Mammalian Genome最新文献

{"title":"Genetic factors underlying Mandibular prognathism: insights from recent human and animal studies.","authors":"Han Fang, Peiran Li, Songsong Zhu, Ruiye Bi","doi":"10.1007/s00335-024-10084-x","DOIUrl":"10.1007/s00335-024-10084-x","url":null,"abstract":"<p><p>This review aims to provide an updated overview of the genetic etiology of mandibular prognathism (MP), focusing on recent research efforts, to summarize the findings from human studies utilizing genome-wide association studies (GWAS), candidate gene analyses, whole exome sequencing (WES) and single-nucleotide polymorphisms (SNPs) in relation to MP. Additionally, insights from animal studies are incorporated to understand the molecular mechanisms underlying mandibular development and the pathogenesis of MP. A comprehensive literature search was conducted to identify relevant studies on the genetic basis of MP. Human studies employing GWAS, candidate gene analyses, and SNPs investigations were reviewed. Animal studies, including European seabass, zebrafish, transgenic mouse and miniature horse were also examined to provide additional insights into mandibular development and MP's pathogenesis using GWAS, WES, transgenic techniques, morpholino antisense oligos and homozygote. Human studies have identified multiple loci and genes potentially associated with MP through GWAS, candidate gene analyses, and SNP investigations. Animal models have contributed valuable information about the molecular mechanisms involved in mandibular development and the development of MP. Recent research efforts have enhanced our understanding of the genetic etiology of MP. Integration of genetic studies with functional analyses has shed light on key signaling pathways and gene regulatory networks implicated in MP.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"293-305"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739882","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}

{"title":"Establishing the hybrid rat diversity program: a resource for dissecting complex traits.","authors":"M R Dwinell, A Takizawa, M Tutaj, L Malloy, R Schilling, A Endsley, W M Demos, J R Smith, S J Wang, J De Pons, A Kundurthi, A M Geurts, A E Kwitek","doi":"10.1007/s00335-024-10102-y","DOIUrl":"10.1007/s00335-024-10102-y","url":null,"abstract":"<p><p>Rat models have been a major model for studying complex disease mechanisms, behavioral phenotypes, environmental factors, and for drug development and discovery. Inbred rat strains control for genetic background and allow for repeated, reproducible, cellular and whole animal phenotyping. The Hybrid Rat Diversity Panel (HRDP) was designed to be a powerful panel of inbred rats with genomic, physiological, and behavioral data to serve as a resource for systems genetics. The HRDP consists of 96-98 inbred rat strains aimed to maximize power to detect specific genetic loci associated with complex traits while maximizing the genetic diversity among strains. The panel consists of 32-34 genetically diverse inbred strains and two panels of recombinant inbred panels. To establish the HRDP program, embryo resuscitation and breeding were done to establish colonies for distribution. Whole genome sequencing was performed to achieve 30X coverage. Genomic, phenotype, and strain information is available through the Hybrid Rat Diversity Panel Portal at the Rat Genome Database ( http://rgd.mcw.edu ).</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"25-37"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189806","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}

{"title":"Integrative approaches to m6A and m5C RNA modifications in autism spectrum disorder revealing potential causal variants.","authors":"Syed Mansoor Jan, Aamir Fahira, Eman S G Hassan, Ali Saber Abdelhameed, Dongqing Wei, Abdul Wadood","doi":"10.1007/s00335-024-10095-8","DOIUrl":"10.1007/s00335-024-10095-8","url":null,"abstract":"<p><p>Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that currently affects approximately 1-2% of the global population. Genome-wide studies have identified several loci associated with ASD; however, pinpointing causal variants remains elusive. Therefore, functional studies are essential to discover potential therapeutics for ASD. RNA modification plays a crucial role in the post-transcriptional regulation of mRNA, with m6A and m5C being the most prevalent internal modifications. Recent research indicates their involvement in the regulation of key genes associated with ASD. In this study, we conducted an integrative genomic analysis of ASD, incorporating m6A and m5C variants, followed by cis-eQTL, gene differential expression, and gene enrichment analyses to identify causal variants from a genome-wide study of ASD. We identified 20,708 common m6A-SNPs and 2,407 common m5C-SNPs. Among these, 647 m6A-SNPs exhibited cis-eQTL signals with a p-value < 0.05, while only 81 m5C-SNPs with a p-value < 0.05 showed cis-eQTL signals. Most of these were functional loss variants, with 38 variants representing the most significant common m6A/m5C-SNPs associated with key ASD-related genes. In the gene differential expression analysis, seven proximal genes corresponding to significant m6A/m5C-SNPs were differentially expressed in at least one of the three microarray gene expression profiles of ASD. Key differentially expressed genes corresponding to m6A/m5C cis-variants included KIAA1671 (rs5752063, rs12627825), INTS1 (rs67049052, rs10237910), VSIG10 (rs7965350), TJP2 (rs3812536), FAM167A (rs9693108), TMEM8A (rs1802752), and NUP43 (rs3924871, rs7818, rs9383844, rs9767113). Cell-specific cis-eQTL analysis for proximal gene identification, combined with gene expression datasets from single-cell RNA-seq analysis, would validate the causal relationship of gene regulation in brain-specific regions, and experimental validation in cell lines would achieve the goal of precision medicine.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"280-292"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909950","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}

{"title":"Investigating DNA damage caused by COVID-19 and influenza in post COVID-19.","authors":"Elaheh Abiri, Mehdi Mirzaii, Majid Moghbeli, Amir Atashi, Ahad Ali Harati","doi":"10.1007/s00335-024-10082-z","DOIUrl":"10.1007/s00335-024-10082-z","url":null,"abstract":"<p><p>The SARS-CoV-2 virus (termed COVID-19) was responsible for over 34 million global deaths. Although the COVID-19 pandemic has subsided, infection by emerging mutant variants of SARS-CoV-2 poses a continuing threat to public health. COVID-19 infection has been associated with the development of cytokine storm syndrome, hypercoagulability, immunological dysregulation and direct viral invasion of organs, and the long-term consequences for the health of COVID-19 survivors are currently unknown. Our research focuses on the possible mutagenic aspects of infection by COVID-19 and measures their harmful effects on DNA composition. DNA damage was investigated, using the comet assay method, during two periods: in the epidemic peak of COVID-19 and during the post-COVID-19 period, both in patients infected with COVID-19 and in those with influenza. During the epidemic peak, the levels of DNA damage ranged from the highest to the lowest levels in the following groups, respectively: intubated-ICU, non-intubated-ICU, non-ICU, and influenza, with a discernible increase in DNA damage in ICU-treated patients. The levels of DNA damage in the post-COVID-19 period were significantly lower compared to those in the epidemic peak period but there was still a discernible increase in DNA damage in the ICU group. Our results indicate that levels of DNA damage may be an effective indicator in prognostic decision-making and may therefore help to reduce mortality. Given that DNA damage and impaired repair processes can contribute to chronic diseases like diabetes, cancer, and neurodegenerative conditions, it will be crucial to investigate potential similar effects in patients with COVID-19.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"200-212"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142623356","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}

{"title":"Biological mechanism and functional verification of key genes related to major depressive disorder and type 2 diabetes mellitus.","authors":"Tao Fang, Na Shen, Zhemin Shi, Weishun Luo, Yanbo Di, Xuan Liu, Shengnan Ma, Jing Wang, Shike Hou","doi":"10.1007/s00335-024-10090-z","DOIUrl":"10.1007/s00335-024-10090-z","url":null,"abstract":"<p><p>Major depressive disorder (MDD) and type 2 diabetes (T₂D) have been shown to be linked, but a comprehensive understanding of the underlying molecular mechanisms remains elusive. The purpose of this study was to explore the biological relationship between MDD and T₂D and verify the functional roles of key genes. We used the Gene Expression Omnibus database to investigate the targets associated with MDD and T₂D. Using linear models for microarray data, differentially expressed genes associated with MDD and T₂D were identified in GSE76826 and GSE95849, respectively, and 126 shared genes were significantly upregulated. Weighted gene coexpression network analysis identified modules associated with MDD and T₂D in the GSE38206 and GSE20966 datasets and identified 8 common genes. Functional enrichment analysis revealed that these genes were enriched in cell signaling, enzyme activity, cell structure and amino acid biosynthesis and involved in cell death pathways. Finally, combined with the CTD and GeneCards databases, lysophosphatidylglycerol acyltransferase 1 (LPGAT1) was identified as a key gene. LPGAT1 was validated in GSE201332 and GSE182117, and the subject operating characteristic curve showed good diagnostic potential for MDD and T₂D. Additionally, we used an in vitro model of MDD related to T₂D to verify the expression of LPGAT1. A subsequent gene knockdown assay revealed that the downregulation of LPGAT1 improved mitochondrial function and reduced apoptosis in damaged neurons. Taken together, our results highlight the role of LPGAT1 in the connection between MDD and T₂D, and these findings provide new insights into potential therapeutic targets for depression associated with diabetes.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"66-82"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801471","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}

{"title":"Identification of a critical interval for type 2 diabetes QTL on chromosome 4 in DDD-A^y mice.","authors":"Jun-Ichi Suto, Misaki Kojima","doi":"10.1007/s00335-025-10106-2","DOIUrl":"10.1007/s00335-025-10106-2","url":null,"abstract":"<p><p>Type 2 diabetes mellitus (T2D) in male KK-A^y and B6-A^y mice is typically associated with hyperinsulinemia, whereas male DDD-A^y mice exhibit a marked decrease in circulating insulin levels due to the loss of pancreatic islet β-cells. T2D in male DDD-A^y mice is linked to Nidd/DDD, a significant quantitative trait locus (QTL) mapped with a 95% confidence interval (CI) between 112.44 and 151.47 Mbp on chromosome 4. Several T2D QTLs involving Nidd/SJL and Nidd/DBA have been identified on this chromosome; however, their allelic relationships remain unclear. In this study, two sets of male F₂-A^y mice produced by crossing C57BL/6J and DDD-A^y mice, and C3H/HeJ and DDD-A^y mice, were used to narrow the 95% CI of the Nidd/DDD to a 9.4 Mbp interval between 114.65 and 125.05 Mbp. Candidate genes underlying Nidd/DDD were identified, assuming that the causative variant is a nonsynonymous single nucleotide variant (nsSNV). The analysis identified 48 potential candidate nsSNVs unique to DDD-A^y mice compared to those in KK, B6, C3H, and DBA mice. Among these nsSNVs, 18 were identified in olfactory receptor genes, which have recently been implicated in the pathogenesis of T2D. The 9.4 Mbp region also contained Zfp69, a potential causative gene for Nidd/SJL, suggesting that Nidd/DDD could be allelic to Nidd/SJL but not to Nidd/DBA. In summary, the findings of this study provide insights into the allelic relationships between T2D QTLs on murine chromosome 4 and their underlying causative genetic variations.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"53-65"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008020","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}

{"title":"Deciphering the molecular drivers for cashmere/pashmina fiber production in goats: a comprehensive review.","authors":"Mahanthi Vasu, Sonika Ahlawat, Reena Arora, Rekha Sharma","doi":"10.1007/s00335-025-10109-z","DOIUrl":"10.1007/s00335-025-10109-z","url":null,"abstract":"<p><p>Cashmere, also known as pashmina, is derived from the secondary hair follicles of Cashmere/Changthangi goats. Renowned as the world's most luxurious natural fiber, it holds significant economic value in the textile industry. This comprehensive review enhances our understanding of the complex biological processes governing cashmere/pashmina fiber development and quality, enabling advancements in selective breeding and fiber enhancement strategies. The review specifically examines the molecular determinants influencing fiber development, with an emphasis on keratins (KRTs) and keratin-associated proteins (KRTAPs). It also explores the roles of key molecular pathways, including Wnt, Notch, BMP, NF-kappa B, VEGF, cAMP, PI3K-Akt, ECM, cell adhesion, Hedgehog, MAPK, Ras, JAK-STAT, TGF-β, mTOR, melanogenesis, FoxO, Hippo, and Rap1 signaling. Understanding these intricate molecular cascades provides valuable insights into the mechanisms orchestrating hair follicle growth, further advancing the biology of this coveted natural fiber. Expanding multi-omics approaches will enhance breeding precision and deepen our understanding of molecular pathways influencing cashmere production. Future research should address critical gaps, such as the impact of environmental factors, epigenetic modifications, and functional studies of genetic variants. Collaboration among breeders, researchers, and policymakers is essential for translating genomic advancements into practical applications. Such efforts can promote sustainable practices, conserve biodiversity, and ensure the long-term viability of high-quality cashmere production. Aligning genetic insights with conservation strategies will support the sustainable growth of the cashmere industry while preserving its economic and ecological value.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"162-182"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189777","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}

{"title":"Unraveling the genetic and physiological potential of donkeys: insights from genomics, proteomics, and metabolomics approaches.","authors":"Ram Parsad, Meena Bagiyal, Sonika Ahlawat, Reena Arora, Ritika Gera, Pooja Chhabra, Upasna Sharma","doi":"10.1007/s00335-024-10083-y","DOIUrl":"10.1007/s00335-024-10083-y","url":null,"abstract":"<p><p>Donkeys (Equus asinus) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultural, and medical industries. Despite their critical importance, research on donkeys has historically been overshadowed with studies on horses. However, recent advancements in high-throughput sequencing and bioinformatics have significantly deepened our understanding of the molecular landscape of donkey genome, uncovering their unique adaptations, genetic diversity, and potential therapeutic applications. Microsatellite and mitochondrial DNA (mtDNA) markers have proven effective in assessing the genetic diversity of donkeys across various regions of the world. Additionally, significant strides have been made in characterizing differentially abundant genes, proteins, and metabolic profiles in donkey milk, meat, and skin, and in identifying specific genes/proteins/metabolites associated with sperm quality, motility, and reproduction. Advanced genomic technologies, such as genome-wide association studies and the identification of selection signatures, have also been instrumental in delineating genomic regions associated with phenotypic and adaptive traits. This review integrates data from diverse studies, including those on genetic diversity, transcriptomics, whole genome sequencing, protein analysis, and metabolic profiling, to provide a comprehensive overview of donkey biology. It underscores the unique characteristics of donkeys and emphasizes the importance of continued research to improve their genetic management, conservation, and agricultural use, ensuring their ongoing contribution to human societies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"10-24"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605183","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}

{"title":"Correction: A fascination with tailless mice: a scientific historical review of studies of the T/t complex.","authors":"Robert P Erickson","doi":"10.1007/s00335-024-10087-8","DOIUrl":"10.1007/s00335-024-10087-8","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"52"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739881","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}

{"title":"The effect of different approaches to determining the regularization parameter of bayesian LASSO on the accuracy of genomic prediction.","authors":"Hamid Sahebalam, Mohsen Gholizadeh, Seyed Hassan Hafezian","doi":"10.1007/s00335-024-10088-7","DOIUrl":"10.1007/s00335-024-10088-7","url":null,"abstract":"<p><p>Using dense genomic markers opens up new opportunities and challenges for breeding programs. The need to penalize marker-specific regression coefficients becomes particularly important when dense markers are available. Therefore, fitting the marker effects to observations using a regularization technique, such as Bayesian LASSO (BL) regression, is of great interesting. When the Laplace prior distribution is applied to the regression coefficients, BL can be interpreted as a regularization of the <math><mrow><mspace></mspace> <mi>L</mi> <mn>1</mn></mrow> </math> norm based on the Bayesian approach. A critical issue is the appropriate selection of hyperparameters values in the prior distributions of regularization techniques, as these values essentially control the sparsity in the estimated model. The purpose of this study was to evaluate different approaches for selecting the regularization parameter in BL, based on fully Bayesian approaches-such as gamma prior (BL_Gamma), beta prior (BL_Beta) and fixed prior (BL_Fixed) as well as data-driven approaches like cross-validation based on mean square error (BL_CV_MSE) and prediction accuracy (BL_CV_PA). Additionally, information-criteria-based methods including Akaike's information criterion (BL_AIC), Bayesian information criterion (BL_BIC) and Deviance information criterion (BL_DIC), were explored. For this purpose, a genome containing eight chromosomes (each 1 Morgan in length) with 100 randomly distributed quantitative trait loci was simulated. The studied scenarios were as follows: Scenario 1 involved 4000 markers and heritability of 0.2, scenario 2 involved 4000 markers and heritability of 0.6, scenario 3 involved 16,000 markers and heritability of 0.2; and scenario 4 involved 16,000 markers and heritability of 0.6. The results showed that among the fully Bayesian and cross-validation approaches, BL_Gamma, BL_Beta, and BL_CV_MSE provided the highest prediction accuracy (PA) in scenario 1 and 3. With increased marker density and heritability (scenario 4), the cross-validation approaches performed slightly better. The information-criteria-based methods demonstrated the lowest PA. Increasing heritability and marker density led to a decrease and an increase in the model penalty on the regression coefficients, respectively. The PA obtained in the target population ranged from 0.210 to 0.413 in Scenario 1, 0.402 to 0.600 in Scenario 2, 0.256 to 0.442 in Scenario 3, and 0.478 to 0.653 in Scenario 4. In generally, fully Bayesian approaches based on random priors for the regularization parameter are recommended for BL, as they provide acceptable PA with lower computational loads.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"331-345"},"PeriodicalIF":2.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807598","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}