Mammalian Genome最新文献

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Hypoxia-induced circ_0017521 enhances glycolysis and promotes NSCLC progression via upregulating the PFKFB3/PI3K-AKT pathway. 缺氧诱导的circ_0017521通过上调PFKFB3/PI3K-AKT通路增强糖酵解并促进NSCLC进展。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-16 DOI: 10.1007/s00335-026-10202-x
Jian Zhu, Jin Yan, Yuanyuan Zhang, Xiaoli Zhu, Guoping Chen
{"title":"Hypoxia-induced circ_0017521 enhances glycolysis and promotes NSCLC progression via upregulating the PFKFB3/PI3K-AKT pathway.","authors":"Jian Zhu, Jin Yan, Yuanyuan Zhang, Xiaoli Zhu, Guoping Chen","doi":"10.1007/s00335-026-10202-x","DOIUrl":"10.1007/s00335-026-10202-x","url":null,"abstract":"<p><p>The hypoxic microenvironment is a critical feature of malignant progression in non-small cell lung cancer (NSCLC). However, the regulatory role of circular RNAs (circRNAs) in this context remains incompletely understood. Hypoxia-related circRNAs were screened by integrating GEO datasets, and the expression of circ_0017521 in hypoxia-treated cells was validated using qRT-PCR. RNase R digestion and actinomycin D assays were employed to assess its stability. Biological functions were evaluated through CCK-8, colony formation, Transwell, flow cytometry, and glycolytic metabolism assays. Dual-luciferase reporter, RNA pull-down, and rescue experiments were conducted to elucidate the circ_0017521/miR-532-3p/PFKFB3 axis. A nude mouse xenograft model was constructed. circ_0017521 was specifically upregulated in NSCLC tissues and hypoxia-treated cells, exhibiting remarkable stability compared to linear AKR1E2 and primarily localizing in the cytoplasm. Under hypoxic conditions, knockdown of circ_0017521 noticeably inhibited NSCLC cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and glycolysis, while promoting apoptosis. Mechanistically, circ_0017521 competitively bound to miR-532-3p, relieving its suppression of PFKFB3 and thereby activating the PI3K/AKT signaling pathway. Upregulation of PFKFB3 drove the expression of glycolytic enzymes (GLUT1, LDHA, HK2) and synergistically activated EMT. Animal experiments confirmed that silencing circ_0017521 suppressed tumor growth and glycolysis. This study revealed that hypoxia-induced circ_0017521 activated the PI3K/AKT pathway through the miR-532-3p/PFKFB3 axis, synergistically driving EMT and glycolysis, thereby promoting NSCLC progression.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"37"},"PeriodicalIF":2.6,"publicationDate":"2026-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146207293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide association study identifies significant SNPs for milk production and stature traits in Karan Fries cattle. 全基因组关联研究发现Karan Fries牛产奶量和身材性状的显著snp。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-05 DOI: 10.1007/s00335-026-10201-y
Pritam Pal, Ishmeet Kumar, Manisha Choudhary, Amritanshu Upadhyay, Irusappan Ilayaraja, Anil Chitra, Lal Muansangi, Gopal Gowane, T V Raja, Anupama Mukherjee, Sabyasachi Mukherjee
{"title":"Genome-wide association study identifies significant SNPs for milk production and stature traits in Karan Fries cattle.","authors":"Pritam Pal, Ishmeet Kumar, Manisha Choudhary, Amritanshu Upadhyay, Irusappan Ilayaraja, Anil Chitra, Lal Muansangi, Gopal Gowane, T V Raja, Anupama Mukherjee, Sabyasachi Mukherjee","doi":"10.1007/s00335-026-10201-y","DOIUrl":"10.1007/s00335-026-10201-y","url":null,"abstract":"<p><p>Crossbreeding indigenous cattle with high-yielding exotic breeds has been a key strategy in Indian dairy systems for increasing milk production. The Karan Fries (KF), a stabilised dairy cattle population derived from the Tharparkar and Holstein Friesian breeds, serves as a valuable genetic resource in India. Despite their adaptability and performance, the genomic architecture underpinning milk traits and stature in KF cattle remains largely unexplored. Therefore, a genome-wide association study (GWAS) was conducted using 777 K SNP genotyping data and estimated breeding values (EBVs) as the dependent variable for four economically important dairy traits: first lactation total milk yield (FLTMY), total fat yield (TFY), total solids-not-fat yield (TSNFY), and stature. After quality control and LD pruning, 347,621 SNPs across 355 KF animals were analysed, revealing 54 significant single-nucleotide polymorphisms (SNPs) associated with these traits, with several exhibiting pleiotropic effects. Candidate genes such as EPHA7, SCFD2, DCUN1D4, CWH43, ZMAT4, KYNU, GINS4, GPAT4, GOLGA7, and OCIAD1 were associated with milk yield and compositional traits, while CBLB, CCDC14, ALCAM, MALRD1, and MUC13 were linked to stature. Protein-protein interaction network analysis identified functionally connected gene clusters involved in lactation, fat metabolism, and structural development. These results provide preliminary insights into the genomic architecture of KF cattle and highlight candidate genes associated with milk production and stature traits. While exploratory in nature, these findings may serve as a starting point for future validation and the development of genomic selection strategies in tropical dairy cattle.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"35"},"PeriodicalIF":2.6,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Large-scale mouse mutagenesis identifies novel genes affecting vertebral anatomy. 大规模小鼠突变鉴定影响椎体解剖的新基因。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-05 DOI: 10.1007/s00335-025-10189-x
Ximena Ibarra-Soria, Elizabeth Webb, John F Mulley
{"title":"Large-scale mouse mutagenesis identifies novel genes affecting vertebral anatomy.","authors":"Ximena Ibarra-Soria, Elizabeth Webb, John F Mulley","doi":"10.1007/s00335-025-10189-x","DOIUrl":"10.1007/s00335-025-10189-x","url":null,"abstract":"<p><p>We analyzed the International Mouse Phenotyping Consortium (IMPC) release 19 set of 8,539 phenotyped whole-gene knockouts to identify 204 genes that alter vertebral anatomy and development. These genes are broadly grouped into six categories based on their phenotype: \"vertebral number\" (22 genes); \"vertebral processes\" (35 genes); \"spine shape\" (16 genes); \"tail morphology\" (73 genes); \"vertebral form\" (62 genes); and \"somitogenesis\" (24 genes), with minimal overlap between groups. Gene expression analysis of somite trios across six developmental stages show that 182 of these genes are expressed in somites, and 60% of them show variable expression during somite maturation. A further 54% show expression changes between developmental stages. Fourteen of the 204 genes affecting vertebral anatomy have a vertebral phenotype as their only phenotype, and for 34 genes vertebral phenotypes represent ≥ 50% of their total phenotypes. We find no evidence for a previous association of the majority of these genes with vertebral defects, and have therefore identified an extensive set of novel candidate genes for association with vertebral malformations in humans, including vertebral fusions, numerical variation, and scoliosis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"34"},"PeriodicalIF":2.6,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12876460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Complement in brain and eye disease: shared mechanisms, convergent pathologies, and common therapeutic opportunities. 脑病和眼病的补体:共同机制、趋同病理和共同治疗机会
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-03 DOI: 10.1007/s00335-026-10199-3
Jacqui Nimmo, Matthew Bright, Zhizhong Yang, Laura Elisabeth Nicholls, Bryan Paul Morgan, Nikoleta Daskoulidou, Wioleta Milena Zelek
{"title":"Complement in brain and eye disease: shared mechanisms, convergent pathologies, and common therapeutic opportunities.","authors":"Jacqui Nimmo, Matthew Bright, Zhizhong Yang, Laura Elisabeth Nicholls, Bryan Paul Morgan, Nikoleta Daskoulidou, Wioleta Milena Zelek","doi":"10.1007/s00335-026-10199-3","DOIUrl":"10.1007/s00335-026-10199-3","url":null,"abstract":"<p><p>The brain and eye share striking anatomical, physiological, and immunological similarities. Both are protected by specialised vascular barriers, the blood-brain barrier (BBB) and blood-retinal barrier (BRB) respectively, that maintain homeostasis through tightly regulated cellular and molecular mechanisms. Increasing evidence implicates complement dysregulation as a key driver of neurodegeneration in both organs, contributing to disorders such as Alzheimer’s disease (AD), and age-related macular degeneration (AMD). Genetic and molecular studies highlight overlapping mechanisms, with variants in complement regulators influencing susceptibility to both retinal and brain pathologies. Locally synthesised complement components modulate glial activation, vascular integrity, and synaptic remodelling at both sites and, when dysregulated, contribute to chronic inflammation, synapse loss and neuronal degradation. Despite these shared pathways, therapeutic development has progressed asymmetrically; several complement therapeutics are already in the clinic for AMD and other ocular pathologies, while none are yet in use for brain diseases. This is in part a consequence of the accessibility of the eye where complement targeted drugs can be directly delivered and impact on pathology monitored, difficult in the brain. Lessons learned from the eye, including local delivery to overcome challenges of barrier penetration, may help accelerate development of complement therapeutics for the brain. Here we present a brief perspective that integrates current understanding of complement-mediated mechanisms across brain and eye, emphasising clues from convergent pathophysiology and ocular translational successes.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"33"},"PeriodicalIF":2.6,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12868058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
m5c-modified LINC01094 participates in epithelial-mesenchymal transition and metastasis of cervical cancer cells via the ZNF582-SIRT1/p53 axis. m5c修饰的LINC01094通过ZNF582-SIRT1/p53轴参与宫颈癌细胞的上皮-间质转移和转移。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-03 DOI: 10.1007/s00335-026-10200-z
Xia Lu, Lili Yao, Xu Xu, Mayinuer Guli Rexiti, Xiaoli He, Yanyan Yang
{"title":"m5c-modified LINC01094 participates in epithelial-mesenchymal transition and metastasis of cervical cancer cells via the ZNF582-SIRT1/p53 axis.","authors":"Xia Lu, Lili Yao, Xu Xu, Mayinuer Guli Rexiti, Xiaoli He, Yanyan Yang","doi":"10.1007/s00335-026-10200-z","DOIUrl":"10.1007/s00335-026-10200-z","url":null,"abstract":"<p><p>Cervical cancer (CC) remains a significant global health burden despite advances in prevention and screening. Emerging evidence highlights the critical role of long non-coding RNAs (lncRNAs) and RNA modifications in tumorigenesis. Here, we identified LINC01094 as a highly expressed lncRNA in CC through TCGA analysis and clinical specimens. Functional studies, including CCK-8 method, flow cytometry, Transwell and Western blot assays, demonstrated that LINC01094 knockdown suppressed cell proliferation, migration, and epithelial-mesenchymal transition while promoting apoptosis in CC cells (Caski and SiHa). Mechanistically, NSUN2-mediated 5-methylcytosine methylation stabilized LINC01094, enhancing its expression in CC. Furthermore, LINC01094 facilitated ZNF582-dependent transcriptional activation of SIRT1, promoted the deacetylation and degradation of p53. Rescue experiments confirmed that ectopic expression of either LINC01094 or SIRT1 reversed the tumor-suppressive effects of NSUN2 or LINC01094 knockdown, respectively. Collectively, NSUN2-mediated stabilization of LINC01094 upregulated SIRT1 expression, thereby suppressing the p53 pathway and accelerating CC progression. These findings uncover a novel NSUN2/LINC01094/SIRT1 axis as an epigenetic-transcriptional driver of CC, offering potential therapeutic targets.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"32"},"PeriodicalIF":2.6,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome-wide in-silico identification and characterization of LTR retrotransposons in domestic goat (Capra hircus). 家山羊(Capra hircus) LTR反转录转座子全基因组的计算机鉴定和表征。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-03 DOI: 10.1007/s00335-025-10175-3
Beenish Ishtiaq, Fiaz Khan, Faisal Nouroz, Shumaila Noreen
{"title":"Genome-wide in-silico identification and characterization of LTR retrotransposons in domestic goat (Capra hircus).","authors":"Beenish Ishtiaq, Fiaz Khan, Faisal Nouroz, Shumaila Noreen","doi":"10.1007/s00335-025-10175-3","DOIUrl":"10.1007/s00335-025-10175-3","url":null,"abstract":"<p><p>This study employs LTR_Finder to identify and characterize mobile genetic elements, specifically long terminal repeat (LTR) retrotransposons, in the whole genome of domestic goats ( Capra hircus). LTR retrotransposons are a class of mobile genetic elements that replicate via an RNA intermediate and are flanked by long terminal repeat sequences. Previous studies have highlighted the complexity and significance of LTR retrotransposons in Capra hircus genome, particularly their role in genetic diversity, genome evolution, and potential functional implications. For the present analysis, the reference genome from NCBI was used, and the annotated results from LTR_Finder were further examined using Microsoft Excel, NCBI, Ensembl, Dfam, and Repbase. A total of 1741 L retrotransposons were identified, representing 23.27% of the complete Capra hircus genome. Among chromosomes, chromosome 23 contained the highest proportion of LTR retrotransposons. The longest LTR retrotransposon, measuring 22 kb, was detected on chromosome 28, and phylogenetic analysis confirmed its presence in other species within the Bovidae family. Conversely, the shortest LTR retrotransposon, with a length of only 1244 bp, was located on chromosome 1. Further classification revealed that 35% of the identified LTR retrotransposons were nested elements. In addition, they exhibited 177 distinct TSD sequences, along with conserved PBS (Primer Binding Site) and PPT (Polypurine Track) motifs, both of which are valuable for evolutionary analysis. Family-level classification using the UCSC Genome Browser identifies groups such as BTLTR, ERVL, ERVL_MaLR, ERVK, and Gypsy, thereby providing insights into the insertion patterns of LTR retrotransposons introduced by various retroviruses. Overall, these findings expand the understanding of the distribution, diversity, and evolutionary significance of LTR retrotransposons in the goat genome, underscoring their pivotal role in shaping genomic architecture and functional dynamics.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"31"},"PeriodicalIF":2.6,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS. GWAS发现的3只安纳托利亚山羊生长和产奶量相关候选基因。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-02-02 DOI: 10.1007/s00335-026-10203-w
Eymen Demir, Umit Bilginer, Huriye Doğru, Burak Karacaören, Hasan Meydan, Zeynep Çiftçi, Serdar Yağci, Sarp Kaya, Taki Karsli
{"title":"Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS.","authors":"Eymen Demir, Umit Bilginer, Huriye Doğru, Burak Karacaören, Hasan Meydan, Zeynep Çiftçi, Serdar Yağci, Sarp Kaya, Taki Karsli","doi":"10.1007/s00335-026-10203-w","DOIUrl":"10.1007/s00335-026-10203-w","url":null,"abstract":"<p><p>This study aimed to identify candidate genes related to birth weight (BW), live weight at 90th day (90-LW), and lactation milk yield (LMY) in Hair (HAI), Honamlı (HNM), and Kabakulak (KBK) goats, providing a genome-wide basis for further selection strategies. The genome-wide efficient mixed model association approach was assessed with 309.342 bi-allelic single nucleotide polymorphisms (SNPs) across 481 animals to detect significant variants and their corresponding genomic regions. False discovery rate (FDR) correction and suggestive significance threshold were applied to identify SNPs having direct and potential effects on traits of interest, respectively. A total of 138 outlier SNPs (20 in HNM, 47 in HAI, and 71 in KBK) exceeded suggestive significance, of which 12 SNPs were identified to meet Benjamini-Hochberg's FDR criterion, suggesting that the overlapped protein-coding genes directly influence the phenotypic traits of interest. This approach revealed that the ID4 and CXCR4 genes directly affect BW and LMY traits in HNM goats, whereas no significant associations were observed regarding these traits in HAI and KBK goats. Additionally, a total of 8 protein-coding genes were identified to directly influence the 90-LW trait in HAI (MFSD1, CHMP4C, and MAP1B) and KBK (IGSF21, RALY, ZNF507, SLC38A10, and PGBD5) goats. The remaining 126 suggestive SNPs, on the other hand, either overlapped or were located near 103 protein-coding genes, indicating their potential effects on growth and milk yield. Both direct and potential protein-coding genes identified in this study seem promising for designing comprehensive selection strategies to improve growth and milk traits in Anatolian goats.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"30"},"PeriodicalIF":2.6,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12864215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic architecture of insertion-deletion (indel) variants in beetal goats of India. 印度山羊插入-缺失(indel)变异的基因组结构。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-01-28 DOI: 10.1007/s00335-026-10197-5
J Saalom King, Marykutty Thomas, Jinty Sukumaran, P M Rojan, M R Akhila, T X Seena, K A Bindu
{"title":"Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.","authors":"J Saalom King, Marykutty Thomas, Jinty Sukumaran, P M Rojan, M R Akhila, T X Seena, K A Bindu","doi":"10.1007/s00335-026-10197-5","DOIUrl":"10.1007/s00335-026-10197-5","url":null,"abstract":"<p><p>Beetal goats, the second largest indigenous goat breed in India, are known for their superior growth and production traits. In this study, we performed a comprehensive genome-wide characterization of insertion-deletion (indel) variants in the Beetal goat genome using pooled whole-genome resequencing. Following stringent filtering criteria, a total of 373,084 high-confidence indels were identified in the Beetal goat genome. Chromosome-wise distribution revealed the highest number of variants on Capra hircus chromosome (CHI) 1 (26,590), while CHI 25 showed the lowest (4303). Insertion variants (57.82%) outnumbered deletion variants (42.12%), yielding a deletion-to-insertion ratio of 0.73:1, a pattern distinct from most other mammalian genomes. The identified indel variants were distributed across intergenic (63.07%) and genic (36.93%) regions of the genome. Functional annotation classified 99.88% of the variants as MODIFIER and 0.05% as HIGH-impact, which included frameshift (144), splice site (31), donor disruptions (8) and start codon (1) mutations. Notably, high-impact indel variants were identified in key genes associated with growth and body conformation-LEPR, LCORL and PLAG1-underscoring their potential as candidate markers for larger body size. Functional enrichment analysis of high-impact indel variants using DAVID revealed significant overrepresentation (p ≤ 0.05) of biological processes related to G protein-coupled receptor signalling, immune regulation and innate immunity; molecular functions such as olfactory receptor activity and metal ion binding and KEGG pathways including olfactory transduction and extracellular matrix (ECM)-receptor interaction. These findings provide valuable insights into the functional relevance of indel variants and establish a foundational resource for future genomic selection strategies in Beetal goats.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"29"},"PeriodicalIF":2.6,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fifteen years of the Diversity Outbred mouse model: a review. 15年的多样性近交小鼠模型:综述。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-01-28 DOI: 10.1007/s00335-026-10196-6
Zachary Tatom, Michael F Miles, Abraham A Palmer
{"title":"Fifteen years of the Diversity Outbred mouse model: a review.","authors":"Zachary Tatom, Michael F Miles, Abraham A Palmer","doi":"10.1007/s00335-026-10196-6","DOIUrl":"10.1007/s00335-026-10196-6","url":null,"abstract":"<p><p>Mouse models have played a critical role in complementing human genetics research due to their genetic similarity to humans and well-annotated and tractable genome. For over 15 years, the Diversity Outbred (DO) mice have existed as a powerful tool for mapping complex traits. With eight founder strains contributing to high levels of genetic diversity, heterozygosity, and large numbers of recombination events, DO mice allow for high-resolution genetic mapping. DO mice have been used to dissect the genetic architecture of physiological traits like blood lipids, behavioral traits such as cocaine self-administration, and molecular phenotypes such as gene expression across various tissues. Here we aim to exhaustively catalog DO mouse studies over the last 15 years, including both mapping and non-mapping studies, as well as to provide an overview of software tools and online resources related to the model.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"28"},"PeriodicalIF":2.6,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12852284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of selection signatures in indigenous African cattle reveals genomic footprints of adaptation, production and temperament traits. 对非洲本土牛的选择特征的检测揭示了适应、生产和气质特征的基因组足迹。
IF 2.6 4区 生物学
Mammalian Genome Pub Date : 2026-01-28 DOI: 10.1007/s00335-026-10193-9
Rodney Okwasiimire, Donald R Kugonza, Junxin Gao, Melak Weldenegodguad, Mahlako L Makgahlela, Nasser Ghanem, Catarina Ginja, Richard P M A Crooijmans, Juha Kantanen, Pekka Uimari, Kisun Pokharel
{"title":"Detection of selection signatures in indigenous African cattle reveals genomic footprints of adaptation, production and temperament traits.","authors":"Rodney Okwasiimire, Donald R Kugonza, Junxin Gao, Melak Weldenegodguad, Mahlako L Makgahlela, Nasser Ghanem, Catarina Ginja, Richard P M A Crooijmans, Juha Kantanen, Pekka Uimari, Kisun Pokharel","doi":"10.1007/s00335-026-10193-9","DOIUrl":"10.1007/s00335-026-10193-9","url":null,"abstract":"<p><p>Indigenous cattle account for approximately 80% of Uganda's cattle population. These animals are well adapted to the country's ten agroecological zones and are mainly kept under pastoral and agropastoral systems. Unlike commercial breeds, they thrive on low-quality feeds, while tolerating major tropical diseases and parasites including tsetse flies, ticks, and vector-borne infections. Whole-genome sequence (WGS) analysis offers opportunities to uncover genomic regions underlying these adaptations and to trace the genetic footprints of long-term breeding decisions taken by cattle keepers. In this study, WGS data from 95 animals representing six indigenous cattle populations (Ankole, Karamojong, Nganda10, Nganda17, Nkedi, and Ntuku) were analyzed to identify genomic regions under putative selection. Two complementary approaches were applied: enumeration of the µ-statistic in RAiSD and runs of homozygosity (ROH) analysis. RAiSD identified population-level signals, while conserved ROH regions were defined using breed-specific SNP-incidence thresholds. The two methods identified 803 and 49 candidate genes respectively. The top genes identified included SLC37A1 (BTA1), CHCHD3 (BTA4), and RAB3GAP1 (BTA2) detected by RAiSD, and IL26 (BTA5), FBXL7 (BTA20), and HSPA9 (BTA7) contained in ROH. Furthermore, the regions harbored 107 novel genes (92 detected by RAiSD and 15 by ROH), corresponding to 255 quantitative trait loci. The identified genes under putative selection are associated with economically important traits including adaptation to tropical environments, resistance to parasites and diseases, and other farmer-preferred characteristics. These findings provide insights into the genetic basis of adaptation, selection and production in Ugandan indigenous cattle, supporting conservation and breeding strategies to enhance resilience and productivity.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"27"},"PeriodicalIF":2.6,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12852251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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