Mammalian Genome最新文献_第10页

Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle. 吉尔牛卵母细胞和胚胎数量的单步全基因组关联研究和gwas后分析。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10009-0

Renata de Fátima Bretanha Rocha, Arielly Oliveira Garcia, Pamela Itajara Otto, Mateus Guimarães Dos Santos, Marcos Vinícius Barbosa da Silva, Marta Fonseca Martins, Marco Antônio Machado, João Claudio do Carmo Panetto, Simone Eliza Facioni Guimarães

{"title":"Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle.","authors":"Renata de Fátima Bretanha Rocha, Arielly Oliveira Garcia, Pamela Itajara Otto, Mateus Guimarães Dos Santos, Marcos Vinícius Barbosa da Silva, Marta Fonseca Martins, Marco Antônio Machado, João Claudio do Carmo Panetto, Simone Eliza Facioni Guimarães","doi":"10.1007/s00335-023-10009-0","DOIUrl":"https://doi.org/10.1007/s00335-023-10009-0","url":null,"abstract":"Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify genomic regions, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO), and number of embryos (EMBR) from 1641 Gir donors was provided by five different stock farms. A genotype file with 2093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. The genomic regions identified in our work were overlapped with QTLs from QTL database on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24, and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR, and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. The protein-coding genes ARNT, EGR1, HIF1A, AHR, and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 3","pages":"497-508"},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10260407","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

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle. 吉尔Indicine牛卵母细胞和胚胎数量的纯合子序列和选择特征。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-09989-w

Renata de Fátima Bretanha Rocha, Arielly Oliveira Garcia, Pamela Itajara Otto, Marcos Vinícius Barbosa da Silva, Marta Fonseca Martins, Marco Antônio Machado, João Claudio do Carmo Panetto, Simone Eliza Facioni Guimarães

{"title":"Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle.","authors":"Renata de Fátima Bretanha Rocha, Arielly Oliveira Garcia, Pamela Itajara Otto, Marcos Vinícius Barbosa da Silva, Marta Fonseca Martins, Marco Antônio Machado, João Claudio do Carmo Panetto, Simone Eliza Facioni Guimarães","doi":"10.1007/s00335-023-09989-w","DOIUrl":"https://doi.org/10.1007/s00335-023-09989-w","url":null,"abstract":"Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 3","pages":"482-496"},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10276201","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: 2

35th International Mammalian Genome Conference: meeting overview. 第35届国际哺乳动物基因组会议:会议综述。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-09983-2

Kristen S Barratt, Yichen Dai, Darla R Miller, Teresa M Gunn, Linda D Siracusa

引用次数: 0

Retraction Note to: miR-217-5p inhibits invasion and metastasis of prostate cancer by targeting clusterin. 注:miR-217-5p通过靶向聚簇蛋白抑制前列腺癌的侵袭转移。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10006-3

Wanli Zhao, Xiuli Wang, Yuqing Jiang, Xiaopeng Jia, Yuexian Guo

引用次数: 0

Retraction Note: Overexpression of ROCK1 promotes cancer cell proliferation and is associated with poor prognosis in human urothelial bladder cancer. 注:ROCK1的过表达促进了人类尿路上皮性膀胱癌的癌细胞增殖，并与预后不良有关。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10002-7

Yanhui Mei, Yuhai Wu, Longbo Ma, Hongli Zhang, Lei Li, Feng Wang

引用次数: 0

Genomic distribution and polymorphism of G-quadruplex motifs occupying ovine promoters and enhancers. 占据绵羊启动子和增强子的g -四重基序的基因组分布和多态性。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-09988-x

Georgios C Stefos, Georgios Theodorou, Ioannis Politis

{"title":"Genomic distribution and polymorphism of G-quadruplex motifs occupying ovine promoters and enhancers.","authors":"Georgios C Stefos, Georgios Theodorou, Ioannis Politis","doi":"10.1007/s00335-023-09988-x","DOIUrl":"https://doi.org/10.1007/s00335-023-09988-x","url":null,"abstract":"G-quadruplexes are non-canonical DNA structures that are formed in regions with short runs of guanines. During the last decade they have gained considerable attention due to their involvement in basic cellular processes, linking them to several physiological processes and pathological conditions. Regulation of gene transcription is among the crucial roles that G-quadruplexes play in the cells. Several ways in which these structures affect transcription have been described, both negatively and positively. Recently, G-quadruplexes have been shown to be implicated in the three-dimensional rearrangement of the chromosomes that enables the interaction of enhancers and gene promoters during regulation of transcription. Sheep is a species for which almost no G-quadruplex-related studies have been conducted and thus research on this species is kept out from the progress that has been made in the G-quadruplex field. In this context, we investigated the DNA sequences with potential to form G-quadruplexes (G4-motifs) in the ovine enhancers and promoters. We describe the distribution of G4-motifs within the regulatory regions which is shown to be enriched in G4-motifs in a way similar to other mammals. Furthermore, our data suggest that G4-motifs promote promoter-enhancer interactions in sheep. The single nucleotide polymorphisms colocalizing with promoter- and enhancer-associated ovine G4-motifs constitute a considerable pool of polymorphism and given the crucial role of these specific G4-motifs on regulation of transcription, we suggest this polymorphism as an interesting target for ovine genetic studies.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 3","pages":"473-481"},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9900368","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: 1

Three-dimensional microCT imaging of mouse heart development from early post-implantation to late fetal stages. 小鼠心脏从植入后早期到胎儿晚期发育的三维显微ct成像。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2023-06-01 Epub Date: 2023-01-03 DOI: 10.1007/s00335-022-09976-7

Nanbing Li-Villarreal, Tara L Rasmussen, Audrey E Christiansen, Mary E Dickinson, Chih-Wei Hsu

{"title":"Three-dimensional microCT imaging of mouse heart development from early post-implantation to late fetal stages.","authors":"Nanbing Li-Villarreal, Tara L Rasmussen, Audrey E Christiansen, Mary E Dickinson, Chih-Wei Hsu","doi":"10.1007/s00335-022-09976-7","DOIUrl":"10.1007/s00335-022-09976-7","url":null,"abstract":"Comprehensive detailed characterization of new mouse models can be challenging due to the individual focus involved in developing these models. Often models are engineered to test a specific hypothesis in a limited number of tissues, stages, and/or other contexts. Whether or not the model produces the desired phenotypes, phenotyping beyond the desired context can be extremely work intensive and these studies are often not undertaken. However, the general information resulting from broader phenotyping can be invaluable to the wider scientific community. The International Mouse Phenotyping Consortium (IMPC) and its subsidiaries, like the Knockout Mouse Project (KOMP), has made great strides in streamlining this process. In particular, the use of microCT has been an invaluable resource in examining internal organ systems throughout fetal/developmental stages. Here, we provide several novel vignettes demonstrating the utility of microCT in uncovering cardiac phenotypes both based on human disease correlations and those that are unpredicted.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 2","pages":"156-165"},"PeriodicalIF":2.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9707740","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

Transcriptome studies of inherited dilated cardiomyopathies. 遗传性扩张型心肌病的转录组研究。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-06-01 Epub Date: 2023-02-07 DOI: 10.1007/s00335-023-09978-z

Matthew Koslow, David Mondaca-Ruff, Xiaolei Xu

{"title":"Transcriptome studies of inherited dilated cardiomyopathies.","authors":"Matthew Koslow, David Mondaca-Ruff, Xiaolei Xu","doi":"10.1007/s00335-023-09978-z","DOIUrl":"10.1007/s00335-023-09978-z","url":null,"abstract":"Dilated cardiomyopathy (DCM) is a group of heart muscle diseases that often lead to heart failure, with more than 50 causative genes have being linked to DCM. The heterogenous nature of the inherited DCMs suggest the need of precision medicine. Consistent with this emerging concept, transcriptome studies in human patients with DCM indicated distinct molecular signature for DCMs of different genetic etiology. To facilitate this line of research, we reviewed the status of transcriptome studies of inherited DCMs by focusing on three predominant DCM causative genes, TTN, LMNA, and BAG3. Besides studies in human patients, we summarized transcriptomic analysis of these inherited DCMs in a variety of model systems ranging from iPSCs to rodents and zebrafish. We concluded that the RNA-seq technology is a powerful genomic tool that has already led to the discovery of new modifying genes, signaling pathways, and related therapeutic avenues. We also pointed out that both temporal (different pathological stages) and spatial (different cell types) information need to be considered for future transcriptome studies. While an important bottle neck is the low throughput in experimentally testing differentially expressed genes, new technologies in efficient animal models such as zebrafish starts to be developed. It is anticipated that the RNA-seq technology will continue to uncover both unique and common pathological events, aiding the development of precision medicine for inherited DCMs.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 2","pages":"312-322"},"PeriodicalIF":2.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10426000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005665","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

A review of standardized high-throughput cardiovascular phenotyping with a link to metabolism in mice. 与小鼠代谢相关的标准化高通量心血管表型研究综述

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2023-06-01 Epub Date: 2023-06-16 DOI: 10.1007/s00335-023-09997-w

Jiri Lindovsky, Zuzana Nichtova, Nathalia R V Dragano, David Pajuelo Reguera, Jan Prochazka, Helmut Fuchs, Susan Marschall, Valerie Gailus-Durner, Radislav Sedlacek, Martin Hrabě de Angelis, Jan Rozman, Nadine Spielmann

{"title":"A review of standardized high-throughput cardiovascular phenotyping with a link to metabolism in mice.","authors":"Jiri Lindovsky, Zuzana Nichtova, Nathalia R V Dragano, David Pajuelo Reguera, Jan Prochazka, Helmut Fuchs, Susan Marschall, Valerie Gailus-Durner, Radislav Sedlacek, Martin Hrabě de Angelis, Jan Rozman, Nadine Spielmann","doi":"10.1007/s00335-023-09997-w","DOIUrl":"10.1007/s00335-023-09997-w","url":null,"abstract":"Cardiovascular diseases cause a high mortality rate worldwide and represent a major burden for health care systems. Experimental rodent models play a central role in cardiovascular disease research by effectively simulating human cardiovascular diseases. Using mice, the International Mouse Phenotyping Consortium (IMPC) aims to target each protein-coding gene and phenotype multiple organ systems in single-gene knockout models by a global network of mouse clinics. In this review, we summarize the current advances of the IMPC in cardiac research and describe in detail the diagnostic requirements of high-throughput electrocardiography and transthoracic echocardiography capable of detecting cardiac arrhythmias and cardiomyopathies in mice. Beyond that, we are linking metabolism to the heart and describing phenotypes that emerge in a set of known genes, when knocked out in mice, such as the leptin receptor (Lepr), leptin (Lep), and Bardet-Biedl syndrome 5 (Bbs5). Furthermore, we are presenting not yet associated loss-of-function genes affecting both, metabolism and the cardiovascular system, such as the RING finger protein 10 (Rfn10), F-box protein 38 (Fbxo38), and Dipeptidyl peptidase 8 (Dpp8). These extensive high-throughput data from IMPC mice provide a promising opportunity to explore genetics causing metabolic heart disease with an important translational approach.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"34 2","pages":"107-122"},"PeriodicalIF":2.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9711482","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

Mouse models of spontaneous atrial fibrillation. 自发性心房颤动小鼠模型

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-06-01 Epub Date: 2022-09-29 DOI: 10.1007/s00335-022-09964-x

Joshua A Keefe, Mohit M Hulsurkar, Svetlana Reilly, Xander H T Wehrens

引用次数: 0