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Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction
- Source :
- Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und ZuchtungsbiologieREFERENCES. 136(5)
- Publication Year :
- 2019
-
Abstract
- Reference populations for genomic selection usually involve selected individuals,which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is,Best Linear Unbiased Prediction of breeding values using pedigree‐based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and aSingle‐Step approach (SSGBLUP) using both. For a scenario with no‐selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices.Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single‐Step approach to obtain accurate and unbiased prediction of GEBV. Refereed/Peer-reviewed
- Subjects :
- 0301 basic medicine
Male
Breeding program
Genotype
selective genotyping
Quantitative Trait Loci
Genome-wide association study
Best linear unbiased prediction
Biology
genomic selection
03 medical and health sciences
Food Animals
prediction bias
Statistics
Genetic model
Animals
Computer Simulation
Selection (genetic algorithm)
GWAS
Assortative mating
0402 animal and dairy science
04 agricultural and veterinary sciences
General Medicine
040201 dairy & animal science
Pedigree
030104 developmental biology
Genetics, Population
Selective genotyping
Animal Science and Zoology
Female
Inbreeding
single‐step GBLUP
Subjects
Details
- ISSN :
- 14390388
- Volume :
- 136
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und ZuchtungsbiologieREFERENCES
- Accession number :
- edsair.doi.dedup.....936c401898a92abe356fa3911f8ea789