Location: Cool and Cold Water Aquaculture Research
Title: Development of a high-density 665 K SNP array for rainbow trout genome-wide genotypingAuthor
BERNARD, MARIA - Inrae | |
DEHAULLON, A - Inrae | |
Gao, Guangtu | |
Palti, Yniv | |
PHOCAS, FLORENCE - Inrae | |
PAUL, K - Inrae | |
LAGARDE, H - Inrae | |
CHARLES, M - Inrae | |
PRCHAL, M - University Of South Bohemia | |
DANON, J - Inrae | |
JAFFRELO, L - Inrae | |
PONCET, C - Inrae | |
PATRICE, P - Inrae | |
HAFFRAY, PATRICK - Inrae | |
QUILLET, EDWIGE - Inrae | |
DUPONT-NIVET, MATILDE - Inrae | |
LALLIA, DELPHINE - 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. https://doi.org/10.1101/2022.04.17.488574. DOI: https://doi.org/10.1101/2022.04.17.488574 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. |