Genome-wide search for quantitative trait loci (QTL) and genes for increased growth and improved fatty acid content in salt tolerant tilapia (oreochromis spp.)

• Main Author: Lin, Grace Xiulin
• Other Authors: Valerie Lin Chun Ling
• Format: Theses and Dissertations
• Language: English
• Published: 2018
• Subjects: DRNTU::Science::Biological sciences::Genetics; DRNTU::Science::Biological sciences::Zoology::Vertebrates
• Online Access: http://hdl.handle.net/10356/74843
• Institution: Nanyang Technological University

Tilapias are the second most important group of farmed fish in the world. Increasing demands for fish as a protein source as well for heart health and decreasing land space due to the growing population has highlighted the importance of breeding fast growing salt tolerant tilapia strains/hybrids with high omega 3 fatty acids for aquaculture. Prior to this project, there was little information about growth and omega 3 fatty acid content in saline tilapia as previous studies were mainly based on freshwater tilapia. This Ph.D. project aims to conduct quantitative trait loci (QTL) mapping for growth traits and fatty acid profiles and to identify for candidate genes located in significant QTL using RNA sequencing in salt tolerant tilapia to accelerate the genetic improvement of these two important traits. It also seeks to improve the understanding of the mechanisms underlying phenotypic variation of growth traits and fatty acid profiles. In the first part of the thesis, QTL mapping for growth, sex and fatty acid content have been conducted in an F2 family of salt tolerant tilapia with 522 individuals. To conduct QTL mapping, linkage maps were constructed. Genotype by sequencing (GBS) technology was utilised to discover and genotype Single Nucleotide Polymorphism (SNP) markers, and together with microsatellites, the first densest linkage map with 784 markers, consisting of 22 linkage groups for saline tilapia was constructed. Phenotyping of growth and fatty acid traits were also carried out. The growth of the salt-tolerant tilapia was comparable to Nile tilapia that were selected for increased growth. The omega 3 fatty acid content of salt tolerant tilapia was much higher than that in freshwater tilapia and was comparable to that of fatty fishes such as mackerel and chinook salmon. QTL mapping was first conducted using the microsatellite-based linkage map and showed that salt tolerant tilapia had two sex associated genomic regions on LG 1 and LG 22, explaining 19.8% and 10.8% of the phenotypic variance respectively. Additionally, growth-associated regions in male and female offspring were generally different; for male offspring, QTL were located on LG 2 and 18, explaining 5.1% to 10.1% and 8.5% to 10.2% of phenotypic variance, respectively and for female offspring, QTL was located xvi on LG 8 and explained 10.4% to 19.9% of phenotypic variance in the population. To improve resolution on the QTL for growth and omega 3 fatty acids, the microsatellite and SNP marker based linkage map was utilized for mapping. This QTL mapping detected two significant QTL for growth on LG 2 and 6, explaining 5.1% and 3.6% to 5.2% of phenotypic variance, respectively. For total lipid and fatty acid content, one genome-wide QTL detected on LG 8, explaining 5.6 to 8.3% phenotypic variance was associated with four traits and 14 significant QTL detected on six LG, namely LG 4, 13, 15, 16, 18 and 20, explaining 6.5% to 17.0% of phenotypic variance were associated with nine traits in the population. The markers flanking the QTL for growth and omega 3 fatty acids can be used in MAS to accelerate the genetic improvements of salt tolerant tilapia for these traits. For the second part of the thesis, a reference transcriptome was generated and differentially expressed genes in the dorsal muscle and liver between fast and slow growing tilapia were identified using RNA sequencing. Pathway analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was conducted to classify these genes into different pathways. From the differentially expressed genes identified, ten genes are found to be located within or at close proximity to QTL detected for growth and omega 3 fatty acid content in salt tolerant tilapia. These ten genes could be candidate genes for growth and omega 3 fatty acid content. In addition, qRT-PCR was conducted and verified the differential expression of these ten genes in the dorsal muscle and liver between fast and slow growing fishes.To summarize, the data obtained through QTL mapping and RNA sequencing clearly suggest the multitude of genomic regions and/or genes that may underlie the phenotypic variations in growth and omega 3 fatty acids in salt tolerant tilapia. Nonetheless, this study lays the groundwork for further investigation of the molecular mechanisms and underlying cause of the phenotypic variation of these two traits. Markers tightly linked to the QTL for growth and omega-3 content could be used in xvii marker-assisted selection (MAS) programmes to accelerate the improvement of growth performance and meat quality of salt tolerant tilapia.