Genome-wide association study comparison analysis based on Hanwoo full-sib family

Abstract

Objective The improvement of carcass traits is essential for the Hanwoo industry because of the Hanwoo grade determination system, and genome-wide association study (GWAS) analysis is an instrumental tool for identifying the genetic factors that impact these traits. While GWAS analysis utilizing family data offers advantages in minimizing genetic bias, research on family-based GWAS in Hanwoo is currently lacking. Methods This study classified Group A using both parental and offspring genetic information, and Group B based solely on offspring genetic information, to compare GWAS analysis results of Hanwoo carcass traits. Results A total of 16 significant single nucleotide polymorphism (SNP) markers were identified in Group A, comprising 7 for carcass weight (CWT), 3 for back fat thickness (BFT), and 6 for marbling score (MS). In Group B, 7 significant SNP markers were identified, including 3 for CWT, 1 for eye muscle area, 1 for BFT, and 2 for MS. Functional annotation analysis revealed only one common function related to carcass traits between the groups, while protein-protein interaction analysis indicated more gene interactions in Group A. The reliability of estimated values for common SNP markers identified between the groups was higher in Group A. Conclusion GWAS analysis utilizing parental genetic information holds greater potential for application, owing to its higher reliability of estimated values and the ability to explore numerous candidate genes.

Keywords

• carcass traits
• family-based gwas
• genome-wide association study (gwas)
• hanwoo