Comparison of the estimated breeding value and accuracy by imputation reference Beadchip platform and scaling factor of the genomic relationship matrix in Hanwoo cattle

Soo Hyun  Lee1   Chang Gwon  Dang1   Mina  Park1   Seung Soo  Lee1   Young Chang Lee1   Jae Gu Lee1   Hyuk Kee  Chang1   Ho Baek  Yoon1   Chung-il  Cho2   Sang Hong  Lee3   Tae Jeong  Choi1,*   

1Animal Genetics & Breeding Division, National Institute of Animal Science, Cheonan 31000, Korea
2Hanwoo Genetic Improvement Center, NongHyup Agribusiness Group Inc., Seosan 31948, Korea
3South Australian Health and Medical Research Institute, University of South Australia, Adelaide 5000, Australia


Hanwoo cattle are a unique and historical breed in Korea that have been genetically improved and maintained by the national evaluation and selection system. The aim of this study was to provide information that can help improve the accuracy of the estimated breeding values in Hanwoo cattle by showing the difference between the imputation reference chip platforms of genomic data and the scaling factor of the genetic relationship matrix (GRM). In this study, nine sets of data were compared that consisted of 3 reference platforms each with 3 different scaling factors (-0.5, 0 and 0.5). The evaluation was performed using MTG2.0 with nine different GRMs for the same number of genotyped animals, pedigree, and phenotype data. A five multi-trait model was used for the evaluation in this study which is the same model used in the national evaluation system. Our results show that the Hanwoo custom v1 platform is the best option for all traits, providing a mean accuracy improvement by 0.1 - 0.3%. In the case of the scaling factor, regardless of the imputation chip platform, a setting of -1 resulted in a better accuracy increased by 0.5 to 1.6% compared to the other scaling factors. In conclusion, this study revealed that Hanwoo custom v1 used as the imputation reference chip platform and a scaling factor of -0.5 can improve the accuracy of the estimated breeding value in the Hanwoo population. This information could help to improve the current evaluation system.

Figures & Tables

Fig. 1. Correlation of marbling score genomic breeding value by Beadchip platform and genomic relationship matrix (GRM) using each scaling factor (SF). v1, Hanwoo custom v1 platform; v2, Illumina bovine v2 platform; v3, Illumina bovine v3 platform; (1), scaling factor 0.5; (0), scaling factor 0; (-1), scaling factor 0.5.