Effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci detection and genomic evaluation in a simulated cattle population

The objective of this study was to assess the effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci (QTL) detection and genomic evaluation using a simulated cattle population. Twelve generations (G1-G12) were simulated from the base generation (G0). The recent population had different effective population sizes, heritability, and number of QTL. G0-G4 were used for pedigree information. A total of 300 genotyped bulls from G5-G10 were randomly selected. Their progenies were generated in G6-G11 with different numbers of progeny per bull. Scenarios were considered according to the number of progenies and whether the genotypes were possessed by the bulls or the progenies. A genome-wide association study and genomic evaluation were performed with a single-step genomic best linear unbiased prediction method to calculate the power of QTL detection and the genomic estimated breeding value (GEBV). We found that genotyped bulls could be available for QTL detection depending on conditions. Additionally, using a reference population, including genotyped bulls, which had more progeny phenotypes, enabled a more accurate prediction of GEBV. However, it is desirable to have more than 4,500 individuals consisting of both genotypes and phenotypes for practical genomic evaluation.