Development of a high-density SNP array for rainbow trout genome-wide genotyping

Authors: BERNARD, MARIA - Inrae; DEHAULLON, A - Inrae; Gao, Guangtu; 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; Palti, Yniv; LALLIAS, DELPHINE - Inrae; PHOCAS, FLORENCE - Inrae

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/24/2022
Publication Date: 7/18/2022
Citation: Bernard, M., Dehaullon, A., Gao, G., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Palti, Y., Lallias, D., Phocas, F. 2022. Development of a high-density SNP array for rainbow trout genome-wide genotyping. Frontiers in Genetics. 13:941340. https://doi.org/10.3389/fgene.2022.941340.
DOI: https://doi.org/10.3389/fgene.2022.941340

Interpretive Summary: The continued development of rainbow trout genomics resources now allows commercial breeders and scientists to accurately predict the genetic merit of fish lacking phenotypic data based on analysis of their DNA, and also to identify the genes or chromosomal loci that affect the trait of interest. In this study, a new tool was developed for genomic and genetic assays. 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 (high density chip) for rainbow trout. Compared to the medium density 50K SNP chip that we have previously developed and used for genomic research in rainbow trout, this new tool enabled detection of much more refined changes in the rainbow trout genome. We demonstrated 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 the usual distances between markers of the commercial medium-density 50K SNP chip.

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.