Inferring relationships between Phosphorus utilization, feed per gain, and bodyweight gain in an F2 cross of Japanese quail using recursive models

Inferring causal structures of gut microbiota diversity and feed efficiency traits in poultry using Bayesian learning and genomic structural equation models

Feed and phosphorus (P) efficiency are of increasing importance in poultry breeding. It has been shown recently that these efficiency traits are influenced by the gut microbiota composition of the birds. The efficiency traits and the gut microbiota composition are partly under control of the host genome. Thus, the gut microbiota composition can be seen as a mediator trait between the host genome and the efficiency traits. The present study used data from 749 individuals of a Japanese quail F2 cross. The birds were genotyped for 4k single-nucleotide polymorphism (SNP) and trait recorded for P utilization (PU) and P retention (PR), body weight gain (BWG), and feed per gain ratio (F:G). The gut microbiota composition was characterized by targeted amplicon sequencing. The alpha diversity was calculated as the Pielou's evenness index (J'). A stable Bayesian network was established using a Hill-Climbing learning algorithm. Pielou's evenness index was placed as the most upstream trait and BWG as the most downstream trait, with direct and indirect links via PR, PU, and F:G. The direct and indirect effects between J', PU, and PR were quantified with structural equation models (SEM), which revealed a causal link from J' to PU and from PU to PR. Quantitative trait loci (QTL) linkage mapping revealed three genome-wide significant QTL regions for these traits with in total 49 trait-associated SNP within the QTL regions. SEM association mapping separated the total SNP effect for a trait into a direct effect and indirect effects mediated by upstream traits. Although the indirect effects were in general small, they contributed to the total SNP effect in some cases. This enabled us to detect some shared genetic effects. The method applied allows for the detection of shared genetic architecture of quantitative traits and microbiota compositions.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

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.

Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome

Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNP markers (false discovery rate less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% False discovery rate threshold, with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.

Phytate degradation, myo-inositol release, and utilization of phosphorus and calcium by two strains of laying hens in five production periods

The objective of this study was to compare 2 laying hen strains in 5 production periods regarding phytase activity, phytate (InsP6) degradation, and myo-inositol (MI) release in the digestive tract and phosphorus (P) and calcium (Ca) utilization. One offspring of 10 nonrelated roosters per strain (Lohmann Brown-classic (LB) or Lohmann LSL-classic (LSL)) was placed in one of 20 metabolic units in a completely randomized block design in week 8, 14, 22, 28, and 58 of life. All hens were fed the same corn and soybean meal-based diet at one time, but the diet composition was adjusted to the requirements in the respective period. For 4 consecutive days, excreta were collected quantitatively at 24-hour intervals. In week 10, 16, 24, 30, and 60, the blood plasma, digesta of crop, gizzard, jejunum, ileum, and ceca, and mucosa of the jejunum was collected. The concentration of inorganic P in the blood plasma was higher in LB than in LSL hens (P = 0.026). Plasma Ca concentrations increased with each period (P < 0.001) in both strains. In jejunum digesta, the MI concentration did not differ between strains, but InsP6 concentration was higher in LB than in LSL hens (P = 0.002) and the highest in week 30 and 60. Total phosphatase and phytase activities were higher in LB than in LSL hens (P ≤ 0.009). Period effects were also significant for these enzymes. Concentrations of some constituents of the cecal content were different between the strains. The MI concentration in the egg albumen and yolk was higher in LB than in LSL hens. Differences in InsP6- and MI-related metabolism of the 2 hen strains existed. These differences were partly dependent of the period. Especially, week 24 was a period of remarkable change of metabolism. Great differences also existed among individuals, making it worth to have a closer look at the metabolism of individuals in addition to evaluating treatment means. Further studies on metabolic, genetic, and microbiome level may help explain these differences.

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome-wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome-wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small-effect QTL that were not detectable in this study.

Phytate Degradation, Transcellular Mineral Transporters, and Mineral Utilization by Two Strains of Laying Hens as Affected by Dietary Phosphorus and Calcium

Laying hens require less phosphorus (P) but markedly more calcium (Ca) in their diet than broilers. These differences may cause more distinct interactions with phytate degradation and utilization of minerals in laying hens than those in broilers. The objective of the study was to characterize intestinal phytate degradation, ileal transcript copy numbers of transcellular Ca and P transporters, and mineral utilization by two laying hen strains fed with standard or reduced levels of dietary Ca and P at the laying peak. The strains showed differences regarding several traits driving Ca and P metabolism along the digestive tract. Thus, the two strains may use different mechanisms to meet their respective P demand, i.e., via effective phytate degradation and transcellular transport. Clear effects of the Ca level on myo-inositol concentrations and mineral utilization revealed the significance of this element for the measured traits. The absence of P-mediated effects confirmed the findings of several studies recommending that P concentrations used in laying hen feeds are too high. Differences were noted between individuals within one treatment. The next step would be to evaluate the data in individual birds to identify birds that better cope with a challenging diet.

The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models

It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.

Effects on the Ileal Microbiota of Phosphorus and Calcium Utilization, Bird Performance, and Gender in Japanese Quail

In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%-15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions

Phosphorus is an essential mineral for all living organisms and a limited resource worldwide. Variation and heritability of phosphorus utilization (PU) traits were observed, indicating the general possibility of improvement. Molecular mechanisms of PU, including host and microbial effects, are still poorly understood. The most promising molecules that interact between the microbiome and host are microRNAs. Japanese quail representing extremes for PU were selected from an F2 population for miRNA profiling of the ileal tissue and subsequent association with mRNA and microbial data of the same animals. Sixty-nine differentially expressed miRNAs were found, including 21 novel and 48 known miRNAs. Combining miRNAs and mRNAs based on correlated expression and target prediction revealed enrichment of transcripts in functional pathways involved in phosphate or bone metabolism such as RAN, estrogen receptor and Wnt signaling, and immune pathways. Out of 55 genera of microbiota, seven were found to be differentially abundant between PU groups. The study reveals molecular interactions occurring in the gut of quail which represent extremes for PU including miRNA-16-5p, miR-142b-5p, miR-148a-3p, CTDSP1, SMAD3, IGSF10, Bacteroides, and Alistipes as key indicators due to their trait-dependent differential expression and occurrence as hub-members of the network of molecular drivers of PU.

Ileal Transcriptome Profiles of Japanese Quail Divergent in Phosphorus Utilization

Phosphorus (P) is an essential component for all living beings. Low P diets prompt phenotypic and molecular adaptations to maintain P homeostasis and increase P utilization (PU). Knowledge of the molecular mechanisms of PU is needed to enable targeted approaches to improve PU efficiency and thus lower P excretion in animal husbandry. In a previous population study, Japanese quail were subjected to a low P diet lacking mineral P and exogenous phytase. Individual PU was determined based on total P intake and excretion. A subset of 20 extreme siblings discordant for PU was selected to retrieve gene expression patterns of ileum (n = 10 per PU group). Sequencing reads have been successfully mapped to the current Coturnix japonica reference genome with an average mapping rate of 86%. In total, 640 genes were found to be differentially abundant between the low and high PU groups (false discovery rate ≤ 0.05). Transcriptional patterns suggest a link between improved PU and mitochondrial energy metabolism, accelerated cell proliferation of enterocytes, and gut integrity. In assessing indicators of the efficient use of macro- and micronutrients, further research on turnover and proliferation rates of intestinal cells could provide an approach to improve P efficiency in poultry species.

Genetic parameters for bone ash and phosphorus utilization in an F2 cross of Japanese quail

The main objective of this study was to perform quantitative genetic analyses of tibia and foot ash traits, which might serve as proxy traits to improve phosphorus utilization (PU) in a breeding program. Additionally, data for ash concentration in tibia and foot were compared with data for total amount of ash. Heritabilities for bone ash traits and genetic and phenotypic correlations between bone ash traits and PU were estimated. A total of 887 F₂ birds, established from 2 Japanese quail lines divergently selected on social reinstatement behavior, were provided a P deficient diet. In a metabolic study, feed consumption was measured and total excreta collected for each bird separately. Afterwards, birds were euthanized, the bones obtained and incinerated. Bone ash data showed a heritability of 0.230 (amount of tibia ash) to 0.342 (amount of foot ash), which was higher than estimated for PU, P retention, calcium utilization (0.120–0.174), and performance traits (0.088–0.114). The strongest genetic and phenotypic correlations between PU and bone ash traits were detected for the amount of foot ash with 0.549 and 0.527, respectively. Genetic and phenotypic correlations were stronger between PU and ash amount than between PU and ash percentage, irrespective of bone. Therefore, ash amount was considered a better trait than ash percentage to reflect PU. Strong genetic and phenotypic correlations were detected between the amount of foot and tibia ash (0.887 and 0.901, respectively). Phenotypic and genetic correlations between ash amount and PU or calcium utilization were almost identical, irrespective of bone. Foot ash is as suitable as tibia ash, but easier to determine. Bone ash data, especially the amount of foot ash, seem to be suitable indirect selection criteria for P efficiency breeding.

Lack of a relationship between plasma fibroblast growth factor-23 and phosphate utilization in young chicks

Fibroblast growth factor 23 (FGF-23) is proposed to be the hormone that controls phosphate (P) homeostasis in chickens. This study was initiated to investigate the effect of feeding young chicks diets that were either adequate (0.45%) or marginal (0.25%) in available P content on plasma FGF-23 levels. The dietary level of available P significantly (P ≤ 0.05) affected bone mineralization and bone length, but was without effect (P > 0.05) on growth rate and circulating FGF-23 concentrations. Substantial individual variation in bone mineralization and plasma FGF-23 levels was observed, and the correlation between these two variables was non-significant (P > 0.05). This suggested that there was no alteration in FGF-23 activity in response to suboptimal dietary P intake. The relationship of these observations to studies on the immunosuppression of FGF-23 activity is subsequentlydiscussed.

Handling the phosphorus paradox in agriculture and natural ecosystems: Scarcity, necessity, and burden of P

This special issue of Ambio compiles a series of contributions made at the 8th International Phosphorus Workshop (IPW8), held in September 2016 in Rostock, Germany. The introducing overview article summarizes major published scientific findings in the time period from IPW7 (2015) until recently, including presentations from IPW8. The P issue was subdivided into four themes along the logical sequence of P utilization in production, environmental, and societal systems: (1) Sufficiency and efficiency of P utilization, especially in animal husbandry and crop production; (2) P recycling: technologies and product applications; (3) P fluxes and cycling in the environment; and (4) P governance. The latter two themes had separate sessions for the first time in the International Phosphorus Workshops series; thus, this overview presents a scene-setting rather than an overview of the latest research for these themes. In summary, this paper details new findings in agricultural and environmental P research, which indicate reduced P inputs, improved management options, and provide translations into governance options for a more sustainable P use.

Results of an international phosphorus digestibility ring test with broiler chickens

The objective of this ring test was to investigate the prececal phosphorus (P) digestibility of soybean meal (SBM) in broiler chickens using the trial protocol proposed by the World's Poultry Science Association. It was hypothesized that prececal P digestibility of SBM determined in the collaborating stations is similar. Three diets with different inclusion levels of SBM were mixed in a feed mill specialized in experimental diets and transported to 17 collaborating stations. Broiler chicks were raised on commercial starter diets according to station-specific management routine. Then they were fed the experimental diets for a minimum of 5 d before content of the posterior half of the ileum was collected. A minimum of 6 experimental replicates per diet was used in each station. All diets and digesta samples were analyzed in the same laboratory. Diet, station, and their interaction significantly affected (P < 0.05) the prececal digestibility values of P and calcium of the diets. The prececal P digestibility of SBM was determined by linear regression and varied among stations from 19 to 51%, with significant differences among stations. In a subset of 4 stations, the prececal disappearance of myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate)-P; InsP6-P) also was studied. The prececal InsP6-P disappearance correlated well with the prececal P digestibility. We hypothesized that factors influencing InsP6 hydrolysis were main contributors to the variation in prececal P digestibility among stations. These factors were probably related to the feeding and housing conditions (floor pens or cages) of the birds in the pre-experimental phase. Therefore, we suggest that the World's Poultry Science Association protocol for the determination of digestible P be should extended to the standardization of the pre-experimental period. We also suggest that comparisons of P digestibility measurements among studies are made only with great caution until the protocol is more refined.

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs

The aim of the present study was to analyze the interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. The study design consisted of 207 pigs that were housed and slaughtered under standardized conditions, and phenotyped for daily gain, feed intake, and feed conversion rate. The pigs were genotyped with a standard 60 K SNP chip. The GIT microbiota composition was analyzed by 16S rRNA gene amplicon sequencing technology. Eight from 49 investigated bacteria genera showed a significant narrow sense host heritability, ranging from 0.32 to 0.57. Microbial mixed linear models were applied to estimate the microbiota variance for each complex trait. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota composition were used to predict the complex traits using genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods, respectively. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, in addition to SNP data, microbiota abundances are an informative source of complex trait predictions. Since the pig is a well-suited animal for modeling the human digestive tract, M-BLUP, in addition to G-BLUP, might be beneficial for predicting human predispositions to some diseases, and, consequently, for preventative and personalized medicine.

Quantitative genetic analysis of causal relationships among feather pecking, feather eating, and general locomotor activity in laying hens using structural equation models

The objective of this research was to analyze the relationship between feather pecking (FP) and feather eating (FE) as well as general locomotor activity (GLA) using structural equation models, which allow that one trait can be treated as an explanatory variable of another trait. This provides an opportunity to infer putative causal links among the traits. For the analysis, 897 F2-hens set up from 2 lines divergently selected for high and low FP were available. The FP observations were Box-Cox transformed, and FE and GLA observations were log and square root transformed, respectively. The estimated heritabilities of FE, GLA, and FP were 0.36, 0.29, and 0.20, respectively. The genetic correlation between FP and FE (GLA) was 0.17 (0.04). A high genetic correlation of 0.47 was estimated between FE and GLA. The recursive effect from FE to FP was [Formula: see text], and from GLA to FP [Formula: see text] These results imply that an increase of FE leads to an increased FP behavior and that an increase in GLA results in a higher FP value. Furthermore, the study showed that the genetic correlation among the traits is mainly caused by indirect effects.