Browsing by Person "Tetens, Jens"

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Mendelian randomisation to uncover causal associations between conformation, metabolism, and production as potential exposure to reproduction in German Holstein dairy cattle
(2025) Schwarz, Leopold; Heise, Johannes; Liu, Zengting; Bennewitz, Jörn; Thaller, Georg; Tetens, Jens; Schwarz, Leopold; Department of Animal Sciences, Georg-August-University, 37077, Göttingen, Germany; Heise, Johannes; Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany; Liu, Zengting; Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany; Thaller, Georg; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany; Tetens, Jens; Department of Animal Sciences, Georg-August-University, 37077, Göttingen, Germany
Background: Reproduction is vital to welfare, health, and economics in animal husbandry and breeding. Health and reproduction are increasingly being considered because of the observed genetic correlations between reproduction, health, conformation, and performance traits in dairy cattle. Understanding the detailed genetic architecture underlying these traits would represent a major step in comprehending their interplay. Identifying known, putative or novel associations in genomics could improve animal health, welfare, and performance while allowing further adjustments in animal breeding. Results: We conducted genome-wide association studies for 25 different traits belonging to four different complexes, namely reproduction (n = 13), conformation (n = 6), production (n = 3), and metabolism (n = 3), using a cohort of over 235,000 dairy cows. As a result, we identified genome-wide significant signals for all the studied traits. The obtained summary statistics collected served as the input for a Mendelian randomisation approach (GSMR) to infer causal associations between putative exposure and reproduction traits. The study considered conformation, production, and metabolism as exposure and reproduction as outcome. A range of 139 to 252 genome-wide significant SNPs per combination were identified as instrumental variables (IVs). Out of 156 trait combinations, 135 demonstrated statistically significant effects, thereby enabling the identification of the responsible IVs. Combinations of traits related to metabolism (38 out of 39), conformation (68 out of 78), or production (29 out of 39) were found to have significant effects on reproduction. These relationships were partially non-linear. Moreover, a separate variance component estimation supported these findings, strongly correlating with the GSMR results and offering suggestions for improvement. Downstream analyses of selected representative traits per complex resulted in identifying and investigating potential physiological mechanisms. Notably, we identified both trait-specific SNPs and genes that appeared to influence specific traits per complex, as well as more general SNPs that were common between exposure and outcome traits. Conclusions: Our study confirms the known genetic associations between reproduction traits and the three complexes tested. It provides new insights into causality, indicating a non-linear relationship between conformation and reproduction. In addition, the downstream analyses have identified several clustered genes that may mediate this association.
Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results
(2022) Blaj, Iulia; Tetens, Jens; Bennewitz, Jörn; Thaller, Georg; Falker-Gieske, Clemens; Blaj, Iulia; Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany; Tetens, Jens; Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany; Bennewitz, Jörn; Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany; Thaller, Georg; Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany; Falker-Gieske, Clemens; Department of Animal Sciences, Georg-August-University, Göttingen, Germany
Background: 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. Results: 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. Conclusions: 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.