Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

Abstract

Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.

Keywords: Abbassa; GIFT; Nile tilapia; SNP array; aquaculture.

Figure 1

MAF categories of SNPs from the ∼65K SNP-chip across nine different Nile tilapia strains / populations.

Figure 2

Number of informative SNPs (MAF > 0) shared among the four distinct strains evaluated in this study: Abbassa, Kenya, GIFT and FaST.

Figure 3

PCA representing the structure of different strains / populations used for the validation of the ∼65k SNP array. The total number of individuals (dots) is 125. Each dot is color coded according to its origin, as shown in the legend at the bottom right corner of the plot.

Figure 4

Linkage disequilibrium decay (r²) over distance (in kb) among different Nile tilapia strains / populations genotyped with the ∼65K SNP array. LD decay after applying a MAF threshold of 0.05 (left panel) and 0.1 (right panel).