{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T14:06:21Z","timestamp":1783951581025,"version":"3.55.0"},"reference-count":63,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T00:00:00Z","timestamp":1631491200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Ministerio de Ciencia e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["RTI2018\u2010093535\u2010B\u2010I00"],"award-info":[{"award-number":["RTI2018\u2010093535\u2010B\u2010I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Animal Genetics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>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\u2010positive results in genome\u2010wide association studies. Currently, whole\u2010genome resequencing (WGR) also offers the potential for variant calling analysis and high\u2010throughput genotyping. WGR might overshadow array\u2010based 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\u2010chip technologies, namely, Affymetrix and Illumina, for high\u2010throughput genotyping in sheep considering high\u2010coverage 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\u2010chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low\u2010reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction.<\/jats:p>","DOI":"10.1111\/age.13139","type":"journal-article","created":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T07:11:26Z","timestamp":1631517086000},"page":"868-880","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Study on the concordance between different SNP\u2010genotyping platforms in sheep"],"prefix":"10.1111","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9226-2902","authenticated-orcid":false,"given":"H.","family":"Marina","sequence":"first","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2047-0208","authenticated-orcid":false,"given":"P.","family":"Chitneedi","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9827-1292","authenticated-orcid":false,"given":"R.","family":"Pelayo","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7726-4288","authenticated-orcid":false,"given":"A.","family":"Su\u00e1rez\u2010Vega","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2425-000X","authenticated-orcid":false,"given":"C.","family":"Esteban\u2010Blanco","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7990-5723","authenticated-orcid":false,"given":"B.","family":"Guti\u00e9rrez\u2010Gil","sequence":"additional","affiliation":[{"name":"Departamento de Producci\u00f3n Animal Facultad de Veterinaria Universidad de Le\u00f3n Campus de Vegazana s\/n Le\u00f3n 24071 Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9058-131X","authenticated-orcid":false,"given":"J. 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