Effect of the number of QTL of carcass weight on the accuracy of genomic estimated breeding values in Hanwoo

Abstract

The objective of this study was to investigate the relationship between the number of QTL (Quantitative Trait Loci) affecting the carcass weight of Hanwoo and the accuracy of GEBV (Genomic Estimated Breeding Values). The study was performed simulation study to generate three populations comprising 100, 500 and 1,000 QTL. Each population consisted of 13,500 individuals which were selected from the 6th to 10th generations of all 10 generations, while keeping litter size constant (N=1) in population parameters. The genetic parameters for these populations were set at 0.45 trait heritability, 0.3 QTL heritability and 48,578 total markers. In order to confirm the number of significant QTL under the threshold of Bonferroni correction, both GWAS (Genome-wide association study) and GWAS based on Random Forest (RF) were performed. In each population, there were 33, 50 and 32 QTL identified by only GWAS, with 100, 500 and 1,000 QTL. Additionally, RF-based GWAS detected 65, 260 and 491. These results showed that the number of significant QTL is not related to the overall number of QTL in the population. Furthermore, machine learning based GWAS is more accurate than solely using GWAS. To estimate the accuracy of GEBV (Genomic Best Linear Unbiased Prediction) in each population, 5-fold cross-validation was employed using SNP effect of the QTL over p-value. In the result of the estimation, GEBV rose with an increase in the number of QTL in the population, and the correlation between TBV (True Breeding Values) followed the same tendency. As a result, this study suggested that the number of QTL related to carcass weight in Hanwoo could exert a significant influence on genetic improvement.