Institut für Nutztierwissenschaften

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Browsing Institut für Nutztierwissenschaften by Journal "BMC genomics"

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    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.
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    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.