| Title: |
Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers |
| Authors: |
Doublet, Mathilde; Degalez, Fabien; Lagarrigue, Sandrine; Lagoutte, Laetitia; Gueret, Elise; Allais, Sophie; Lecerf, Frédéric |
| Contributors: |
Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage Rennes (PEGASE); Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro); Montpellier GenomiX (MGX); BioCampus (BCM); Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM); ANR-10-GENM-0015,UtOpIGe,Vers une Utilisation Optimale de l'Information Génomique dans les schémas pyramidaux(2010) |
| Source: |
ISSN: 1932-6203. |
| Publisher Information: |
CCSD; Public Library of Science |
| Publication Year: |
2024 |
| Collection: |
Université de Montpellier: HAL |
| Subject Terms: |
[SDV.GEN]Life Sciences [q-bio]/Genetics |
| Description: |
Data is deposited in the European Nucleotide Archive (ENA) with the accession number PRJEB58821 and PRJEB71464. ; International audience ; Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens. Until now, breeding companies have been using or developing SNP chips. Nevertheless, alternatives methods based on sequencing have been developed. Among these, reduced representation sequencing approaches can offer sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability of double digested Restriction site Associated DNA sequencing (ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CR SNP ) and mean depth of sequencing per SNP (DP SNP ) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CR SNP of 0.55, a DP SNP of 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CR SNP and DP SNP values were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CR SNP (0.25) and DP SNP (1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CR SNP , DP SNP , genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a ... |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
WOS: 001282321500018 |
| DOI: |
10.1371/journal.pone.0298565 |
| Availability: |
https://hal.inrae.fr/hal-04666242; https://hal.inrae.fr/hal-04666242v1/document; https://hal.inrae.fr/hal-04666242v1/file/journal.pone.0298565.pdf; https://doi.org/10.1371/journal.pone.0298565 |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.3D06C242 |
| Database: |
BASE |