RNA-seq analysis of the kidneys of broiler chickens fed diets containing different concentrations of calcium

Calcium (Ca) is required for normal growth and is involved in cellular physiology, signal transduction, and bone mineralization. In humans, inadequate Ca intake causes hypocalcaemia, and excessive Ca intake causes hypercalcemia. In chicken, Ca is also required for body weight gain and eggshell formation. However, transcriptomic responses to low/high Ca intake, and mechanisms affecting body weight have not been explored. In this study, we performed comparative RNA sequencing (RNA-seq) using the kidney of broiler chickens fed diets containing 0.8, 1.0, and 1.2% Ca. Annotation of RNA-seq data revealed a significant number of differentially expressed genes (DEGs) in the kidney via pairwise comparison using Cufflinks and edgeR. Using edgeR, we identified 12 DEGs; seven overlapped with those found by cufflinks. Seven DEGs were validated by real-time quantitative-PCR (qRT-PCR) in Ca-supplemented kidneys, and the results correlated with the RNA-seq data. DEGs identified by cufflinks/edgeR were subjected to pathway enrichment, protein/protein interaction, and co-occurrence analyses to determine their involvement in disease. The National Research Council (NRC) recommended Ca intake for 21-day post-hatch broilers is about 1.0%. Our findings suggest that higher-than-recommended Ca intake (1.2%) could reduce body weight gain in broilers, and that affected DEGs are related to stress-induced diseases, such as hypertension.