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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

40103 - Fishery

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

Kód důvěrnosti údajů

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

Název periodika

Frontiers in Genetics

ISSN

1664-8021

e-ISSN

—

Svazek periodika

13

Číslo periodika v rámci svazku

neuvedeno

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

16

Strana od-do

nestrankovano

Kód UT WoS článku

000835528600001

EID výsledku v databázi Scopus

2-s2.0-85135254783