Development and application of genomic tools for the genetic improvement of Nile Tilapia

Abstract

Nile Tilapia (Oreochromis niloticus) is the main aquaculture species in Brazil and the second most produced in the world. This species features high quality meat and great adaptation to a diversity of production systems. Tilapia production chain is the fastest growing sector within aquaculture and its annual growth rate has been of 10% for the past decade in Brazil. It is also believed that production growth will keep steady in the future due to the expanding market demand. On the other hand, profit margins have decreased significantly in the Brazilian tilapia market as a result of the competition with other domestic and foreign products. The genetic improvement of economically important production traits and those associated with diseases, where the use of genomics has demonstrated great potential with other species, is one of the paths to assure the future sustainability for the production of this important species. The economic impact of increasing fillet yield is very significant. For example, a 1.0% increase in fillet yield (from 31% to 32%) would increase gross receipts for a fish processing plant in 3,3%, without demanding any additional costs. The genetic improvement of tilapia aiming for better production performance is one alternative to assure its sustainability. Recent biotechnological developments, such as the use of SNP (Single Nucleotide Polymorphism) in the form of SNP chips, has allowed for new strategies in identifying the genes or genomic regions responsible for desirable characteristics. The genetic selection and improvement processes gain in time, efficiency and accuracy with this technology, as it has been shown in the poultry, swine, dairy and beef industries, which adopted such tools as the basis for their genetic programs. In aquaculture, the Atlantic Salmon (Salmo salar) is an example of the successful application of the SNP chips on genetic improvement programs. Considering that a commercial SNP chip for tilapia is unavailable up to date, it is not possible to have an in-depth information on the genetic tilapia lines available in Brazil and neither to make phenotype to genotype associations from the phenotypic data collected from individuals to integrate them into breeding or selection programs. This innovative research project aims to develop a genomic analysis tool for the Nile tilapia (SNP chip) with 50,000 SNP (TilapiaTG 50K), as well as the processes for analyzing the genomic data generated by the SNP chip focusing on the information required by genetic improvement programs (PMG) for tilapia (TRI-lapia Max). The objective is to develop an integrated system based on genomics tools (SNP chip and analysis of genomic data) that will allow for faster and more precise methods of selection of tilapia individuals that feature higher fillet yield and faster growth rate. In order to develop the SNP chip, biological samples (fin tissue) of fish specimens that represent the tilapia genetic variability in Brazil and around the world will be collected, their DNA prepared and undergone the NGS (Next Generation Sequencing). Then, the sequences will be aligned against the reference genome of the species to identify the best SNP. The SNP selected will be evenly spaced along the 22 tilapia chromosomes in order to access the entire genome in one test. Once the SNP chip is made available, a Genome-wide association study (GWAS) will be carried out by using specific bioinformatic processes to identify genomic markers associated with fillet yield and growth rate on commercially produced tilapia populations. (AU)