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

• DOI: 10.3389/fgene.2022.941340
• Publication Date: 2022-07-18T07:46:25Z
• Authors: Maria Bernard; Audrey Dehaullon; Guangtu Gao; Katy Paul; Henri Lagarde; Mathieu Charles; Martin Prchal; Jeanne Danon; Lydia Jaffrelo; Charles Poncet; Pierre Patrice; Pierrick Haffray; Edwige Quillet; Mathilde Dupont-N...; Yniv Palti; Delphine Lallias; Florence Phocas
• Keywords: SNP; SNP genotyping

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