RT info:eu-repo/semantics/article
T1 Study on the concordance between different SNP‐genotyping platforms in sheep
A1 Marina García, Héctor
A1 Chitneedi, Praveen Krishna
A1 Pelayo, Rocío
A1 Suárez Vega, Aroa
A1 Esteban-Blanco, Cristina
A1 Gutiérrez Gil, Beatriz
A1 Arranz Santos, Juan José
A2 Producción Animal
K1 Producción animal
K1 Affymetrix
K1 Genotype concordance
K1 High-throughput genotyping technologies
K1 Illumina
K1 Sheep
K1 Whole-genome resequencing
K1 3104 Producción Animal
AB [EN] Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction
PB Wiley-Blackwell
SN 0268-9146
LK http://hdl.handle.net/10612/14522
UL http://hdl.handle.net/10612/14522
NO Marina, H., Chitneedi, P., Pelayo, R., Suárez-Vega, A., Esteban-Blanco, C., Gutiérrez-Gil, B. and Arranz, J.J. (2021), Study on the concordance between different SNP-genotyping platforms in sheep. Anim Genet, 52: 868-880. https://doi.org/10.1111/age.13139
DS BULERIA. Repositorio Institucional de la Universidad de León
RD 19-abr-2024