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Open Access Research article

Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle)

Seung-Hwan Lee123*, Cedric Gondro24, Julius van der Werf2, Nam-Kuk Kim1, Da-jeong Lim1, Eung-Woo Park1, Sung-Jong Oh1, John P Gibson23 and John M Thompson23

Author Affiliations

1 Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon 441-706, Korea

2 School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia

3 The Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, NSW 2351, Australia

4 The Centre for Genetic Analysis and Applications, University of New England, Armidale, NSW 2351, Australia

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BMC Genomics 2010, 11:623  doi:10.1186/1471-2164-11-623

Published: 9 November 2010

Abstract

Background

Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular fat deposition on highly divergent marbling phenotypes in adult Hanwoo cattle.

Results

Bovine genome array analysis was conducted to detect differentially expressed genes (DEGs) in m. longissimus with divergent marbling phenotype (marbling score 2 to 7). Three data-processing methods (MAS5.0, GCRMA and RMA) were used to test for differential expression (DE). Statistical analysis identified 21 significant transcripts from at least two data-processing methods (P < 0.01). All 21 differentially expressed genes were validated by real-time PCR. Results showed a high concordance in the gene expression fold change between the microarrays and the real time PCR data. Gene Ontology (GO) and pathway analysis demonstrated that some genes (ADAMTS4, CYP51A and SQLE) over expressed in high marbled animals are involved in a protein catabolic process and a cholesterol biosynthesis process. In addition, pathway analysis also revealed that ADAMTS4 is activated by three regulators (IL-17A, TNFα and TGFβ1). QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFβ1 are associated with increasing marbling fat. An ADAMTS4/TGFβ1 pathway seems to be associated with the phenotypic differences between high and low marbled groups.

Conclusions

Marbling differences are possibly a function of complex signaling pathway interactions between muscle and fat. These results suggest that ADAMTS4, which is involved in connective tissue degradation, could play a role in an important biological pathway for building up marbling in cattle. Moreover, ADAMTS4 and TGFβ1could potentially be used as an early biological marker for marbling fat content in the early stages of growth.