Browsing by Subject "Japanese quail"

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Analysis of phosphorus utilization using the host genome and microbiota variability in Japanese quail
(2021) Vollmar, Solveig Deniece; Bennewitz, Jörn
Phosphorus (P) is an essential element for growth and performance of avian species. It is predominantly bound as phytic acids and salts (phytate) in plant seeds. Phytases and other phosphatases can harness P by cleaving P groups. Nonruminants have low endogenous phytase activity in the gastrointestinal tract, and thus, the requirement of this element is not met from exclusive plant-based diets. Therefore, mineral P or phytase enzymes are supplemented in poultry feed. Due to the finite quantities of high quality mineral P worldwide, it is of great economic interest. P supplementation is increasingly causing environmental problems. Past studies investigated the P utilization (PU) of different poultry species. They revealed a high phenotypic variation in PU among individuals. Moderate heritabilities indicates that breeding for this trait is in principle possible. The overall aim of this thesis was to gain a deeper understanding of the variability of P utilization in relation to host genetics, ileal microbiota composition and their interaction in the model species Japanese quail. The objective of chapter two was to verify whether variation in PU in quail is a heritable trait conditioned by a few quantitative trait loci (QTL) with detectable effects. For this purpose, individuals were genome-wide genotyped with a 4k SNP chip, and a linkage map was generated. Based on this map, QTL linkage analysis was performed using multimarker regression analysis in a line-crossing model to map QTL for PU. We identified a few QTL regions with significant effects. Among them was a QTL peak at Coturnix japonica chromosome (CJA) 3 for PU. Several genes were found in the region surrounding this peak, which requires further functional gene analysis. Based on these results, we hypothesized that these traits are polygenically determined due to several small QTL effects, which we could not detect significantly. The overlap of the QTL regions indicated linkage of the traits and confirmed their genetic correlations. With the aim of predicting microbiota-related host traits, chapter three examined the composition of the ileum microbiota and differential abundance analysis (DAA). Based on this study, it was shown that a sex-specific influence on microbiota composition exists. The digesta samples of all animals were dominated by five genera, which contributed to more than 70% of the total ileum microbial community. In examining the microbiota composition of each of the 50 animals with the highest and lowest PU, DAA revealed genera significantly associated with PU. In chapter four, we characterized the influence of performance-related gut microbiota to unravel the microbial architecture of the traits evaluated. The aim of this study was to determine whether the variation in PU is partly driven by the microbial community in the ileum. We used microbial mixed linear models to estimate microbiabilities (m^2). This determines the fraction of phenotypic variance that can be explained by the gut microbiota. The estimation of m^2 was 0.15 for PU and was highly significant. It was also highly significant for feed intake, body weight gain and feed per gain. This model was bivariately extended and showed a high microbial correlation of the traits. Based on both results, the ileum microbiota composition plays a substantial role in PU as well as in performance traits, and there is a considerable animal microbiota correlation, showing that the microbiota affects multiple traits. The microbial drivers of this microbial fraction were identified by applying microbiome-wide association studies (MWAS). By back-solving the microbial linear mixed model, we approximated the effect of single OTUs on the phenotypic traits from the microbial model solutions. An MWAS at the genus level uncovered several traits associated with bacterial genera. Subsequently, we assessed whether the microbial community in the ileum is a heritable host trait that can be used for breeding individuals with improved PU. In chapter five we applied QTL analysis using specific genera to examine whether they are linked with genomic SNP markers. These QTL analyses revealed a link between some microbiota species and host genomic regions of chromosomes and SNP markers. By estimating significant heritabilities for some genera, we were able to provide evidence for the hypothesis that the microbial community and microbial features are at least partially related to host genetics. We predicted the animal microbial effects on PU and correlated performance traits by applying microbial best linear unbiased predictions (M-BLUP). In addition, genomic best linear unbiased predictions (G-BLUP) were used to predict the SNP effect for the predicted animal microbial effect. A combination of those two may help to predict genomic breeding values of the microbiota effects for future hologenomic breeding programs.
Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)
(2022) Haas, Valentin; Vollmar, Solveig; Preuß, Siegfried; Rodehutscord, Markus; Camarinha-Silva, Amélia; Bennewitz, Jörn; Haas, Valentin; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Vollmar, Solveig; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Preuß, Siegfried; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Rodehutscord, Markus; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
Background: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.