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 57K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2 kb to 10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50 kb to 100 kb which are usual distances between markers of the medium-density chip.

Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

“…Among the genotyped individuals, eight offspring from B2 and one sire had less than 90% of the SNP genotyped and their genotypes were therefore removed from the analysis. SNP with probe polymorphism and multiple locations on the Arlee genome assembly (accession number: GCA_013265735.3; [35]) were also discarded from the analysis as described by Bernard et al [31]. In addition, only SNP with a call rate higher than 0.97, a test of deviation from Hardy- Weinberg equilibrium with a p-value > 0.00001 and a minor allele frequency higher than 0.05 were kept for the study.…”

“…The collected fin samples from the 99 sires, the 76 [30]. The 175 parents were genotyped for 664,531 SNP (high density (HD) genotypes) with the 665K SNP AxiomTM Trout Genotyping array from Thermo Fisher [31].…”

“…The 2,888 offspring of B1 and B2 were genotyped for 57,501 SNP (medium-density (MD) genotypes) with the 57K SNP AxiomTM Trout Genotyping array from Thermo Fisher 12 [30]. The 175 parents were genotyped for 664,531 SNP (high density (HD) genotypes) with the 665K SNP AxiomTM Trout Genotyping array from Thermo Fisher [31].…”

“…Therefore, heterozygous isogenic lines A32h and A22h shared the same maternal genetic basis but had different paternal genetic basis. Homozygous isogenic lines A32 and A22 have previously been sequenced to establish a catalogue of variants (Bernard et al, 2022). We only looked at the paternal genetic sequences A22 and A32 as maternal genetic sequence B57 was identical between A22h and A32h.…”

“…For this purpose, a group of fish issued from 76 females mated with 99 males in ten independent full- factorial blocks families was phenotyped at nine months for acute hyperthermia resistance and their sibs were phenotyped at twenty months, which is near harvest age (body weight around 1 kg), for production traits using a robust experimental design with over 1,300 phenotyped fish in each group. Phenotyped fish were genotyped for 57K SNP (Single Nucleotide Polymorphism markers) [30] and imputed to 665K SNP thanks to their parents being genotyped with a new high-density SNP array [31]. The main issues addressed in this study were to i) assess genetic parameters for acute hyperthermia resistance in juveniles, ii) estimate genetic correlations between acute hyperthermia resistance and production traits at harvest age, iii) detect with a powerful tool (665K SNP array) QTL associated with acute hyperthermia resistance and (iv) identify functional candidate genes.…”