High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus)

Abstract

25Nile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a 26 sustainable source of protein for human consumption. Several genetic improvement programs have been 27 established for this species in the world and so far, they are mainly based on conventional selection using 28 genealogical and phenotypic information to estimate the genetic merit of breeders and make selection 29 decisions. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to 30 measure in the breeding goal. Thus, SNPs are required to investigate phenotype-genotype associations 31 and determine the genomic basis of economically important traits. We performed de novo SNP discovery 32 in three different populations of farmed tilapias. A total of 29.9 million non-redundant SNPs were 33 identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After 34 applying several filtering steps including removing SNP based on genotype and site quality, presence of 35Mendelian errors, and non unique position in the genome, a total of high quality 50,000 SNP were selected 36 for validation purposes. These SNPs were highly informative in the three populations analyzed showing 37 between 43,869 (94%) and 46,139 (99%) SNP in HWE; 37,843 (76%) and 45,171(90%) SNP with a MAF 38 higher than 0.05 and; 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The final list 39 of 50K SNPs will be very useful for the dissection of economically relevant traits, enhancing breeding 40 programs through genomic selection as well as supporting genetic studies in farmed populations Nile 41 tilapia using dense genome-wide information. 42 43

Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia (Oreochromis niloticus)

“…Genomic DNA was extracted from fin clip samples from 108 parents (45 sires and 63 dams) and 1,364 offspring from year-class 2017. Samples were then genotyped using a 50K SNP Illumina BeadChip, which is described in detail by Yáñez et al (2019). Genomic DNA was purified from all the samples using the DNeasy Blood & Tissue Kit (QIAGEN) according to the manufacturer’s protocol.…”

“…The incorporation of genomic information for genetic analysis has not been evaluated or implemented in tilapia breeding programs. This is mainly due to the fact that dense SNP panels were not available until recently (Joshi et al 2018; Yáñez et al 2019). The use of genomic information for the implementation of genomic selection has already been assessed in various aquaculture species, e.g.…”

Genome-Wide Patterns of Population Structure and Linkage Disequilibrium in Farmed Nile Tilapia (Oreochromis niloticus)

“…The genotypes were selected from a whole-genome sequencing experiment aimed at designing a 50K SNP Illumina BeadChip, which is described in detail by Yáñez et al (2019). Briefly, caudal fin-clip were sampled from 59, 126 and 141 individuals belonging to POP A, POP B and POP C, respectively.…”

“…About 36 million polymorphic sites were discovered after variant calling using the Genome Analysis Toolkit GATK (McKenna et al, 2010). A list of 50K SNP were selected based on quality of genotype and site, number of missing values, minor allele frequency (MAF), unique position in the genome, and even distribution across the genome as described by Yáñez et al (2019). Genotype quality control (QC) was performed within each population separately, excluding SNPs with MAF lower than 5%, Hardy–Weinberg Equilibrium P-value < 1e −06 , and missing genotypes higher than 70%.…”

“…The recent development of dense SNP panels for Nile tilapia (Joshi et al, 2018; Yáñez et al, 2019) will provide new opportunities for uncovering the genetic basis of important commercial traits; especially in those traits that are difficult or expensive to measure in selected candidates. As has been demonstrated for different traits in salmonid species, the incorporation of genomic evaluations in breeding programs is expected to increase the accuracy of breeding values, compared to pedigree-based methods (Tsai et al, 2016; Bangera et al, 2017; Correa et al, 2017; Sae-Lim et al, 2017; Yoshida et al, 2017; Barria et al, 2018b; Vallejo et al, 2018; Yoshida et al, 2019a).…”