Ileal Transcriptome Profiles of Japanese Quail Divergent in Phosphorus Utilization

Abstract

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.

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

“…2020) and transcriptomic profiles (Oster et al . 2020) as well as miRNA–mRNA and gut microbiota (Ponsuksili et al . 2020) on the focal trait PU and other related traits.…”

“…In addition, ileal transcriptome profiles, miRNA–mRNA and gut microbiome interactions of subsets of quails with divergent PU have been studied (Oster et al . 2020; Ponsuksili et al . 2020).…”

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

“…The mRNA expression data of the same samples from our previous study [20] were used for pairwise correlation analysis. The threshold for differential expression was set at an s-value of 0.10 for miRNA and a q-value of 0.10 for mRNA for the pairwise correlation analysis.…”

“…DESeq2 was used for calculating variance-stabilizing transformations of the miRNA and the mRNA count matrices derived from the same animals in a complementary study [20]. Afterwards, the function removeBatchEffect() from the R package limma [62] was used to remove the batch effects of sequencing lane, BV1, and BV2 from the transformed miRNA expression matrix.…”

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

“…The most promising molecules mediating between gut microbiota and host are microRNAs (miRNAs), which are conserved between species and can regulate gene expression across species. We previously identified differentially abundant miRNAs, mRNAs and microbiota in the gut of Japanese quail representing extremes for PU [1,2].…”