Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.
Trop Anim Health Prod
; 54(2): 90, 2022 Feb 08.
Article
em En
| MEDLINE
| ID: mdl-35133512
ABSTRACT
Imputation may be used to rescue genomic data from animals that would otherwise be eliminated due to a lower than desired call rate. The aim of this study was to compare the accuracy of genotype imputation for Afrikaner, Brahman, and Brangus cattle of South Africa using within- and multiple-breed reference populations. A total of 373, 309, and 101 Afrikaner, Brahman, and Brangus cattle, respectively, were genotyped using the GeneSeek Genomic Profiler 150 K panel that contained 141,746 markers. Markers with MAF ≤ 0.02 and call rates ≤ 0.95 or that deviated from Hardy Weinberg Equilibrium frequency with a probability of ≤ 0.0001 were excluded from the data as were animals with a call rate ≤ 0.90. The remaining data included 99,086 SNPs and 360 Afrikaner, 75,291 SNPs and 288 animals Brahman, and 97,897 SNPs and 99 Brangus animals. A total of 7986, 7002, and 7000 SNP from 50 Afrikaner and Brahman and 30 Brangus cattle, respectively, were masked and then imputed using BEAGLE v3 and FImpute v2. The within-breed imputation yielded accuracies ranging from 89.9 to 96.6% for the three breeds. The multiple-breed imputation yielded corresponding accuracies from 69.21 to 88.35%. The results showed that population homogeneity and numerical representation for within and across breed strategies, respectively, are crucial components for improving imputation accuracies.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Bovinos
/
Genoma
/
Genótipo
Limite:
Animals
País/Região como assunto:
Africa
Idioma:
En
Revista:
Trop Anim Health Prod
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
África do Sul