Genome-wide identification of DNA methylation marks associated with resistance to Streptococcus agalactiae in the GIFT strain of Nile Tilapia (Oreochromis niloticus)

Abstract

Epigenetic mechanism plays a pivotal role in the immune responses of fish. Streptococcus agalactiae (SA) infection is a significant challenge to tilapia aquaculture. DNA methylation involved in immune responses in tilapia against SA is unclear. Here, by using a QTLseq strategy integrated with whole-genome bisulfite sequencing-based DNA methylation analysis (methyl-QTLseq) and RNA sequencing (RNA-seq), we identified 3608 differentially methylated regions (DMRs) and 4355 differentially expressed genes (DEGs) in the spleen of Nile tilapia Oreochromis niloticus. Compared to the susceptible group, the up-regulated DMRs (2449) were approximately twice as many as the down-regulated DMRs (1159). Compared to the susceptible group, lower methylation levels for CpG, CHG and CHH in TEs and for CHG and CHH in genes and significant decreased expression for 8 of the 11 DNA methyltransferase genes in the resistant group were detected. 46 DEGs with differentially methylated promoter regions (DMPs) were significantly enriched in immune processes such as T cell differentiation and adaptive immunity. We detected 4 methyl-QTLs located on LG8:5332501–5,336,400, LG14:2307301–2,353,500, LG16:16889101–16,903,500, and LG22:25238401–2,536,880 across the tilapia genome. The methyl-QTL region located within the chromosome LG22:25238401–25,368,800 contains the most DMRs (91) and DMGs (7). Interestingly, most of the annotated genes that located within or under the peak of the methyl-QTL interval belong to the HOX protein family including hoxa1, hoxa2, hoxa4a and hoxa5a. Bisulfite sequencing PCR and expression analysis indicated that DNA methylation in the promoter regions of hoxa4a, lcp2a, and ccr9a regulated gene expression in spleen in response to SA infection. Overall, our study provides epigenetics evidences involving in immune responses against SA infection in tilapia.