Lee et al. BMC Genomics 2010, 11:623 http://www.biomedcentral.com/1471-2164/11/623 gene in pig. This study showed that the SREBP1 gene was highly expressed in muscle from female compared with males. In addition there were differences in expres- sion within the genotypes showing a strong positive cor- relation with intramuscular fat content. The CYP51A pathway which is driven by the SREBP1 transcription factor might be one of the biological pathways asso- ciated to intramuscular fat in cattle. In this study SREBP1 was not differentially expressed in the arrays. Pathway for the ADAMTS4 gene Marbling fat accumulates in a connective tissue matrix in close proximity to a blood capillary network between the bundle of muscle fibres in bovine skeletal muscle [21]. Under electron microscopy, reorganization and degradation of intramuscular connective tissue is observed in highly marbled muscle [1]. The relationship between marbling fat and protein content showed a negative correlation in longissimus of cattle; for example, longissimus with high level of fat decreased composition of moisture and protein in the carcasses [3]. Microarray analysis identified that ADAMTS4 is highly expressed in highly marbling muscle. ADAMTS4 has a function of metalopetidase that degrades the extracellular matrix of connective tissue [22]. Recently, one gene of the ADAM gene family, ADAM12 was reported as overexpressed in transgenic mice exhibiting increased intramuscular adi- pogenesis [23]. These findings suggest that ADAMTS4 might be one of the key genes controlling the relation- ship between marbling fat deposition and connective tis- sue degradation through a complex biological pathway in skeletal muscle. Pathway analysis (Figure 5) suggested that ADAMTS4 is activated by three regulators; IL-17A, TNFa and transforming growth factor b 1 (TGFb1) that have not been previously considered to be associated with mar- bling fat. While only ADAMTS4 was detected as differ- entially expressed in the arrays (TNFa was excluded in the quality control step), the RT-PCR gene expression analysis found that ADAMTS4 and TGFb1 are highly co-expressed in highly marbled muscle while these two genes have a lower expression with higher protein con- tent (Figure 4). The TGFb1 is known to be a member of the GDF8 family that is a major gene known to affect carcass fatness and double muscling in cattle [24]. The GDF8 gene not only affects the size of muscle but also the proportion of connective tissue within the muscle and intramuscular fat % [19]. Also, the GDF8 gene pro- duct is a growth regulator for muscle development. In cattle the mutation of this gene product causes a decrease in fat deposition and an increase in muscle mass of carcasses [25,26]. However, this study only shows that the ADAMTS4/TGFb1 pathway might be Page 7 of 11 Figure 5 ADAMTS4 pathway. The blue solid arrow with square indicates that the regulator changes the gene expression of the target gene. The dot arrow with square indicates that the regulator changes the protein activity of the target gene. The black solid arrow indicates that the regulator changes the localization of the target gene. The blue closed line indicates that the regulator inhibits gene expression of the target gene. involved in phenotypic differences between high and low marbled cattle. Therefore, an ADAMTS4/TGFb1 path- way could be an important biological pathway related to increase of marbling fat in bovine skeletal muscle. Conclusion Genome wide microarray analysis was undertaken to explore novel biological pathways associated with mar- bling in Hanwoo (Korean cattle). In this study, microar- ray analysis identified 21 differentially expressed genes (DEGs) in muscle with divergent marbling phenotypes. Pathway analysis for the 21 DEGs showed 5 unique pathway hubs associated with steroid biosynthesis, cho- lesterol metabolism and common transcription factors in lipid metabolism. These biological pathways might represent a phenomenon occurring in muscle with highly divergent marbling phenotypes. Out of these 5 main pathways, ADAMTS4 is involved in protein cata- bolic process (GO0006516), which is biologically related to the connective tissue degradation that is observed in highly marbled muscle. Pathway analysis revealed that ADAMTS4 gene is activated by three regulators; IL-17A, TNFa, and transforming growth factor b 1 (TGFb1) that have not previously been considered to be associated with marbling fat. Gene expression analysis found that ADAMTS4 and TGFb1 are co-expressed in highly marbled muscle while these two genes have a lower expression with higher protein content. We conclude ADAMTS4 might be one of the key genes controlling the relationship between marbling fat deposition and connective tissue degradation through a complex biolo- gical pathway in skeletal muscle. Further studies will be necessary to unveil the biological function of this path- way (ADAMTS4/TGFb1).