Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 R E S E A R C H A R T I C L E Open Access Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle) Seung-Hwan Lee1,2,3*, Cedric Gondro2,4, Julius van der Werf2, Nam-Kuk Kim1, Da-jeong Lim1, Eung-Woo Park1, Sung-Jong Oh1, John P Gibson2,3, John M Thompson2,3 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, TNFa and TGFb1). QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFb1 are associated with increasing marbling fat. An ADAMTS4/TGFb1 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 TGFb1could potentially be used as an early biological marker for marbling fat content in the early stages of growth. Background Intramuscular fat deposition in cattle starts to become visible at 12 months of age and the rate of deposition increases from 15 months to 24 months [1]. The initial formation of visible intramuscular fat seems to be driven through the development of adipocytes in combination with declining muscle growth [2]. It has been shown * Correspondence: slee46@une.edu.au 1Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon 441-706, Korea Full list of author information is available at the end of the article that marbling fat content is negatively correlated with protein content in beef muscle [3]. In addition the development of adipose tissues in longissimus muscle of high-marbled cattle appears to disorganize the structure of the intramuscular connective tissue during growth [1]. This suggests that there might be an interaction between fat development and collagen structure in mus- cle. Kokta et al [4] reviewed the interaction between myogenic cells and adipocytes to determine the rate and extent of myogenesis and adipogenesis during animal growth. Fat and muscle development are regulated by a © 2010 Lee et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.