</p><p><strong>Result: </strong>In this study, healthy Simmental with similar birth date and weight were selected as dams, Simmental (Combination I), Belgian Blue (Combination II) and Red Angus (Combination III) were used as parents for crossbreeding. The progeny of the three combination crosses were measured for growth performance under identical conditions from birth rearing to 18 months of age (n = 30). Rumen fluid and plasma were collected for macro-genomic and non-targeted metabolomic analysis (n = 8). The results showed that Combination II was superior to Combination I and Combination III in body weight (BW) and body height (BH) (P < 0.05). Mycoplasma, Succinivibrio, Anaerostipes, Methanosphaera, Aspergillus, and Acidomyces were significantly increased in the rumen of Combination II (P < 0.05), whereas differentially expressed metabolites (DEMs) 9,10,13-Trihome (11), 9,12,13-Trihome and 9(10)-Epome, and 9(S)-Hpode were reduced in abundance. In addition, plasma DEM PC (14:0/P-18:1(11Z)), PC (16:0/0:0), and PC (17:0/0:0) were down-regulated in combination II. Correlation analysis revealed that Anaerostipes, Methanosphaera, and Succinivibrio were associated with PC (14:0/P-18:1(11Z)), 9(10)-Epome, 9,10,13-Trihome (11), 9(S)-Hpode, 9,10,13-Trihome, PC (17:0/0:0), and PC (16:0/0:0). Growth traits were significantly positively correlated with the three dominant genera, Anaerostipes, Methanosphaera, and Succinivibrio, while significantly negatively correlated with key rumen metabolites and plasma metabolites (P < 0.05).</p><p><strong>Conclusions: </strong>Our study reveals the role of rumen microorganisms and its metabolites with host metabolism in the regulation of growth performance of crossbred cattle, which will contribute to the development of modern cattle breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"278"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676605","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":"Whole-genome bisulfite sequencing of X and Y sperm in Holstein bulls reveals differences in autosomal methylation status.","authors":"Aishao Shangguan, Fengling Ding, Rui Ding, Wei Sun, Xihe Li, Xiangnan Bao, Tiezhu Zhang, Huihui Chi, Qi Xiong, Mingxin Chen, Yang Zhou, Shujun Zhang","doi":"10.1186/s12864-025-11402-6","DOIUrl":"10.1186/s12864-025-11402-6","url":null,"abstract":"<p><p>A comprehensive understanding of the molecular differences between X and Y sperm in Holstein bull semen is crucial for advancing sex control technologies. While previous studies have primarily focused on proteomic and transcriptomic differences, the genome-wide DNA methylation differences between these sperm types remains largely unexplored. In this study, we employed whole-genome bisulfite sequencing to systematically compare the autosomal methylation profiles of X and Y sperm. Although global methylation patterns showed remarkable consistency between the two sperm types, our localized comparative analysis revealed 12,175 differentially methylated regions mapping to 2,041 genes (differentially methylated genes, DMGs). Functional enrichment analysis of these DMGs revealed their involvement in essential biological processes, particularly in energy metabolism and membrane voltage regulation. Notably, SPA17 and CHCHD3, identified as hypermethylated genes in X sperm in this study, have also been reported to show lower protein expression levels in X sperm compared to Y sperm. Furthermore, we identified 28 DMGs functionally associated with spermatogenesis and 5 DMGs related to fertilization. Our findings lay the foundation for thorough understanding of molecular differences between X and Y sperm in bull, providing essential insights for the development of more advanced sex control technologies in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"282"},"PeriodicalIF":3.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676688","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":"JSNMFuP: a unsupervised method for the integrative analysis of single-cell multi-omics data based on non-negative matrix factorization.","authors":"Bai Zhang, Mengdi Nan, Liugen Wang, Hanwen Wu, Xiang Chen, Yongle Shi, Yibing Ma, Jie Gao","doi":"10.1186/s12864-025-11462-8","DOIUrl":"10.1186/s12864-025-11462-8","url":null,"abstract":"<p><p>With the rapid advancement of sequencing technology, the increasing availability of single-cell multi-omics data from the same cells has provided us with unprecedented opportunities to understand the cellular phenotypes. Integrating multi-omics data has the potential to enhance the ability to reveal cellular heterogeneity. However, data integration analysis is extremely challenging due to the different characteristics and noise levels of different molecular modalities in single-cell data. In this paper, an unsupervised integration method (JSNMFuP) based on non-negative matrix factorization is proposed. This method integrates the information extracted from the latent variables of each omic through a consensus graph. High-dimensional geometrical structure is captured in the original data and biologically-related feature links across modalities are incorporated into the model using regularization terms. JSNMFuP can be utilized for data visualization and clustering, facilitating marker characterization and gene ontology enrichment analysis, providing rich biological insights for downstream analysis. The application on real datasets shows that JSNMFuP has superior performance in cell clustering. The factors are interpretable, making it an effective method for analyzing cell heterogeneity using single-cell multi-omics data.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"274"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668884","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":"Genome-wide identification of the P4ATPase gene family and its response to biotic and abiotic stress in soybean (Glycine max L.).","authors":"Jingjing Wei, Gaoyang Zhang, Huanhuan Lv, Saidi Wang, Xingyu Liu, Yanli Qi, Zhongke Sun, Chengwei Li","doi":"10.1186/s12864-025-11468-2","DOIUrl":"10.1186/s12864-025-11468-2","url":null,"abstract":"<p><strong>Background: </strong>Soybean is an important legume crop and has significant agricultural and economic value. P4-ATPases (aminophospholipid ATPases, ALAs), one of the classes of P-type ATPases, can transport or flip phospholipids across membranes, creating and maintaining lipid asymmetry and playing crucial roles in plant growth and development. To date, however, the ALA gene family and its expression patterns under abiotic and biotic stresses have not been studied in the soybean genome.</p><p><strong>Results: </strong>A total of 27 GmALA genes were identified in the soybean genome and these genes were unevenly distributed on 15 chromosomes and classified into five groups based on phylogenetic analysis. The GmALAs family had diverse intron-exon patterns and a highly conserved motif distribution. A total of eight domains were found in GmALAs, and all GmALAs had conserved PhoLip_ATPase_C, phosphorylation and transmembrane domains. Cis-acting elements in the promoter demonstrated that GmALAs are associated with cellular development, phytohormones, environmental stress and photoresponsiveness. Analysis of gene duplication events revealed 24 orthologous gene pairs in soybean and synteny analysis revealed that GmALAs had greater collinearity with AtALAs than with OsALAs. Evolutionary constraint analyses suggested that GmALAs have undergone strong selective pressure for purification during the evolution of soybeans. Tissue-specific expression profiles revealed that GmALAs were differentially expressed in roots, stems, seeds, flowers, nodules and leaves. The expression pattern of these genes appeared to be diverse in the different developmental tissues. Combined transcriptome and qRT-PCR data confirmed the differential expression of GmALAs under abiotic (dehydration, saline, low temperature, ozone, light, wounding and phytohormones) and biotic stresses (aphid, fungi, rhizobia and rust pathogen).</p><p><strong>Conclusion: </strong>In summary, genome-wide identification and evolutionary and expression analyses of the GmALAs gene family in soybean were conducted. Our work provides an important theoretical basis for further understanding GmALAs in biological functional studies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"277"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668878","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":"Identification and characterization of the TmSnRK2 family proteins related to chicoric acid biosynthesis in Taraxacum mongolicum.","authors":"Qun Liu, Zhiqing Wu, Changyang Yu, Xiwu Qi, Hailing Fang, Xu Yu, Li Li, Yang Bai, Dongmei Liu, Zequn Chen, Guoyin Kai, Chengyuan Liang","doi":"10.1186/s12864-025-11460-w","DOIUrl":"10.1186/s12864-025-11460-w","url":null,"abstract":"<p><strong>Background: </strong>Taraxacum mongolicum is rich in phenolic acids and is widely utilized in food and medicine globally. Our previous research demonstrated that the abscisic acid (ABA) hormone significantly enhances chicoric acid accumulation in T. mongolicum. SNF1-related protein kinase 2s (SnRK2s) are extensively involved in ABA signaling and have the potential to regulate the biosynthesis of phenolic acids.</p><p><strong>Results: </strong>In this study, liquid chromatography-mass spectrometry (LC-MS) and transcriptomic analyses revealed that the TmbZIP1-Tm4CL1 pathway plays a crucial role in the transcriptional regulation of chicoric acid biosynthesis. Seven TmSnRK2s were identified in T. mongolicum and classified into three groups. Analysis of the TmSnRK2s promoters (2000 bp in length) indicated that the three most prevalent stress-related elements were ABA, methyl jasmonate (MeJA), and light. ABA treatments (0 h, 2 h, 4 h, 8 h, and 24 h) showed that all seven TmSnRK2s were significantly modulated by ABA, with the exception of SnRK2.7. TmSnRK2.2, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 were localized in both the cytoplasm and nucleus, whereas TmSnRK2.1 and TmSnRK2.5 were exclusively observed in the cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that TmSnRK2.1, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 interact with TmbZIP1. The motifs 'Q(S/G)(V/D)(D/E)(I/L)××I(I/V)×EA' and 'D×(D/ED××D)' are identified as the core sites that facilitate the binding of TmSnRK2s to TmbZIP1. Dual-luciferase reporter assays demonstrated that TmSnRK2.3 and TmSnRK2.6 enhance the stability of TmbZIP1 binding to proTm4CL1.</p><p><strong>Conclusion: </strong>These findings enhance our understanding of the specific roles of certain members of the TmSnRK2 family in the biosynthesis pathway of chicoric acid.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"276"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668881","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":"Abnormal DNA methylation of EBF1 regulates adipogenesis in chicken.","authors":"Xiaohuan Chao, Lijin Guo, Meiling Hu, Mao Ye, Zhexia Fan, Kang Luan, Jiahao Chen, Chunlei Zhang, Manqing Liu, Bo Zhou, Xiquan Zhang, Zhenhui Li, Qingbin Luo","doi":"10.1186/s12864-025-11464-6","DOIUrl":"10.1186/s12864-025-11464-6","url":null,"abstract":"<p><strong>Background: </strong>DNA methylation influences gene expression and is involved in numerous biological processes, including fat production. It is involved in lipid generation in numerous animal species, including poultry. However, the effect of DNA methylation on adipogenesis in chickens remains unclear.</p><p><strong>Results: </strong>A total of 12 100-day-old chickens were divided into high and low-fat groups based on their abdominal fat ratios. Subsequently, genome-wide bisulfite sequencing (WGBS) was performed on their abdominal fat, and 1877 differentially methylated region (DMR) genes were identified, among which SLC45A3, EBF1, PLA2G15, and ACAD9 were associated with lipid metabolism. Interestingly, EBF1 showed a lower level of DNA methylation and higher mRNA expression in the low-fat group, as determined by comprehensive RNA-seq analysis. Cellular verification showed that EBF1 expression was upregulated by 5-azacytidine (5-Aza) and downregulated by betaine. EBF1 facilitated the differentiation of immortalized chicken preadipocyte 1 (ICP-1) through the PPAR-γ pathway, thereby affecting chicken adipogenesis.</p><p><strong>Conclusion: </strong>A combination of WGBS and RNA-seq analyses revealed 48 DMGs in the abdominal fat tissue of chickens. Notably, the DNA methylation status of EBF1 was inversely related to its mRNA expression. Mechanistically, DNA methylation regulates EBF1 expression, which in turn mediates the differentiation of ICP-1 through the PPARγ pathway. This study provides a theoretical framework for investigating the effects of DNA methylation on adipogenesis in chickens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"275"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668905","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":"Evolution and amplification of the trehalose-6-phosphate synthase gene family in Theaceae.","authors":"Zaibao Zhang, Tao Xiong, Kejia Li, Kexin Huang, Chunxia Liao, Guangqu Liu","doi":"10.1186/s12864-025-11475-3","DOIUrl":"10.1186/s12864-025-11475-3","url":null,"abstract":"<p><strong>Background: </strong>Trehalose-6-phosphate synthase (TPS) is an essential enzyme involved in the production of trehalose, and the genes associated with TPS are crucial for various processes such as growth, development, defense mechanisms, and resistance to stress. However, there has been no documentation regarding the evolution and functional roles of the TPS gene family within Theaceae.</p><p><strong>Results: </strong>Here, we uncovered the lineage-specific evolution of TPS genes in Theaceae. A total of 102 TPS genes were discovered across ten Theaceae species with sequenced genomes. Consistent with the previous classification, our phylogenetic analysis indicated that the TPS genes in Theaceae can be categorized into two primary subfamilies and six distinct clades (I, II-1, II-2, II-3, II-4, II-5), with clade I containing a greater number of introns compared to those found in clade II. Segmental duplication served as the main catalyst for the evolution of TPS genes within Theaceae, and numerous TPS genes exhibited inter-species synteny among various Theaceae species. Most of the TPS genes were ubiquitously expressed, and expression divergence of TPS paralogous pairs was observed. The cis-acting elements found in TPS genes indicated their involvement in responses to phytohormones and stress.</p><p><strong>Conclusion: </strong>This research enhanced our understanding of the lineage-specific evolution of the TPS gene family in Theaceae and offered important insights for future functional analyses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"273"},"PeriodicalIF":3.5,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662179","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":"Short-term heat exposure affects thermogenesis and mitophagy in goat brown adipocytes.","authors":"Yulong Song, Die Li, Duo Su, Tingting Jiang, Longrui Li, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Linjie Wang","doi":"10.1186/s12864-025-11467-3","DOIUrl":"10.1186/s12864-025-11467-3","url":null,"abstract":"<p><strong>Background: </strong>Brown adipose tissue (BAT) has a significant impact in newborn goats on maintaining body temperature through non-shivering thermogenesis in response to cold exposure. However, the roles of heat treatment on BAT thermogenesis are still limited.</p><p><strong>Results: </strong>This study focused on the effects of short-term heat exposure on goat brown adipocytes. We found that the content of mitochondria and the proteins of UCP1 and PGC1α were increased after 12 h of heat exposure. Additionally, the triglyceride (TG) content was significantly decreased after 1, 2, 6 h of heat exposure. Furthermore, RNA-seq analysis of brown adipocytes after 12 h of heat exposure identified 1091 differentially expressed genes (DEGs). The KEGG enrichment analysis were mainly enriched in thermogenesis, fatty acid metabolism and mitophagy. In addition, we found that the amount of mitophagosomes and expression levels of mitophagy-related protein (LC3BII/LC3BI, BNIP3, and BECN) were elevated after 12 h of heat treatment.</p><p><strong>Conclusion: </strong>These findings collectively indicate that heat exposure enhances the thermogenic capacity and mitophagy level of goat brown adipocytes. Our study provides evidence that heat exposure facilitates adaptive thermogenesis in goat brown adipocytes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"272"},"PeriodicalIF":3.5,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662193","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}