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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12520%2F22%3A43904534" target="_blank" >RIV/60076658:12520/22:43904534 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.3389/fgene.2022.941340" target="_blank" >https://doi.org/10.3389/fgene.2022.941340</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fgene.2022.941340" target="_blank" >10.3389/fgene.2022.941340</a>

Result language

angličtina

Original language name

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

Original language description

Single nucleotide polymorphism (SNP) arrays, also named &lt;&lt; SNP chips &gt;&gt;, 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.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

40103 - Fishery

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Frontiers in Genetics

ISSN

1664-8021

e-ISSN

—

Volume of the periodical

13

Issue of the periodical within the volume

neuvedeno

Country of publishing house

CH - SWITZERLAND

Number of pages

16

Pages from-to

nestrankovano

UT code for WoS article

000835528600001

EID of the result in the Scopus database

2-s2.0-85135254783