Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia (Oreochromis aureus)

Abstract

Tilapias are very important to the world's aquaculture. As befitting fish of their tropical origin, their distribution, and culture practices are highly affected by low temperatures. In this study, we used genetic and genomic methodologies to reveal pathways involved in the response and tolerance of blue tilapia (Oreochromis aureus) to low temperature stress. Cold tolerance was characterized in 66 families of blue tilapia. Fish from cold-tolerant and cold-sensitive families were sampled at 24 and 12°C, and the transcriptional responses to low-temperature exposure were measured in the gills and liver by high-throughput mRNA sequencing. Four hundred and ninety four genes displayed a similar temperature-dependent expression in both tolerant and sensitive fish and in the two tissues, representing the core molecular response to low temperature exposure. KEGG pathway analysis of these genes revealed down-regulation of focal-adhesion and other cell-extracellular matrix (ECM) interactions, and up-regulation of proteasome and various intra-cellular proteolytic activities. Differential responses between cold-tolerant and cold-sensitive fish were found with genes and pathways that were up-regulated in one group and down-regulated in the other. This reverse response was characterized by genes involved in metabolic pathways such as glycolysis/gluconeogenesis in the gills and biosynthesis of amino-acids in the liver, with low temperature down-regulation in tolerant fish and up-regulation in sensitive fish.

Keywords: Oreochromis; carbon metabolism; cold tolerance; selective breeding; tilapia; transcriptome.

Figure 1

Phenotypic distribution of cold tolerance, as measured in median survival day, of 66 blue tilapia families that were challenged under declined temperature regime (n = 10–15 fish/family). Resistant families are highlighted in purple and tolerant families in green. Families used for transcriptome sequencing are marked with stripes.

Figure 2

Non-metric multidimensional scaling (NMDS) of gene expression profiles, based on Jaccard similarity (presence/absence of genes), in (A) both the gills and liver of cold-tolerant and cold-sensitive fish, (B) only the gills, and (C) only the liver, at warm (24°C) and cold (12°C) water.

Figure 3

Number of Differentially Expressed Genes (DEGs) (A) and differentially enriched KEGG pathways (B) in the gills and liver of the cold tolerant and sensitive families, showing both up- (red) and down-regulation (blue).

Figure 4

Up- and down-regulated fold changes belonging to different KEGG pathways in the gills and liver of cold tolerant and sensitive fish.

Figure 5

KEGG pathways with differential temperature-dependent regulation between cold sensitive and cold tolerant blue tilapia, glycolysis/gluconeogenesis in the gills (A) and biosynthesis of amino-acids in the liver (B). Up-regulated genes in these pathways were found only in the cold sensitive fish and are marked in red, whereas down-regulated genes in these pathways were found only in the cold tolerant fish and are marked in blue.

Figure 6

qPCR validation of eight DEG obtained from the Illumina deep-sequencing (NGS) analysis. Comparison of transcript expression levels measured using NGS (black bars), and as calculated from qPCR reactions (gray bars), in the same fish from families 480 and 740 (A). Temperature-dependent expression of the same genes in fish from additional four families (430, 460, 720, 730), analyzed by qPCR (B).