Abstract
Simple SummaryIn this study, we investigated the brain, gill, liver, and muscle transcriptomic responses of Taiwan tilapia towards cold stress. Some key genes and molecular markers involved in cold biological pathways were screened through differential expression. Among them, energy-related metabolic pathways and nucleotide genotypes were highly correlated with cold tolerance traits. This suggested that single nucleotide polymorphism (SNP) genetic variation can be used as a molecular marker to assist the selection and verification of cold-tolerant populations. Our study results will accelerate the understanding of different farmed tilapia tolerance mechanisms to environmental temperature changes and provide insights for the molecular breeding of cold-tolerant Taiwan tilapia species.Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.
Highlights
Due to the extreme climate and environmental changes caused by global warming that include unusual snowfall and frequent winter cold currents, all biological communities and ecosystems have been impacted [1]
The results revealed that the low-temperature treatment process resulted in significant differences in gene expression between cold-tolerance (CT) and cold-sensitivity (CS) fish
Research comparing the cold-tolerance characteristics among the different Nile tilapia species located in different geographic locations such as Egypt, Ghana, and the Ivory Coast revealed that Nile tilapia have survived through natural selection for many years, and the physiologies and lethal temperature ranges reflect different cold-tolerant phenotypic characteristics acquired from their ancestral populations [42,43]
Summary
Due to the extreme climate and environmental changes caused by global warming that include unusual snowfall and frequent winter cold currents, all biological communities and ecosystems have been impacted [1]. Taiwan is located in a tropical/subtropical region. The majority of aquaculture production is dominated by subtropical fish species. High temperatures in summer and typhoons, heavy rainfall, low temperature, and cold currents in winter along with other extreme abnormal weather have caused serious damage to aquaculture fisheries and economic losses [4]. Given the tropical origin of these fish, 20–30 ◦ C is the optimal growth temperature for most tilapia. In addition to many genetic studies examining low temperature tolerance in different tilapia species, a number of countries have developed cultivated tilapia strains exhibiting different degrees of cold-tolerance through selection and hybridization [6,7]. In Taiwan, after years of research, genetic improvement, and certification, tilapia fish have gradually become a unique and high-quality strain. The industry termed these fish “Taiwan tilapia” [8]
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