Mammalian Genome最新文献

Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-02 DOI: 10.1007/s00335-025-10125-z

Maria Victória Henrique Genuíno, Ayrton Fernandes de Oliveira Bessa, Roney Teixeira da Silva, Giovanna Maria Dos Santos Câmara, João Cláudio do Carmo Panetto, Marco Antônio Machado, Sabrina Luzia Caetano, Salvador Boccaletti Ramos, Danísio Prado Munari, Tad Sonstegard, Marcos Vinícius Gualberto Barbosa da Silva, Marcos Eli Buzanskas

{"title":"Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.","authors":"Maria Victória Henrique Genuíno, Ayrton Fernandes de Oliveira Bessa, Roney Teixeira da Silva, Giovanna Maria Dos Santos Câmara, João Cláudio do Carmo Panetto, Marco Antônio Machado, Sabrina Luzia Caetano, Salvador Boccaletti Ramos, Danísio Prado Munari, Tad Sonstegard, Marcos Vinícius Gualberto Barbosa da Silva, Marcos Eli Buzanskas","doi":"10.1007/s00335-025-10125-z","DOIUrl":"https://doi.org/10.1007/s00335-025-10125-z","url":null,"abstract":"Technological advances in genomics and bioinformatics made it possible to study the genetic structure of breeds and understand genome changes caused by selection over generations. Our objective was to evaluate selection signatures (SS) in Nelore, Gir, and Red Sindhi cattle from Brazil and the Asian continent to identify divergent variants due to the history of formation and selection of populations, with a focus on the SS of animals from Brazil. Extended haplotype homozygosities between populations (XP-EHH), the ratio of site-specific extended haplotype homozygosity between populations (Rsb), and the allelic fixation index (Fst) were used to detect SS. Considering a window size of 50-kb, a non-sliding window approach was used to define SS regions. A total of 62, 57, and 72 genes were co-located within SS regions for Nelore, Gir, and Red Sindhi, respectively, and used to perform functional analyses per breed. Most genes were associated with productive and reproductive traits, while others were related to thermotolerance, the immune system, temperament, and coat color. The identified SS demonstrate how animal breeding programs shape the genetic makeup of these breeds to meet production system requirements, given that animals from Brazil and the Asian continent have undergone different selection processes. The identification of genes related to thermotolerance, temperament, and the immune system suggests specific alleles have enabled animals to adapt to environmental conditions and selection criteria in Brazil. Understanding SS can support breeding strategies for Nelore, Gir, and Red Sindhi cattle, contributing to enhanced resistance, adaptation, and productivity to meet food production demands.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772465","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

Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-02 DOI: 10.1007/s00335-025-10122-2

Nidhi Sukhija, K K Kanaka, Indrajit Ganguly, Satpal Dixit, Sanjeev Singh, Rangasai Chandra Goli, Pallavi Rathi, P B Nandini, Subrata Koloi

{"title":"Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India.","authors":"Nidhi Sukhija, K K Kanaka, Indrajit Ganguly, Satpal Dixit, Sanjeev Singh, Rangasai Chandra Goli, Pallavi Rathi, P B Nandini, Subrata Koloi","doi":"10.1007/s00335-025-10122-2","DOIUrl":"https://doi.org/10.1007/s00335-025-10122-2","url":null,"abstract":"Huge genetic diversity is evident among the diverse goat breeds in terms of production, reproduction, adaptability, growth, disease resistance and thermo-tolerance. This diversity is an outcome of both natural and artificial selection acting on the caprine genome over the years. A fine characterization of whole genome variation is now possible by employing Next Generation Sequencing (NGS) technologies. To explore underlying genetics, genome-wide analysis of genetic markers is the best resolution. The study strived to capture variation in terms of CNV/CNVRs among 11 Indian goat breeds. In this study, the first ever resequencing-based CNV/CNVR distribution of Indigenous goat breeds was delineated, providing a sizable addition to the prior caprine CNVRs reported. Different diversity metrics were analyzed using identified CNVR. Principal component analysis (PCA) showed separate clustering of Kanniadu (KAN) and Jharkhand Black (JB) from other breeds under the study, indicating their unique genetic profile as the former breeds were sampled from institutional farms. The admixture analysis and introgression revealed by f3 statistics suggested distinct genetic structuring of JB, KAN and TEL(Tellicherry) as compared to the rest of the studied populations. Apart from this, we also identified 32 selection signatures through VST (Variance-stabilizing transformation) method and key genes such as ZBTB7C, BHLHE22, AGT were found elucidating the genetic architecture of hot and cold adaptation in Indian goats. Information generated hereby in the form of 32,711 autosomal CNVRs and the custom scripts ( https://github.com/kkokay07/Climate-Variables-Analysis.git , https://github.com/chau-mau/SelectCNVR.git and https://github.com/chau-mau/CNVrecaller.git ) will be of relevance in further studies on copy number based genetics.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772349","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

Identification and validation of mitochondrial endoplasmic reticulum membrane-related genes in atherosclerosis.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-28 DOI: 10.1007/s00335-025-10124-0

Li-Rong Wang, Chun-Xi Zhang, Lv-Bo Tian, Jie Huang, Li-Jun Jia, Hao Tao, Neng-Wei Yu, Bing-Hu Li

引用次数: 0

The mouse resource at National Resource Center for Mutant Mice of China.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-27 DOI: 10.1007/s00335-025-10118-y

Bingzhou Han, Dongshen Chen, Zhong Chen, Ting Wang, Kaiyuan Zi, Rui Feng, Xiaoliu Yang, Ling'en Li, Juan Liang, Xiang Gao

引用次数: 0

The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-25 DOI: 10.1007/s00335-025-10123-1

Lucie Chevallier, Marin Green, Julia Vo, Karen Vernau, Denis J Marcellin-Little, Vidhya Jagannathan, Tosso Leeb, Danika Bannasch

{"title":"The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas.","authors":"Lucie Chevallier, Marin Green, Julia Vo, Karen Vernau, Denis J Marcellin-Little, Vidhya Jagannathan, Tosso Leeb, Danika Bannasch","doi":"10.1007/s00335-025-10123-1","DOIUrl":"https://doi.org/10.1007/s00335-025-10123-1","url":null,"abstract":"Bilateral anterior amelia (BAA) is the congenital absence of thoracic limbs and has been reported in the Chihuahua as an autosomal recessive disorder. In some cases, the digits of the pelvic limbs can be variably affected, but otherwise, the pelvic limbs are generally spared. A GWAS performed with nine BAA affected Chihuahuas identified a significant association on chromosome 13, and homozygosity mapping delineated a 2.1 Mb chromosomal region containing the RSPO2 gene. Loss of function variants of RSPO2 in humans and cattle has been associated with the absence of all limbs. Six affected Chihuahuas were whole genome sequenced (WGS) and aligned to the CanFam4 assembly. SNVs, small indels, and structural variants within the critical interval that fitted a recessive model were investigated. Three SNVs (NC_049234.1:g.8891861C > T; NC_049234.1:g.8974204C > T and NC_049234.1:g.9789424G > A) were homozygous in five cases and absent from 3,418 genetically diverse control genome sequences, except for one Small Poodle that was heterozygous. One SNV resided in RSPO2's second intron, while the two others were intergenic. The three candidate variants were genotyped in 7 additional cases and 100 control Chihuahuas. Twelve of 13 cases were homozygous for the mutant allele, and one case was heterozygous. Controls were either homozygous for the reference allele (97%) or heterozygous (3%). Our data should facilitate genetic testing of Chihuahuas to prevent the unintentional production of BAA affected dogs. Moreover, the identification of these variants enhances understanding of RSPO2 gene function in limb development.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710595","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

Identification of NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-19 DOI: 10.1007/s00335-025-10117-z

Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen

{"title":"Identification of NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis.","authors":"Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen","doi":"10.1007/s00335-025-10117-z","DOIUrl":"https://doi.org/10.1007/s00335-025-10117-z","url":null,"abstract":"Neutrophil extracellular traps (NETs) are increasingly recognized for their involvement in ischemic stroke (IS), yet their precise contribution to IS outcomes is not fully understood. This study aims to elucidate the role of NETs in IS progression and identify potential biomarkers and therapeutic targets. In this study, mice were subjected to middle cerebral artery occlusion (MCAO). RNA sequencing was conducted on brain tissue samples to identify differentially expressed genes (DEGs) using the \"limma\" package. The diagnostic potential of these biomarkers was assessed using receiver operating characteristic (ROC) curve analysis. Additionally, single-cell RNA sequencing data were analyzed with the Seurat package to further investigate the cellular dynamics. We identified DEGs, and NETs-related genes associated with IS progression. Specifically, Ceacam3, Tnf, Selp, and Fcgr4 were found to be upregulated in MCAO samples, exhibiting diagnostic value as biomarkers for IS. Immune infiltration analysis indicated associations between these genes and various immune cell types. Gene Set Enrichment Analysis (GSEA) revealed their involvement in IS-related pathways, including ferroptosis, IL-17 signaling, leukocyte transendothelial migration, necroptosis, and NETs formation. Single-cell data confirmed the expression of Tnf, Selp, and Fcgr4 in neutrophils. CellChat analysis uncovered key cell-cell interactions in IS, emphasizing the role of neutrophils in communicating with microglia and T cells via the JAM pathway, with Thbs1 and Cd47 as key mediators. The findings provide insights into the cellular and molecular mechanisms underlying IS and may pave the way for novel therapeutic strategies targeting NETs in IS patients.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663921","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

Rat models of musculoskeletal lysosomal storage disorders and their role in pre-clinical evaluation of gene therapy approaches.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-18 DOI: 10.1007/s00335-025-10121-3

Sara Marcó, Sergio Muñoz, Fatima Bosch, Veronica Jimenez

{"title":"Rat models of musculoskeletal lysosomal storage disorders and their role in pre-clinical evaluation of gene therapy approaches.","authors":"Sara Marcó, Sergio Muñoz, Fatima Bosch, Veronica Jimenez","doi":"10.1007/s00335-025-10121-3","DOIUrl":"https://doi.org/10.1007/s00335-025-10121-3","url":null,"abstract":"Mice have been a cornerstone of biomedical research for decades for studying a wide range of biological processes, disease mechanisms, and the assessment of therapies. Moreover, mice present several practical advantages such as small size, low cost and ease of genetic manipulation. While mice offer numerous benefits, for certain disease areas, rat models provide a closer representation of human disease progression, offering better insights for translational research and therapeutic development. This closer resemblance is particularly important for research focusing on diseases involving the cardiovascular and musculoskeletal system. In rats, the pathophysiology of these diseases mirrors the clinical alterations observed in humans. This review focuses on the key phenotypic differences between mouse and rat models of lysosomal storage disorders that specifically manifest with cardiac, skeletal muscle, and bone and joint involvement (Pompe and Danon diseases, and Maroteaux-Lamy and Morquio A syndromes). Furthermore, we discuss the therapeutic potential of various adeno-associated viral vector-mediated gene therapies that have been evaluated in these rat models, highlighting their contributions to advancing treatment options for these debilitating conditions.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657668","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

The power of mouse models in the diagnostic odyssey of patients with rare congenital anomalies.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-18 DOI: 10.1007/s00335-025-10114-2

Stephen R F Twigg, Nicholas D E Greene, Deborah J Henderson, Pleasantine Mill, Karen J Liu

{"title":"The power of mouse models in the diagnostic odyssey of patients with rare congenital anomalies.","authors":"Stephen R F Twigg, Nicholas D E Greene, Deborah J Henderson, Pleasantine Mill, Karen J Liu","doi":"10.1007/s00335-025-10114-2","DOIUrl":"https://doi.org/10.1007/s00335-025-10114-2","url":null,"abstract":"Congenital anomalies are structural or functional abnormalities present at birth, which can be caused by genetic or environmental influences. The availability of genome sequencing has significantly increased our understanding of congenital anomalies, but linking variant identification to functional relevance and definitive diagnosis remains challenging. Many genes have unknown or poorly understood functions, and with a lack of clear genotype-to-phenotype correlations, it can be difficult to move from variant discovery to diagnosis. Thus, for most congenital anomalies, there still exists a \"diagnostic odyssey\" which presents a significant burden to patients, families and society. Animal models are essential in the gene discovery process because they allow researchers to validate candidate gene function and disease progression within intact organisms. However, use of advanced model systems continues to be limited due to the complexity of efficiently generating clinically relevant animals. Here we focus on the use of precisely engineered mice in variant-to-function studies for resolving molecular diagnoses and creating powerful preclinical models for congenital anomalies, covering advances in genomics, genome editing and phenotyping approaches as well as the necessity for future initiatives aligning animal modelling to deep patient multimodal datasets.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657669","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

Unraveling the brain-joint axis: genetic, transcriptomic, and cohort insights from neuroticism to osteoarthritis.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-13 DOI: 10.1007/s00335-025-10112-4

Jingwei Zhang, Yingjie Li, Yongzhen Li, Hongwei Liu

{"title":"Unraveling the brain-joint axis: genetic, transcriptomic, and cohort insights from neuroticism to osteoarthritis.","authors":"Jingwei Zhang, Yingjie Li, Yongzhen Li, Hongwei Liu","doi":"10.1007/s00335-025-10112-4","DOIUrl":"https://doi.org/10.1007/s00335-025-10112-4","url":null,"abstract":"The causal relationships between neuroticism and osteoarthritis (OA) were inconclusive in observational studies. We conducted bidirectional two-sample Mendelian randomization (MR) and transcriptome-wide association studies to determine the associations and the underlying transcriptomic basis. The summary-level genome-wide association study data for any site OA, knee OA, erosive hand OA, and hip OA were mainly derived from UK Biobank, and neuroticism was derived from CTGlab. We then utilized weighted regression and propensity score matching (PSM) models to investigate the relationship between neuroticism and OA in 11,948 participants of European ancestry from the National Health and Nutrition Examination Survey from 2005 to 2018. Bidirectional two-sample MR studies revealed that feelings of being fed-up, a sense of miserableness, mood swings, and a higher neuroticism score were all linked to an increased risk of OA. These factors were specifically associated with OA at various sites, including the knee. Conversely, there was no evidence to suggest that OA had any influence on traits related to neuroticism. In a comprehensive analysis that accounted for variables such as age, sex, blood lipids, blood glucose, body weight, smoking, alcohol consumption, and physical activity, it was determined that mental fluctuation significantly increased the incidence of self-reported OA (OR 1.37, 95% CI 1.20-1.58, P < 0.001) based on weighted regression. Further confirmation was provided by PSM analysis, which showed that mental fluctuation was associated with a higher incidence of self-reported OA (OR 1.28, 95% CI 1.08-1.52, P = 0.004). Moreover, differentially expressed genes were enriched in several biological processes, including the cell cycle, lipid metabolism, RNA processing, and immuno-inflammatory responses. The results revealed significant genetic and population-based associations, as well as underlying mechanisms, between neuroticism and osteoarthritis, supporting the concept of a brain-joint axis.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625263","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

Exploring the therapeutic effect of melatonin targeting common biomarkers in testicular germ cell tumor, prostate adenocarcinoma, and male infertility: an integrated biology approach.

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-08 DOI: 10.1007/s00335-025-10119-x

Uddesh Ramesh Wanjari, Abilash Valsala Gopalakrishnan

{"title":"Exploring the therapeutic effect of melatonin targeting common biomarkers in testicular germ cell tumor, prostate adenocarcinoma, and male infertility: an integrated biology approach.","authors":"Uddesh Ramesh Wanjari, Abilash Valsala Gopalakrishnan","doi":"10.1007/s00335-025-10119-x","DOIUrl":"10.1007/s00335-025-10119-x","url":null,"abstract":"Globally, male infertility (MI) is a major concern. Several other comorbidities related to MI are testicular germ cell tumor (TGCT) and prostate adenocarcinoma (PRAD). This study focuses on finding the common biomarkers among these diseases and their interaction with Melatonin (MLT). The differential expressed genes were retrieved using the GEPIA2 database for TGCT and PRAD, whereas the DISGENET database for MI-related genes. InteractiVenn was performed in response to identify the common genes. The STAG3, RNF212, DDX3Y, DPY19L2, TPCN1, KLK3, GNRH1, DMD, CCDC146, and DNAH1 are found to be involved in all these diseases. The gene ontologies and pathway enrichment analysis were done for these significant genes in response to identifying and accessing the involvement of these genes in other processes. MLT is a neuroendocrine hormone with high therapeutic properties. MLT showed the best binding energy with DDX3Y among all the proteins. Molecular dynamic simulation (MDS) of MLT with DDX3Y was performed and found to be -52.382 ± 13.110 kJ/mol binding energy. The RMSD, RMSF, SASA, RG, H-bond, FEL, PCA, and MM-PBSA analysis confirm the stability and compactness of the DDX3Y-MLT complex. The MDS results indicate that MLT is a promising therapeutic option for enhancing DDX3Y expression, which will support spermatogenesis. Additionally, the hub genes were identified based on MCC parameters from the merged interactive network of common genes in response to finding significant genes that can be a potential biomarker for the diagnosis of diseases.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582319","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