Investigation of high correlation with carcass traits of SNPs of the PLCB1, C/EBPα, and TDRKH genes and the combinations of SNPs using the MDR method in the Hanwoo

• Published in: Genes & genomics Vol. 43; no. 8; pp. 961 - 973
• Main Authors: Kim, Songmi, Lee, Yong-Moon, Kim, Dong Hee, Ha, Jae Jung, Yi, Jun Koo, Kim, Dae Hyun, Oh, Dongyep, Han, Kyudong
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01.08.2021; Springer Nature B.V; 한국유전학회
• Subjects: Animal Genetics and Genomics; Animals; backfat; Beef; beef quality; Biomedical and Life Sciences; carcass weight; Carcasses; Cattle; CCAAT-Enhancer-Binding Protein-alpha - genetics; Consumers; Flavors; Food Analysis; Food consumption; Gene polymorphism; Genes; Genetic markers; Genetic relationship; Genome-Wide Association Study; genomics; Genotype; Genotyping; Human Genetics; Humans; intramuscular fat; Investigations; Life Sciences; longissimus muscle; marbling; Meat; Meat - analysis; Microbial Genetics and Genomics; Multifactor Dimensionality Reduction; Phenotype; Phospholipase C beta - genetics; Physical growth; Plant Genetics and Genomics; Polymorphism, Single Nucleotide - genetics; Research Article; RNA-Binding Proteins - genetics; Single-nucleotide polymorphism; Statistical analysis; taste; Whole Exome Sequencing; 생물학; Beef quality; MDR method; SNP genotypes; Hanwoo; DNA marker
• ISSN: 1976-9571; 2092-9293; 2092-9293
• DOI: 10.1007/s13258-021-01122-y

Background Recently, many researchers focus on the best way to produce high-quality meat, as the trend in food consumption today is to focus on quality. In general, consumers’ preferences in beef differ depending on taste and meatiness. Therefore, researchers are interested in how the marbling score affects the flavors of meat or the various factors that make up the meatiness to captivate the consumers’ tastes. Objective This study identifies single nucleotide polymorphisms (SNPs) or gene combinations that affect the carcass traits of Korean cattle (Hanwoo) by using the multifactor dimensionality reduction (MDR) method. Methods We collected the candidate SNPs to identify SNPs related to marbling scores from whole-exome sequencing and bovine SNP genotyping data. Using 96 Hanwoo samples, we performed PCR amplification to investigate the polymorphism status. In addition, we investigated genetic relationships between carcass traits and SNPs using 612 Hanwoo samples. Furthermore, each candidate SNP genotype and the combinations of SNP genotypes were verified to improve the accuracy of genetic relationships using MDR method. Results Twenty-four candidate SNPs associated with carcass trait and marbling scores were identified from SNP genotyping and whole-exome sequencing. Among them, three SNP markers (c.459 T > C of the PLCB1 gene, c.271 A > C of the C/EBPα gene, and g.17257 A > G of the TDRKH gene) were showed statistically significant differences between intramuscular fat and genotypes. Especially, two candidate SNPs, including c.459 T > C located in the PLCB1 gene and c.271 A > C located in the C/EBPα gene, could be highly associated with the intramuscular fat of Hanwoo quality grade. In addition, the combination of SNP genotypes is showed higher significant differences with carcass weight, backfat thickness, and longissimus dorsi muscle area. Conclusion Three SNP genotypes and the combination of SNP genotypes in the PLCB1 , C/EBPα , and TDRKH genes may be useful genetic markers for improving beef quality.