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Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping

item BERNARD, MARIA - Inrae
item DEHAULLON, A - Inrae
item Gao, Guangtu
item Palti, Yniv
item PAUL, K - Inrae
item LAGARDE, H - Inrae
item CHARLES, M - Inrae
item PRCHAL, M - University Of South Bohemia
item DANON, J - Inrae
item JAFFRELO, L - Inrae
item PONCET, C - Inrae
item PATRICE, P - Inrae
item QUILLET, EDWIGE - Inrae

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 4/18/2022
Publication Date: 4/19/2022
Citation: Bernard, M., Dehaullon, A., Gao, G., Palti, Y., Phocas, F., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Lallia, D. 2022. Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. bioRxiv. 488574.

Interpretive Summary:

Technical 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 prexisting variant datasets from USDA, 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 identied 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, prioritising 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 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 initial 57K chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2kb 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 commercial medium-density chip.