Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping.
SNP
doubled haploid lines
high-density chip
isogenic lines
linkage disequilibrium
rainbow trout
sequence
single nucleotide polymorphism
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2022
2022
Historique:
received:
11
05
2022
accepted:
24
06
2022
entrez:
4
8
2022
pubmed:
5
8
2022
medline:
5
8
2022
Statut:
epublish
Résumé
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 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2-10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50-100 kb which are usual distances between markers of the medium-density chip.
Identifiants
pubmed: 35923696
doi: 10.3389/fgene.2022.941340
pii: 941340
pmc: PMC9340366
doi:
Types de publication
Journal Article
Langues
eng
Pagination
941340Informations de copyright
Copyright © 2022 Bernard, Dehaullon, Gao, Paul, Lagarde, Charles, Prchal, Danon, Jaffrelo, Poncet, Patrice, Haffray, Quillet, Dupont-Nivet, Palti, Lallias and Phocas.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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