2024-03-28T10:25:41Zhttp://buleria.unileon.es/oai/requestoai:buleria.unileon.es:10612/145222022-11-10T12:01:30Zcom_10612_17col_10612_18
Facultad de Veterinaria
Marina, H.
Chitneedi, Praveen Krishna
Pelayo, Rocío
Suárez Vega, Aroa
Esteban-Blanco, Cristina
Gutiérrez Gil, Beatriz
Arranz Santos, Juan José
Producción Animal
2021
2022-04-06T12:52:00Z
2022-04-06T12:52:00Z
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
0268-9146
https://onlinelibrary.wiley.com/doi/10.1111/age.13139
http://hdl.handle.net/10612/14522
10.1111/age.13139
1365-2052
[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
SI
eng
Wiley-Blackwell
Attribution-NonCommercial-NoDerivatives 4.0 Internacional
http://creativecommons.org/licenses/by-nc-nd/4.0/
info:eu-repo/semantics/openAccess
Producción animal
Affymetrix
Genotype concordance
High-throughput genotyping technologies
Illumina
Sheep
Whole-genome resequencing
3104 Producción Animal
Study on the concordance between different SNP‐genotyping platforms in sheep
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
info: eu-repo/grantAgreement/AEI/Programa Estatal de I+D+i Orientada a los Retos de la Sociedad/RTI2018-093535-B-I00/ANALISIS DEL PAPEL DE LAS DE MARCAS EPIGENETICAS Y DE LA VARIABILIDAD GENOMICA EN LA REGULACION DE LA TRANSCRIPCION EN TEJIDOS DE INTERES PRODUCTIVO EN EL GANADO OVINO LECHERO
Animal Genetics
52
6
868
880