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

Abstract

Tilapia are amongst 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 programmes 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 with known utility across multiple tilapia strains 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 several other farmed and wild 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.

Development and validation of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

“…When evaluating the MAF across European seabass and gilthead seabream populations, the allele frequency profiles were similar within species, and did not vary significantly by origin (either wild or farmed) ( Fig S1). The mean MAF across the European seabass (0.33) and gilthead seabream (0.31) populations was higher than that reported when validating SNP arrays in Nile tilapia (0.29) and rainbow trout (0.25) [15,22]. However, the high average MAF observed in this study is most likely influenced by the fact that most of the discovery populations were also used for the validation of the SNP chip.…”

“…Substantial genomic tools have been developed for both species, including the assembly and characterization of highquality reference genomes [13,14]. Medium or high density SNP arrays have been developed for several other important finfish aquaculture species such as rainbow trout (Oncorhynchus mykiss) [15], Atlantic salmon (Salmo salar) [16,17], catfish (Ictalurus furcatus and I. punctatus) [18,19], common carp (Cyprinus carpio) [20], Arctic charr (Salvelinus alpinus) [21], and Nile tilapia (Oreochromis niloticus) [22][23][24], which have been used for studies into population structure, genetic diversity, signatures of domestication, genetic architecture of traits of interest, and testing of genomic selection. A 57K SNP array was also recently developed for European sea bass [25] and has been applied to assess the genetic basis of resistance to viral nervous necrosis.…”

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

“…Nevertheless, we need to acknowledge the fact that a low‐density genotyping approach was followed in our study which could limit our ability to discriminate between populations of low genetic distance. Therefore, high‐density genotyping approaches through the application of either more frequent cutting restriction enzymes or the recently developed open access tilapia SNP array (Peñaloza et al, 2020) could be of value for predicting with higher accuracy the population of origin even among closely related samples.…”

Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Larimichthys crocea)

“…A high polymorphic SNP rate (83.38%) was observed during the evaluation of NingXin-I in the wild and cultured large yellow croaker populations. Compared with the other aquaculture species, about 67.5% polymorphic SNPs were identified during the assessment of the 690K catfish array (Zeng et al, 2017); 64.5 and 86.0% polymorphic SNPs were identified in the 50K (Salem et al, 2018) and 57K (Palti et al, 2015) rainbow trout arrays, respectively, 74.0 and 83.4% polymorphic SNPs were identified in the 58K (Joshi et al, 2018) and 65K (Peñaloza et al, 2020) Nile tilapia arrays, respectively; 70.4% polymorphic SNPs were identified in the 190K Pacific oyster array (Qi et al, 2017); 74.6% polymorphic SNPs were identified in the 38K combined-species SNPs array for Pacific and European oysters (Gutierrez et al, 2017); 67.5% polymorphic SNPs were identified in the 9K Pacific white shrimp array (Jones et al, 2017); 70.6% polymorphic SNPs were identified in the 6K black tiger shrimp array (Baranski et al, 2014); 79.6% polymorphic SNPs were identified in the 200K Atlantic salmon array (Yáñez et al, 2016); 74.06% polymorphic SNPs were identified in the 250K common carp array (Xu et al, 2014); and 74.7% polymorphic SNPs were identified in the 50K Japanese flounder array (Zhou et al, 2020). The polymorphic SNP rate of NingXin-I (83.38%) is one of the highest among aquaculture SNP arrays, although others have achieved also a high polymorphism rate, such as rainbow trout with 86.0%, and Nile tilapia with 83.4%.…”