Institut für Nutztierwissenschaften

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Effects of a transient lack of dietary mineral phosphorus on renal gene expression and plasma metabolites in two high-yielding laying hen strains
(2025) Qasir, Hiba; Reyer, Henry; Oster, Michael; Ponsuksili, Siriluck; Trakooljul, Nares; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus
Background: There is an emerging body of evidence that current poultry feed is formulated in excess for phosphorus (P), which results in unnecessarily high P excretions. Sustainable concepts for agricultural P flows should trigger animal-intrinsic mechanisms for efficient P utilization. In the current study, Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) laying hens were fed either a high P diet (P+) with 1 g/kg mineral P supplement or a low P diet (P-) with 0 g/kg mineral P supplement for a period of 4 weeks prior to sampling. Before and after onset of laying, i.e., at 19 and 24 weeks of life, kidney and plasma samples were collected to investigate the endogenous P utilization in response to restricted dietary P, laying hen strain, and sexual maturation. Results: Plasma analyses of minerals and metabolites confirmed the response to a low P diet, which was characterized by a significant reduction in plasma P levels at week 19 in both strains. The plasma calcium (Ca) levels were tightly regulated throughout the entire experimental period. Notably, there was a numerical trend of increased plasma calcitriol levels in P- fed birds of both strains compared to the P + group, which might have mediated a substantial role regarding the adaptive responses to low P supply. At week 19, RNA sequencing of kidney identified 1,114 and 556 differentially expressed genes (DEGs) unique to the LB and LSL strains, respectively. The number of DEGs declined with increasing maturity of the hens culminating in 90 and 146 DEGs for LB and LSL strains at week 24. Analyses revealed an enrichment of pathways related to energy metabolism and cell cycle, particularly at week 19 in both strains. The diet-specific expression of target genes involved in P homeostasis highlighted transcripts related to active ( SLC34A1 , SLC20A2 ) and passive mineral transport ( CLDN14 , CLDN16 ), Ca utilization ( STC1 , CALB1 ), and acid-base balance ( CA2 , SLC4A1 ). Conclusions: Results suggest that both laying hen strains adapted to the lack of mineral P supplements and achieved a physiological Ca: P-ratio in body compartments through endogenous regulation as evidenced via the endocrine profile.
Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows
(2024) Schneider, Helen; Krizanac, Ana-Marija; Falker-Gieske, Clemens; Heise, Johannes; Tetens, Jens; Thaller, Georg; Bennewitz, Jörn; Schneider, Helen; Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany; Krizanac, Ana-Marija; Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany; Falker-Gieske, Clemens; Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany; Heise, Johannes; Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany; Tetens, Jens; Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany; Thaller, Georg; Institute of Animal Breeding and Husbandry, Christian-Albrechts University of Kiel, 24098, Kiel, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany
Background: Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. Results: In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits’ genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets’ high effect. Conclusion: Our results confirm the connection of milk production and health traits in dairy cattle via the animals’ metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits’ connection in more detail.
Mapping genes for resilient dairy cows by means of across-breed genome-wide association analysis
(2025) Keßler, Franziska; Zölch, Maximilian; Wellman, Robin; Bennewitz, Jörn; Keßler, Franziska; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Zölch, Maximilian; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Wellman, Robin; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
Background: Indicator traits based on variance and autocorrelation of longitudinal data are increasingly used to measure resilience in animal breeding. While these traits show promising heritability and can be routinely collected, their genetic architecture remains poorly understood. We conducted GWAS for three resilience indicators across German Holstein ( n = 2,300), Fleckvieh ( n = 2,330), and Brown Swiss ( n = 1,073) dairy cattle ( Bos Taurus ) populations. The indicators included variance ( ) and autocorrelation ( ) of deviations of observed from predicted daily milk yield and variance of relative daily milk yield ( ). Additionally, we analysed a selection index combining these traits. Prior to GWAS, we examined population structure through multi-dimensional scaling (MDS) and LD patterns, revealing distinct genetic clusters for each breed and similar LD decay patterns. Results: The GWAS results confirmed the polygenic nature of resilience, with multiple genomic regions showing significant associations. Notable signals were detected on BTA5 ( ), BTA14 ( ), BTA2 and BTA8 ( ) for single indicator traits. For selection index resilience, strong suggestive SNPs are located on BTA4 , BTA16 , BTA21 , and BTA27 . Detected regions overlapped with previously reported QTLs for performance, reproduction, longevity and health, providing new insights into the biological pathways underlying dairy cattle resilience. Conclusions: Our findings demonstrate that resilience indicators have a complex genetic architecture with both breed-specific and shared components, supporting their potential use in selective breeding programs while highlighting the importance of careful trait definition.
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
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.
Transcriptional responses in jejunum of two layer chicken strains following variations in dietary calcium and phosphorus levels
(2021) Reyer, Henry; Oster, Michael; Ponsuksili, Siriluck; Trakooljul, Nares; Omotoso, Adewunmi O.; Iqbal, Muhammad A.; Muráni, Eduard; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus
Background: Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and egg laying performance and environmental burden due to excessive P excretion rates. Improved utilization of minerals in particular of P sources contributes to healthy growth while preserving the finite resource of mineral P and mitigating environmental pollution. In the current study, high performance Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) hens at peak laying performance were examined to approximate the consequences of variable dietary Ca and P supply. The experimental design comprised four dietary groups with standard or reduced levels of either Ca or P or both (n = 10 birds per treatment group and strain) in order to stimulate intrinsic mechanisms to maintain homeostasis. Jejunal transcriptome profiles and the systemic endocrine regulation of mineral homeostasis were assessed (n = 80). Results: Endogenous mechanisms to maintain mineral homeostasis in response to variations in the supply of Ca and P were effective in both laying hen strains. However, the LSL and LB appeared to adopt different molecular pathways, as shown by circulating vitamin D levels and strain-specific transcriptome patterns. Responses in LSL indicated altered proliferation rates of intestinal cells as well as adaptive responses at the level of paracellular transport and immunocompetence. Endogenous mechanisms in LB appeared to involve a restructuring of the epithelium, which may allow adaptation of absorption capacity via improved micro-anatomical characteristics. Conclusions: The results suggest that LSL and LB hens may exhibit different Ca, P, and vitamin D requirements, which have so far been neglected in the supply recommendations. There is a demand for trial data showing the mechanisms of endogenous factors of Ca and P homeostasis, such as vitamin D, at local and systemic levels in laying hens.

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