Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.
Journal
Genetics, selection, evolution : GSE
ISSN: 1297-9686
Titre abrégé: Genet Sel Evol
Pays: France
ID NLM: 9114088
Informations de publication
Date de publication:
04 Sep 2022
04 Sep 2022
Historique:
received:
28
02
2022
accepted:
17
08
2022
entrez:
3
9
2022
pubmed:
4
9
2022
medline:
8
9
2022
Statut:
epublish
Résumé
In 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) (r 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.
Sections du résumé
BACKGROUND
BACKGROUND
In 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.
RESULTS
RESULTS
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) (r
CONCLUSIONS
CONCLUSIONS
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.
Identifiants
pubmed: 36057548
doi: 10.1186/s12711-022-00751-5
pii: 10.1186/s12711-022-00751-5
pmc: PMC9441065
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
58Subventions
Organisme : Bill and Melinda Gates Foundation
ID : OPP1127286
Organisme : Bill and Melinda Gates Foundation
ID : OPP1125367
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/30002275
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/10002070
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/20002172
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s).
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