Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Abstract

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.

GenoTriplo: A SNP genotype calling method for triploids

“…The experimental stock was established from 190 dams and 98 sires of a commercial selected all-female line of Aquaculteurs Bretons breeding company (Plouigneau, France) and 1232 triploid offspring and the 190 dams and 98 sires were genotyped for 57,501 SNPs using the medium-density Rainbow Trout Axiom® 57K SNP array from Thermo Fisher [30]. We retained the allelic signals for 38,033 high quality markers present in both SNP array [31,32]. Luminescence values of probsets A and B (S A and S B ) for each marker and individual were obtained through the AXAS software.…”

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

“…High-density genotypes were obtained at the INRAE genotyping Platform Gentyane (Clermont-Ferrand, France) for all the 176 French samples using the Affymetrix 665K SNP array recently developed for rainbow trout (Bernard et al, 2022). We only considered the genotypes for the 576,118 SNPs of the Rainbow Trout Axiom® 665K SNP array that were positioned on the Arlee genome (GCA_013265735.…”

“…We only considered the genotypes for the 576,118 SNPs of the Rainbow Trout Axiom® 665K SNP array that were positioned on the Arlee genome (GCA_013265735. 3, Gao et al, 2021;Bernard et al, 2022).…”

“…The first study in domesticated rainbow trout was performed on a single Chilean population (Cádiz et al, 2021) genotyped with a 57K SNP array; identified signatures of selection were associated with early development, growth, reproduction and immune system. Recently, a highdensity array (665K SNPs) was developed for rainbow trout (Bernard et al, 2022), allowing us to potentially more accurately detect signatures of selection and to compare them across various domesticated rainbow trout populations. The existence of signatures of selection shared by farmed populations from different geographical areas is essential to understand the importance of genetic diversity in several genomic regions in rainbow trout and then to identify genes having key roles in either the domestication process or fitness because conserved by all populations (Bruford et al, 2003;Yáñez et al, 2022).…”

SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array

“…Therefore, SNP‐arrays have valuable applications for the study of both wild and farmed populations and have been successfully applied across multiple taxa (Houston et al, 2014; Kranis et al, 2013; Michelizzi et al, 2011; Stoffel et al, 2012). Arrays are currently available for several farmed aquatic species including the Pacific ( Crassostrea gigas ) and European flat oysters ( Ostrea edulis ) (Gutierrez et al, 2017; Lapègue et al, 2014; Qi et al, 2017), Atlantic salmon ( Salmo sala r) (Houston et al, 2014), Rainbow trout ( Onchorynchus mykiss ) (Bernard et al, 2022; Palti et al, 2015) and Nile Tilapia ( Oreochromis niloticus ) (Joshi et al, 2018; Peñaloza et al, 2020), offering a rapid, accessible and cost‐effective approach for medium‐ and high‐density genotyping.…”