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

ABSTRACT:

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

We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. O

SUBMITTER: Riggio V 

PROVIDER: S-EPMC9441065 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature