Tetens, Jens

[["dc.bibliographiccitation.artnumber","e0122325"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","PLoS ONE"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Ha, Ngoc-Thuy"],["dc.contributor.author","Gross, Josef Johann"],["dc.contributor.author","van Dorland, Annette"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Schlather, Martin"],["dc.contributor.author","Bruckmaier, Rupert"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T09:59:31Z"],["dc.date.available","2018-11-07T09:59:31Z"],["dc.date.issued","2015"],["dc.description.abstract","The metabolic adaptation of dairy cows during the transition period has been studied intensively in the last decades. However, until now, only few studies have paid attention to the genetic aspects of this process. Here, we present the results of a gene-based mapping and pathway analysis with the measurements of three key metabolites, (1) non-esterified fatty acids (NEFA), (2) beta-hydroxybutyrate (BHBA) and (3) glucose, characterizing the metabolic adaptability of dairy cows before and after calving. In contrast to the conventional single-marker approach, we identify 99 significant and biologically sensible genes associated with at least one of the considered phenotypes and thus giving evidence for a genetic basis of the metabolic adaptability. Moreover, our results strongly suggest three pathways involved in the metabolism of steroids and lipids are potential candidates for the adaptive regulation of dairy cows in their early lactation. From our perspective, a closer investigation of our findings will lead to a step forward in understanding the variability in the metabolic adaptability of dairy cows in their early lactation."],["dc.description.sponsorship","Swiss Commission for Technology and Innovation CTI [13948.2 PFLS-LS]"],["dc.identifier.doi","10.1371/journal.pone.0122325"],["dc.identifier.isi","000351425400212"],["dc.identifier.pmid","25789767"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11763"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/37606"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Public Library Science"],["dc.relation.issn","1932-6203"],["dc.rights.access","openAccess"],["dc.title","Gene-Based Mapping and Pathway Analysis of Metabolic Traits in Dairy Cows"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","6095"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Scientific Reports"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Felkel, Sabine"],["dc.contributor.author","Vogl, Claus"],["dc.contributor.author","Rigler, Doris"],["dc.contributor.author","Dobretsberger, Viktoria"],["dc.contributor.author","Chowdhary, Bhanu P."],["dc.contributor.author","Distl, Ottmar"],["dc.contributor.author","Fries, Ruedi"],["dc.contributor.author","Jagannathan, Vidhya"],["dc.contributor.author","Janečka, Jan E."],["dc.contributor.author","Leeb, Tosso"],["dc.contributor.author","Lindgren, Gabriella"],["dc.contributor.author","McCue, Molly"],["dc.contributor.author","Metzger, Julia"],["dc.contributor.author","Neuditschko, Markus"],["dc.contributor.author","Rattei, Thomas"],["dc.contributor.author","Raudsepp, Terje"],["dc.contributor.author","Rieder, Stefan"],["dc.contributor.author","Rubin, Carl-Johan"],["dc.contributor.author","Schaefer, Robert"],["dc.contributor.author","Schlötterer, Christian"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Velie, Brandon"],["dc.contributor.author","Brem, Gottfried"],["dc.contributor.author","Wallner, Barbara"],["dc.date.accessioned","2019-07-09T11:51:39Z"],["dc.date.available","2019-07-09T11:51:39Z"],["dc.date.issued","2019"],["dc.description.abstract","Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago."],["dc.identifier.doi","10.1038/s41598-019-42640-w"],["dc.identifier.pmid","30988347"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16162"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59981"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","630"],["dc.title","The horse Y chromosome as an informative marker for tracing sire lines"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","18"],["dc.contributor.author","Schaefer, Robert J."],["dc.contributor.author","Schubert, Mikkel"],["dc.contributor.author","Bailey, Ernest"],["dc.contributor.author","Bannasch, Danika L."],["dc.contributor.author","Barrey, Eric"],["dc.contributor.author","Bar-Gal, Gila Kahila"],["dc.contributor.author","Brem, Gottfried"],["dc.contributor.author","Brooks, Samantha A."],["dc.contributor.author","Distl, Ottmar"],["dc.contributor.author","Fries, Ruedi"],["dc.contributor.author","Finno, Carrie J."],["dc.contributor.author","Gerber, Vinzenz"],["dc.contributor.author","Haase, Bianca"],["dc.contributor.author","Jagannathan, Vidhya"],["dc.contributor.author","Kalbfleisch, Ted"],["dc.contributor.author","Leeb, Tosso"],["dc.contributor.author","Lindgren, Gabriella"],["dc.contributor.author","Lopes, Maria Susana"],["dc.contributor.author","Mach, Núria"],["dc.contributor.author","da Câmara Machado, Artur"],["dc.contributor.author","MacLeod, James N."],["dc.contributor.author","McCoy, Annette"],["dc.contributor.author","Metzger, Julia"],["dc.contributor.author","Penedo, Cecilia"],["dc.contributor.author","Polani, Sagi"],["dc.contributor.author","Rieder, Stefan"],["dc.contributor.author","Tammen, Imke"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Verini-Supplizi, Andrea"],["dc.contributor.author","Wade, Claire M."],["dc.contributor.author","Wallner, Barbara"],["dc.contributor.author","Orlando, Ludovic"],["dc.contributor.author","Mickelson, James R."],["dc.contributor.author","McCue, Molly E."],["dc.date.accessioned","2019-07-09T11:43:43Z"],["dc.date.available","2019-07-09T11:43:43Z"],["dc.date.issued","2017"],["dc.description.abstract","BACKGROUND: To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. RESULTS: Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. CONCLUSIONS: Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse."],["dc.format.extent","18"],["dc.identifier.doi","10.1186/s12864-017-3943-8"],["dc.identifier.pmid","28750625"],["dc.identifier.pmid","Equine genomics; Linkage disequilibrium; SNP chip; SNP discovery; SNP informativeness; SNP validation; SNP-tagging; Variant recalibration; Whole genome sequence"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14662"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58959"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/15122 but duplicate"],["dc.rights.holder","The Author(s)."],["dc.title","Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","e0205576"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","PLoS One"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Blaj, Iulia"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Preuß, Siegfried"],["dc.contributor.author","Bennewitz, Jörn"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.editor","Óvilo, Cristina"],["dc.date.accessioned","2020-12-10T18:42:09Z"],["dc.date.available","2020-12-10T18:42:09Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1371/journal.pone.0205576"],["dc.identifier.eissn","1932-6203"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15706"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/77827"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.relation.orgunit","Fakultät für Agrarwissenschaften"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1039"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Genes"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Bögeholz, Anke"],["dc.contributor.author","Falker-Gieske, Clemens"],["dc.contributor.author","Guélat, Monika"],["dc.contributor.author","Gurtner, Corinne"],["dc.contributor.author","Hunziker, Sibylle"],["dc.contributor.author","Oevermann, Anna"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Drögemüller, Cord"],["dc.contributor.author","Tetens, Jens"],["dc.date.accessioned","2021-08-12T07:45:57Z"],["dc.date.available","2021-08-12T07:45:57Z"],["dc.date.issued","2021"],["dc.description.abstract","Bilateral convergent strabismus with exophthalmos (BCSE) is a malformation of the eyes and is recognized as a mild but progressive disorder that affects cattle in the first two years of life. This most likely inherited disorder is rarely described in cattle resembling autosomal dominantly inherited forms of human progressive external ophthalmoplegia (PEO). In German Braunvieh cattle, two linked genome regions were found that could be responsible for the development and/or progression of BCSE. The goal of this study was to phenotypically characterize BCSE in Holstein cattle from Germany and Switzerland as well as to identify associated genome regions by GWAS. The clinicopathological phenotype of 52 BCSE-affected Holstein cattle was in accordance with the phenotype described in German Braunvieh cattle, but in addition, signs of degeneration and cellular infiltration in the eye muscles were found. By using imputed sequence level genotype data, three genome-wide significant GWAS hits were revealed on different chromosomes that were not detected by initial GWAS based on high density SNP array data highlighting the usefulness of this approach for mapping studies. The associated genome regions include the ABCC4 gene as well as markers adjacent to the NCOR2 and DNAJC3 genes all illustrating possible functional candidate genes. Our results challenge a monogenic mode of inheritance and indicate a more complex inheritance of BCSE in Holstein cattle. Furthermore, in comparison to previous results from German Braunvieh cattle, it illustrates an obvious genetic heterogeneity causing BSCE in cattle. Subsequent whole genome sequencing (WGS)-based analyses might elucidate pathogenic variants in the future."],["dc.description.abstract","Bilateral convergent strabismus with exophthalmos (BCSE) is a malformation of the eyes and is recognized as a mild but progressive disorder that affects cattle in the first two years of life. This most likely inherited disorder is rarely described in cattle resembling autosomal dominantly inherited forms of human progressive external ophthalmoplegia (PEO). In German Braunvieh cattle, two linked genome regions were found that could be responsible for the development and/or progression of BCSE. The goal of this study was to phenotypically characterize BCSE in Holstein cattle from Germany and Switzerland as well as to identify associated genome regions by GWAS. The clinicopathological phenotype of 52 BCSE-affected Holstein cattle was in accordance with the phenotype described in German Braunvieh cattle, but in addition, signs of degeneration and cellular infiltration in the eye muscles were found. By using imputed sequence level genotype data, three genome-wide significant GWAS hits were revealed on different chromosomes that were not detected by initial GWAS based on high density SNP array data highlighting the usefulness of this approach for mapping studies. The associated genome regions include the ABCC4 gene as well as markers adjacent to the NCOR2 and DNAJC3 genes all illustrating possible functional candidate genes. Our results challenge a monogenic mode of inheritance and indicate a more complex inheritance of BCSE in Holstein cattle. Furthermore, in comparison to previous results from German Braunvieh cattle, it illustrates an obvious genetic heterogeneity causing BSCE in cattle. Subsequent whole genome sequencing (WGS)-based analyses might elucidate pathogenic variants in the future."],["dc.description.sponsorship","H. Wilhelm Schaumann Stiftung"],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.3390/genes12071039"],["dc.identifier.pii","genes12071039"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/88582"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-448"],["dc.relation.eissn","2073-4425"],["dc.rights","CC BY 4.0"],["dc.title","GWAS Hits for Bilateral Convergent Strabismus with Exophthalmos in Holstein Cattle Using Imputed Sequence Level Genotypes"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Genetics Selection Evolution"],["dc.bibliographiccitation.volume","52"],["dc.contributor.author","Gehrke, Lilian Johanna"],["dc.contributor.author","Capitan, Aurélien"],["dc.contributor.author","Scheper, Carsten"],["dc.contributor.author","König, Sven"],["dc.contributor.author","Upadhyay, Maulik"],["dc.contributor.author","Heidrich, Kristin"],["dc.contributor.author","Russ, Ingolf"],["dc.contributor.author","Seichter, Doris"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Medugorac, Ivica"],["dc.contributor.author","Thaller, Georg"],["dc.date.accessioned","2020-12-10T18:38:50Z"],["dc.date.available","2020-12-10T18:38:50Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1186/s12711-020-0525-z"],["dc.identifier.eissn","1297-9686"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/17159"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/77450"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Are scurs in heterozygous polled (Pp) cattle a complex quantitative trait?"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2823"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","G3: Genes, Genomes, Genetics"],["dc.bibliographiccitation.lastpage","2834"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Falker-Gieske, Clemens"],["dc.contributor.author","Blaj, Iulia"],["dc.contributor.author","Preuß, Siegfried"],["dc.contributor.author","Bennewitz, Jörn"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Tetens, Jens"],["dc.date.accessioned","2020-12-10T18:42:41Z"],["dc.date.available","2020-12-10T18:42:41Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1534/g3.119.400452"],["dc.identifier.eissn","2160-1836"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16481"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/78045"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","GWAS for Meat and Carcass Traits Using Imputed Sequence Level Genotypes in Pooled F2-Designs in Pigs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","631"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","23"],["dc.contributor.author","Blaj, Iulia"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Bennewitz, Jörn"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Falker-Gieske, Clemens"],["dc.date.accessioned","2022-09-05T09:03:00Z"],["dc.date.available","2022-09-05T09:03:00Z"],["dc.date.issued","2022-09-03"],["dc.date.updated","2022-09-04T03:12:20Z"],["dc.description.abstract","Abstract\r\n \r\n Background\r\n Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study.\r\n \r\n \r\n Results\r\n A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation.\r\n \r\n \r\n Conclusions\r\n The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation."],["dc.identifier.citation","BMC Genomics. 2022 Sep 03;23(1):631"],["dc.identifier.doi","10.1186/s12864-022-08716-0"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/114071"],["dc.language.iso","en"],["dc.rights","CC BY 4.0"],["dc.rights.holder","The Author(s)"],["dc.subject","Structural variants"],["dc.subject","Tandem repeats"],["dc.subject","Genome wide association studies"],["dc.subject","Imputation"],["dc.subject","Pig"],["dc.subject","Whole-genome sequencing"],["dc.subject","lncRNA"],["dc.title","Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]