Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle

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cg.authorship.typesCGIAR and developing country institute
cg.authorship.typesCGIAR and advanced research institute
cg.contributor.affiliationUniversity of Edinburgh
cg.contributor.affiliationInternational Livestock Research Institute
cg.contributor.affiliationNational Veterinary Research Institute, Nigeria
cg.contributor.affiliationGhent University
cg.contributor.affiliationUniversity of Nigeria
cg.contributor.affiliationUniversity of Pretoria
cg.contributor.affiliationUniversity of Ghana
cg.contributor.affiliationLaboratoire National d'Appui au Dévéloppement Agricole, Côte d'Ivoire
cg.contributor.affiliationSokoine University of Agriculture
cg.contributor.affiliationCentral Vétérinaire de Diagnostic, Guinea
cg.contributor.affiliationÉcole Inter-États des Sciences et Médecine Vétérinaires de Dakar
cg.contributor.affiliationUniversité Polytechnique de Bobo-Dioulasso
cg.contributor.affiliationBill & Melinda Gates Foundation
cg.contributor.affiliationClinvet
cg.contributor.affiliationClinomics
cg.contributor.affiliationClinGlobal
cg.contributor.donorBill & Melinda Gates Foundation
cg.contributor.donorForeign, Commonwealth and Development Office, United Kingdom
cg.coverage.regionAfrica
cg.creator.identifierKaren Marshall: 0000-0003-4197-1455
cg.creator.identifierAppolinaire Djikeng: 0000-0001-9271-3419
cg.creator.identifierJames Prendergast: 0000-0001-8916-018X
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.1186/s12711-022-00751-5
cg.isijournalISI Journal
cg.issn1297-9686
cg.issue1
cg.journalGenetics Selection Evolution
cg.number58
cg.reviewStatusPeer Review
cg.subject.ilriANIMAL BREEDING
cg.subject.ilriCATTLE
cg.subject.ilriGENETICS
cg.subject.ilriLIVESTOCK
cg.volume54
dc.contributor.authorRiggio, V.
dc.contributor.authorTijjani, Abdulfatai
dc.contributor.authorCallaby, R.
dc.contributor.authorTalenti, A.
dc.contributor.authorWragg, D.
dc.contributor.authorObishakin, E.T.
dc.contributor.authorEzeasor, C.K.
dc.contributor.authorJongejan, F.
dc.contributor.authorOgo, N.I.
dc.contributor.authorAboagye-Antwi, F.
dc.contributor.authorTouré, A.
dc.contributor.authorNzalawahej, J.
dc.contributor.authorDiallo, B.
dc.contributor.authorMissohou, A.
dc.contributor.authorBelem, A.M.G.
dc.contributor.authorDjikeng, Appolinaire
dc.contributor.authorJulef, Nick
dc.contributor.authorFourie, J.
dc.contributor.authorLabuschagne, Maryke T.
dc.contributor.authorMadder, M.
dc.contributor.authorMarshall, Karen
dc.contributor.authorPrendergast, James G.D.
dc.contributor.authorMorrison, Liam J.
dc.date.accessioned2022-09-06T16:52:16Zen
dc.date.available2022-09-06T16:52:16Zen
dc.identifier.urihttps://hdl.handle.net/10568/121149
dc.titleAssessment of genotyping array performance for genome-wide association studies and imputation in African cattleen
dcterms.abstractIn cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array.We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS.Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.en
dcterms.accessRightsOpen Access
dcterms.audienceScientists
dcterms.available2022-09-04
dcterms.bibliographicCitationRiggio, V., Tijjani, A., Callaby, R., Talenti, A., Wragg, D., Obishakin, E.T., Ezeasor, C., Jongejan, F., Ogo, N.I., Aboagye-Antwi, F., Toure, A., Nzalawahej, J., Diallo, B., Missohou, A., Belem, A.M.G., Djikeng, A., Julef, N., Fourie, J., Labuschagne, M., Madder, M., Marshall, K., Prendergast, J.G.D. and Morrison, L.J. 2022. Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle. Genetics Selection Evolution 54:58.en
dcterms.issued2022-09-04
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringer
dcterms.subjectcattleen
dcterms.subjectanimal breedingen
dcterms.subjectgeneticsen
dcterms.subjectlivestocken
dcterms.typeJournal Article

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