Transcriptomic responses to yam ( Dioscorea oppositifolia L .) extract dietary supplementation in rainbow trout ( Oncorhynchus mykiss ) liver

Abstract

Infectious diseases in rainbow trout (Oncorhynchus mykiss) have been seen in rainbow trout farming industry. Yam (Dioscorea oppositifolia L.) has a functional impact upon anti-disease and strengthens immunity. Understanding the molecular mechanisms which occur in rainbow trout in response to yam will be useful to decrease disease-related morbidity and mortality. In the present study, we conducted transcriptome analysis of liver in rainbow trout fed diets including yam extract (0, 0.2% and 0.4%), to identify yam extract-induced genes and pathways. Over 451 million clean reads were obtained from nine liver libraries. Two comparisons were separately implemented between yam extract groups and control group. Using |log2Fold-change|>1 and p-value < .05 as the threshold, a total of 2,693 differentially expressed unigenes (DEGs) were identified, including 1599 up-regulated and 1,094 down-regulated unigenes. The RNA-Seq results were verified by RT-qPCR. DEGs were classified into three categories by GO annotation and functional enrichment analysis: biological process (23 subclasses), cellular component (16 subclasses) and molecular function (16 subclasses). KEGG annotation and classifications of DEGs indicated endocrine system, immune system, lipid metabolism, carbohydrate metabolism and signal transduction pathways include a large number of DEGs. In addition, 526 overlap DEGs in two comparisons were annotated to 174 pathways in KEGG analysis, 7 top significantly enriched pathway terms include chemokine signalling pathway, platelet activation, progesterone-mediated oocyte maturation, insulin signalling pathway, FoxO signalling pathway, cGMP-PKG signalling pathway and sphingolipid signalling pathway. These findings provide valuable information for further analysis of the disease resistance mechanisms of rainbow trout fed yam.