Mammalian Genome最新文献_第7页

Elucidation of genetic determinants of dyslipidaemia using a global screening array for the early detection of coronary artery disease. 利用冠状动脉疾病早期检测的全球筛选阵列阐明血脂异常的遗传决定因素。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-09-05 DOI: 10.1007/s00335-023-10017-0

Ananthaneni Radhika, Sandeepta Burgula, Chandan Badapanda, Tajamul Hussain, Shaik Mohammad Naushad

{"title":"Elucidation of genetic determinants of dyslipidaemia using a global screening array for the early detection of coronary artery disease.","authors":"Ananthaneni Radhika, Sandeepta Burgula, Chandan Badapanda, Tajamul Hussain, Shaik Mohammad Naushad","doi":"10.1007/s00335-023-10017-0","DOIUrl":"10.1007/s00335-023-10017-0","url":null,"abstract":"Dyslipidemia is a major risk factor for the development of coronary artery disease (CAD). Understanding the genetic determinants of dyslipidemia can provide valuable information on the pathogenesis of CAD and aid in the development of early detection strategies. In this study, we used a Global Screening Array (GSA) to elucidate the genetic factors associated with dyslipidemia and their potential role in the prediction of CAD. We conducted a GSA-based association study in 265 subjects to identify the genetic loci associated with dyslipidemia traits using Multiple Linear Regression (MLR) and Logistic Regression (LR), Classification and Regression Tree (CART), and Manhattan plots. We identified an association between dyslipidemia and variants identified in genes such as JCAD, GLIS3, CD38, FN1, CELSR2, MTNR1B, GIPR, DYM, APOB, APOE, ADCY5. The MLR models explained 62%, 71%, and 81% of the variability in HDL, LDL, and triglycerides, respectively. The Area Under the Curve (AUC) values in the LR models of HDL, LDL, and triglycerides were 1.00, 0.94, and 0.95, respectively. CART models identified novel gene-gene interactions influencing the risk for dyslipidemia. To conclude, we have identified the association of 12 SNVs with dyslipidemia and demonstrated their clinical utility in four different models such as MLR, LR, CART, and Manhattan plots. The identified genetic variants and associated pathways shed light on the underlying biology of dyslipidemia and offer potential avenues for precision medicine strategies in the management of CAD.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10508800","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

Recent advances in the genomic resources for sheep. 绵羊基因组资源的最新进展。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-09-26 DOI: 10.1007/s00335-023-10018-z

Shernae A Woolley, Mazdak Salavati, Emily L Clark

引用次数: 0

Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale. 巴基斯坦杂交奶牛的遗传学见解：在全基因组范围内探索等位基因频率、连锁不平衡和有效种群规模。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-10-07 DOI: 10.1007/s00335-023-10019-y

Fakhar Un Nisa, Haiba Kaul, Muhammad Asif, Imran Amin, Raphael Mrode, Shahid Mansoor, Zahid Mukhtar

{"title":"Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale.","authors":"Fakhar Un Nisa, Haiba Kaul, Muhammad Asif, Imran Amin, Raphael Mrode, Shahid Mansoor, Zahid Mukhtar","doi":"10.1007/s00335-023-10019-y","DOIUrl":"10.1007/s00335-023-10019-y","url":null,"abstract":"Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r2 statistics. LD value declined as inter-marker distance increased. The average r2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50-100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41137787","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

GWAS reveals genomic associations with swine inflammation and necrosis syndrome. GWAS揭示了与猪炎症和坏死综合征的基因组关联。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-08-01 DOI: 10.1007/s00335-023-10011-6

Katharina Gerhards, Sabrina Becker, Josef Kuehling, Mirjam Lechner, Jochen Bathke, Hermann Willems, Gerald Reiner

{"title":"GWAS reveals genomic associations with swine inflammation and necrosis syndrome.","authors":"Katharina Gerhards, Sabrina Becker, Josef Kuehling, Mirjam Lechner, Jochen Bathke, Hermann Willems, Gerald Reiner","doi":"10.1007/s00335-023-10011-6","DOIUrl":"10.1007/s00335-023-10011-6","url":null,"abstract":"The recently identified swine inflammation and necrosis syndrome (SINS) occurs in high prevalence from newborn piglets to fattening pigs and resembles an important concern for animal welfare. The primary endogenous syndrome affects the tail, ears, teats, coronary bands, claws and heels. The basis of clinical inflammation and necrosis has been substantiated by histopathology, metabolomic and liver transcriptomic. Considerable variation in SINS scores is evident in offspring of different boars under the same husbandry conditions. The high complexity of metabolic alterations and the influence of the boar led to the hypothesis of a polygenic architecture of SINS. This should be investigated by a genome-wide association study. For this purpose, 27 sows were simultaneously inseminated with mixed semen from two extreme boars. The mixed semen always contained ejaculate from a Pietrain boar classified as extremely SINS susceptible and additionally either the ejaculate from a Pietrain boar classified as SINS stable or from a Duroc boar classified as SINS stable. The 234 piglets were phenotyped on day 3 of life, sampled and genetically assigned to the respective boar. The piglets showed the expected genetic differentiation with respect to SINS susceptibility. The suspected genetic complexity was confirmed both in the number and genome-wide distribution of 221 significantly associated SNPs, and led to 49 candidate genes. As the SNPs were almost exclusively located in noncoding regions, functional nucleotides have not yet been identified. The results suggest that the susceptibility of piglets to SINS depends not only on environmental conditions but also on genomic variation.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9912110","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

Swine global genomic resources: insights into wild and domesticated populations. 全球猪基因组资源：对野生和驯养种群的深入了解。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-10-07 DOI: 10.1007/s00335-023-10012-5

Neal R Benjamin, Richard P M A Crooijmans, Luke R Jordan, Courtni R Bolt, Lawrence B Schook, Kyle M Schachtschneider, Martien A M Groenen, Alfred L Roca

{"title":"Swine global genomic resources: insights into wild and domesticated populations.","authors":"Neal R Benjamin, Richard P M A Crooijmans, Luke R Jordan, Courtni R Bolt, Lawrence B Schook, Kyle M Schachtschneider, Martien A M Groenen, Alfred L Roca","doi":"10.1007/s00335-023-10012-5","DOIUrl":"10.1007/s00335-023-10012-5","url":null,"abstract":"Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41154981","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

Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data. 利用纯种和杂交基因组数据对奶牛进行综合选择特征分析。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-10-16 DOI: 10.1007/s00335-023-10021-4

Sonali Sonejita Nayak, Manjit Panigrahi, Divya Rajawat, Kanika Ghildiyal, Anurodh Sharma, Subhashree Parida, Bharat Bhushan, B P Mishra, Triveni Dutt

{"title":"Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data.","authors":"Sonali Sonejita Nayak, Manjit Panigrahi, Divya Rajawat, Kanika Ghildiyal, Anurodh Sharma, Subhashree Parida, Bharat Bhushan, B P Mishra, Triveni Dutt","doi":"10.1007/s00335-023-10021-4","DOIUrl":"10.1007/s00335-023-10021-4","url":null,"abstract":"The main objective of the current research was to locate, annotate, and highlight specific areas of the bovine genome that are undergoing intense positive selection. Here, we are analyzing selection signatures in crossbred (Bos taurus X Bos indicus), taurine (Bos taurus), and indicine (Bos indicus) cattle breeds. Indicine cattle breeds found throughout India are known for their higher heat tolerance and disease resilience. More breeds and more methods can provide a better understanding of the selection signature. So, we have worked on nine distinct cattle breeds utilizing seven different summary statistics, which is a fairly extensive approach. In this study, we carried out a thorough genome-wide investigation of selection signatures using bovine 50K SNP data. We have included the genotyped data of two taurine, two crossbreds, and five indicine cattle breeds, for a total of 320 animals. During the 1950s, these indicine (cebuine) cattle breeds were exported with the aim of enhancing the resilience of taurine breeds in Western countries. For this study, we employed seven summary statistics, including intra-population, i.e., Tajima's D, CLR, iHS, and ROH and inter-population statistics, i.e., FST, XP-EHH, and Rsb. The NCBI database, PANTHER 17.0, and CattleQTL database were used for annotation after finding the important areas under selection. Some genes, including EPHA6, CTNNA2, NPFFR2, HS6ST3, NPR3, KCNIP4, LIPK, SDCBP, CYP7A1, NSMAF, UBXN2B, UGDH, UBE2K, and DAB1, were shown to be shared by three or more different approaches. Therefore, it gives evidence of the most intense selection in these areas. These genes are mostly linked to milk production and adaptability traits. This study also reveals selection regions that contain genes which are crucial to numerous biological functions, including those associated with milk production, coat color, glucose metabolism, oxidative stress response, immunity and circadian rhythms.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41236689","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 alliance of genome resources: transforming comparative genomics. 基因组资源联盟:转化比较基因组学。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-12-01 Epub Date: 2023-09-04 DOI: 10.1007/s00335-023-10015-2

Carol J Bult, Paul W Sternberg

{"title":"The alliance of genome resources: transforming comparative genomics.","authors":"Carol J Bult, Paul W Sternberg","doi":"10.1007/s00335-023-10015-2","DOIUrl":"10.1007/s00335-023-10015-2","url":null,"abstract":"Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene Ontology resource. The Alliance uses a common set of gene ortholog assertions as the basis for comparing biological annotations across the organisms represented in the Alliance. The major types of knowledge associated with genes that are represented in the Alliance database currently include gene function, phenotypic alleles and variants, human disease associations, pathways, gene expression, and both protein-protein and genetic interactions. The Alliance has enhanced the ability of researchers to easily compare biological annotations for common data types across model organisms and human through the implementation of shared programmatic access mechanisms, data-specific web pages with a unified \"look and feel\", and interactive user interfaces specifically designed to support comparative biology. The modular infrastructure developed by the Alliance allows the resource to serve as an extensible \"knowledge commons\" capable of expanding to accommodate additional model organisms.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10628019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10151505","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: 2

The spontaneous mouse mutant low set ears (Lse) is caused by tandem duplication of Fgf3 and Fgf4. 小鼠自发性低置耳突变体(Lse)是由Fgf3和Fgf4的串联重复引起的。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-09999-8

Alana Luzzio, Sarah Edie, Kristina Palmer, L Brianna Caddle, Rachel Urban, Leslie O Goodwin, Ian C Welsh, Laura G Reinholdt, David E Bergstrom, Timothy C Cox, Leah Rae Donahue, Stephen A Murray

{"title":"The spontaneous mouse mutant low set ears (Lse) is caused by tandem duplication of Fgf3 and Fgf4.","authors":"Alana Luzzio, Sarah Edie, Kristina Palmer, L Brianna Caddle, Rachel Urban, Leslie O Goodwin, Ian C Welsh, Laura G Reinholdt, David E Bergstrom, Timothy C Cox, Leah Rae Donahue, Stephen A Murray","doi":"10.1007/s00335-023-09999-8","DOIUrl":"https://doi.org/10.1007/s00335-023-09999-8","url":null,"abstract":"The external ear develops from an organized convergence of ventrally migrating neural crest cells into the first and second branchial arches. Defects in external ear position are often symptomatic of complex syndromes such as Apert, Treacher-Collins, and Crouzon Syndrome. The low set ears (Lse) spontaneous mouse mutant is characterized by the dominant inheritance of a ventrally shifted external ear position and an abnormal external auditory meatus (EAM). We identified the causative mutation as a 148 Kb tandem duplication on Chromosome 7, which includes the entire coding sequences of Fgf3 and Fgf4. Duplications of FGF3 and FGF4 occur in 11q duplication syndrome in humans and are associated with craniofacial anomalies, among other features. Intercrosses of Lse-affected mice revealed perinatal lethality in homozygotes, and Lse/Lse embryos display additional phenotypes including polydactyly, abnormal eye morphology, and cleft secondary palate. The duplication results in increased Fgf3 and Fgf4 expression in the branchial arches and additional discrete domains in the developing embryo. This ectopic overexpression resulted in functional FGF signaling, demonstrated by increased Spry2 and Etv5 expression in overlapping domains of the developing arches. Finally, a genetic interaction between Fgf3/4 overexpression and Twist1, a regulator of skull suture development, resulted in perinatal lethality, cleft palate, and polydactyly in compound heterozygotes. These data indicate a role for Fgf3 and Fgf4 in external ear and palate development and provide a novel mouse model for further interrogation of the biological consequences of human FGF3/4 duplication.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9902195","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

Retraction Note: CircRNA circ-ATAD1 is downregulated in endometrial cancer and suppresses cell invasion and migration by downregulating miR-10a through methylation. 注:CircRNA circ-ATAD1在子宫内膜癌中下调，通过甲基化下调miR-10a来抑制细胞的侵袭和迁移。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10007-2

Pengxia Yang, Kunlun Yun, Ruying Zhang

引用次数: 0

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. aganimalgenomics:用于查看和手动注释农场动物基因组的浏览器。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10008-1

Deborah A Triant, Amy T Walsh, Gabrielle A Hartley, Bruna Petry, Morgan R Stegemiller, Benjamin M Nelson, Makenna M McKendrick, Emily P Fuller, Noelle E Cockett, James E Koltes, Stephanie D McKay, Jonathan A Green, Brenda M Murdoch, Darren E Hagen, Christine G Elsik

{"title":"AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes.","authors":"Deborah A Triant, Amy T Walsh, Gabrielle A Hartley, Bruna Petry, Morgan R Stegemiller, Benjamin M Nelson, Makenna M McKendrick, Emily P Fuller, Noelle E Cockett, James E Koltes, Stephanie D McKay, Jonathan A Green, Brenda M Murdoch, Darren E Hagen, Christine G Elsik","doi":"10.1007/s00335-023-10008-1","DOIUrl":"https://doi.org/10.1007/s00335-023-10008-1","url":null,"abstract":"Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9905274","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