High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus)

Abstract

Nile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world and so far, they are mainly based on conventional selection using genealogical and phenotypic information to estimate the genetic merit of breeders and make selection decisions. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure in the breeding goal. Thus, SNPs are required to investigate phenotype-genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed tilapias. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps including removing SNP based on genotype and site quality, presence of Mendelian errors, and non unique position in the genome, a total of high quality 50,000 SNP were selected for validation purposes. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNP in HWE; 37,843 (76%) and 45,171(90%) SNP with a MAF higher than 0.05 and; 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The final list of 50K SNPs will be very useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection as well as supporting genetic studies in farmed populations Nile tilapia using dense genome-wide information.

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

“…SNP arrays are powerful high-throughput genotyping tools that are increasingly becoming available for aquaculture species including Atlantic salmon (Salmo salar) (Houston et al 2014;Yáñez et al 2016), common carp (Cyprinus carpio) (Xu et al 2014), rainbow trout (Oncorhynchus mykiss) (Palti et al 2015), Pacific (Crassostrea gigas) and European (Ostrea edulis) oysters (Lapègue et al 2014;Qi et al 2017;Gutierrez et al 2017), catfish (Ictalurus punctatus and Ictalurus furcatus) (Liu et al 2014;Zeng et al 2017;), Arctic charr (Salvelinus alpinus) (Nugent et al 2019), tench (Tinca tinca) (Kumar et al 2019), and indeed Nile tilapia (Joshi et al 2018;Yáñez et al 2020). Compared to other high-throughput genotyping methods, such as RAD-Seq (Baird et al 2008), SNP arrays have the advantage of increased genotyping accuracy and SNP stability, as the same markers are interrogated each time (Robledo et al 2018a).…”

“…The two Nile tilapia SNP arrays developed to date are both focused on the broodstock strains of specific commercial breeding programs. One of the platforms was designed based on the analysis of the GenoMar Supreme Tilapia (GST) strain (Joshi et al 2018), whereas the other platform derived from the evaluation of two strains belonging to Aquacorporación Internacional (Costa Rica) and a GIFT population from AquaAmerica (Brazil) (Yáñez et al 2020). These SNP arrays have been shown to be highly effective in the discovery populations, and have been used to generate high-density linkage maps and perform tests of genomic selection (Joshi et al 2020;Yoshida et al 2019a).…”

Multi-trait GWAS using high-density genotypes identifies genes associated with body traits in Nile tilapia

“…We used a total of 1,309 phenotyped animals from 72 families (mean = 18, minimum = 7, and maximum = 25 animals per family) belonging to a breeding nucleus owned by Aquacorporación International group (ACI), Costa Rica. More details about the breeding program and the origin of the Nile tilapia population is described in detail [17,19,75].…”

“…The availability of a chromosome-level reference genome assembly [14] and highthroughput whole-genome sequencing (WGS) methods [15,16], has allowed for the assessment of genetic variation of different Nile tilapia populations at a genome-wide level and the recent development of single nucleotide polymorphism (SNP) panels [17,18]. The availability of Nile tilapia SNP panels made it possible to use modern molecular breeding approaches; including mapping of quantitative trait loci (QTL) through genome-wide association studies (GWAS), marker-assisted selection (MAS) and genomic selection [19,20].…”

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

“…Compared with RAD sequencing, the high-throughput SNP arrays showed higher repeatability and reproducibility, and more straightforward experimental procedures and bioinformatic analyses (Robledo et al, 2018). SNP arrays are efficient and robust tools for genomescale genotyping, which have been developed in many fish species including the 250K common carp array (Xu et al, 2014); the 250K and 690K catfish arrays (Liu et al, 2014;Zeng et al, 2017); the 50K and 58K Nile tilapia arrays (Joshi et al, 2018;Yáñez et al, 2020); the 50K and 57K rainbow trout arrays (Palti et al, 2015;Salem et al, 2018); the 15K, 286K, and 400K Atlantic salmon arrays (Gidskehaug et al, 2010;Houston et al, 2014;Yáñez et al, 2016); the 50K Japanese flounder array (Zhou et al, 2020); the 6K giant tiger shrimp array (Baranski et al, 2014); the 9K Pacific white shrimp array (Jones et al, 2017); and the 38K and 190K oyster arrays (Gutierrez et al, 2017;Qi et al, 2017). The applications of the high-density SNP array in GWAS have identified QTL associated with various traits in multiple species, including growth, disease resistance, heat stress, hypoxia tolerance, morphometric, sex, and body conformation (Abdelrahman et al, 2017;Zenger et al, 2019).…”