Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia.

Grace Lin,Z Y Wan,Natascha M Thevasagayam,B Q Ye,Gen Hua Yue

doi:10.3389/fgene.2019.00244

Abstract

Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage.

Highlights

Candidate genes are important for understanding the phenotypic variations (Yue, 2014)
We focused on the differentially expressed genes (DEGs) that are located in QTL for growth and omega-3 contents, which were identified in a previous study (Lin et al, 2018), to facilitate the identification of candidate genes and their polymorphisms that underlie the phenotypic variation of growth and fatty acid content, especially omega-3 fatty acids, in the population
We used RNA-seq in combination with a previous study on QTL mapping (Lin et al, 2018) to identify candidate genes to improve our understanding of the molecular mechanisms underlying growth and lipid biosynthesis in saline tilapia

Summary

Introduction

Candidate genes are important for understanding the phenotypic variations (Yue, 2014). Genes for Omega-3 in Tilapia (Schuster, 2007), transcriptome analysis (Wang et al, 2009) becomes a powerful tool for identifying candidate genes related to important traits (Qian et al, 2014). RNA-seq is one of the important tools for analysis of transcriptomes (Wang et al, 2009). Through RNA-seq, many candidate genes have been identified for some important traits (Qian et al, 2014). By combining transcriptome analysis and QTL mapping, it is possible to identify causative genes underlying important traits (Yue, 2014; Yue and Wang, 2017). The knowledge on the relationship between genotypes and phenotypes will enhance our understanding about phenotypic variations and identify DNA markers for markerassisted selection (MAS) to accelerate the genetic improvement (Liu, 2008; Yue, 2014)

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Conclusion