CIMB, Vol. 44, Pages 6075-6092: Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

Meat quality is a generic concept utilized to describe satisfaction or consumer perception of beef palatability, which is determined by multiple factors such as flavor, juiciness, tenderness, and marbling [22]. In this context, back fat thickness (subcutaneous fat) is one of the most significant attributes and has a considerable impact on meat quality by protecting the muscle from cold-shortening that occurs in the carcass-chilling process after the slaughter [23]. Another trait is marbling (intramuscular fat), which is known to be a main factor influencing the sensory meat quality. These traits are influenced by several factors, including breed, genetic, age, management, feeding regime, and growth stages [24]. Moreover, in efforts to improve meat quality, earlier studies have focused on the detection of key genes along with a precise understanding of the underlying biology of quantitative traits to better meet consumer expectations [1,25,26,27,28]. Hence, the screening of potential candidate genes to comprehend the connection between gene variations and back fat thickness and intramuscular fat is necessary. The ANGPTL3, DGAT1, FASN, LPL, SCD, FABP3, FABP4, STAT6, and MAP2K6 genes are some candidate genes that have been demonstrated to be involved in regulating fat deposition and lipid metabolism (Table 1). One of the important parameters of meat quality is fatty acid (FA) composition, which affects the firmness of adipose tissue, and the associations of five well-known candidate genes (FABP3, FABP4, FASN, SCD, and DGAT1) with FA composition in beef cattle have been reported previously. The FABPs are members of a family of fatty acid-binding proteins, classified as FABP1–FABP9 [29], that play an essential role in the metabolism of long-chain fatty acids, transport, and uptake. Among them, the FABP3 and FABP4 genes have been shown to be related to marbling and back fat thickness in Hanwoo cattle. The FABP3 (fatty acid-binding protein 3) gene, also known as heart-type FABP, is involved in the transport of fatty acid from the plasma membrane to intracellular sites [30] and is mainly expressed in tissues, including lactating mammary gland, skeletal muscles, heart muscle, and adipose tissues [31]. In bovine, this gene, located at 122 Mb on chromosome 2, contains 4 exons [32], and its function is to bind unsaturated long-chain and non-esterified saturated fatty acids and other lipids for storage or transportation inside a cell [33,34]. The results of gene expression analysis revealed that the FABP3 gene was down-regulated in the high-marbled compared to the low-marbled group of Hanwoo cattle [35]. In another study, it has been found that variation in the FABP3 gene was related to back fat thickness in Hanwoo cattle [36]. The FABP4 (fatty acid-binding protein 4) gene, mapped on chromosome 14 and encoding adipocyte fatty acid-binding proteins, is mainly expressed in adipocytes [37]. This gene has a key function in lipid catabolism through changes in the intracellular targeting of fatty acids and lipid hydrolysis [38], and is involved in the Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathway. It was suggested that the PPAR signaling pathway is related to energy metabolism, regulating adipocyte tissue development, and lipogenesis. Moreover, it has been shown that the FABP4 gene is associated with back fat thickness [36], fatty acid composition [39,40], and marbling score [41,42] in Hanwoo cattle. Another interesting finding by Lim et al. [35] showed that the FABP4 gene was up-regulated in muscle with high marbling levels in Hanwoo cattle. The bovine FASN (fatty acid synthase) encodes a complex homodimeric enzyme involved in the regulation of long-chain fatty acid biosynthesis [43], and is extensively expressed in the adipose tissue. The FASN gene has seven active sites and catalyzes the formation of fatty acids of palmitate from malonyl coenzyme A and acetyl-coenzyme A [43]. This gene is a candidate gene located in the position of 50 Mb on chromosome 19, and it has been related to FA composition in various beef cattle breeds [44,45]. Mutations in the FASN gene have been reported in several studies of Hanwoo cattle. It was shown that five exonic SNPs (g.12870 T > C, g.13126 T > C, g.15532 C > A, g.16907 T > C, and g.17924 G > A) in the gene encoding FASN were connected to FA composition and marbling score [46]. In addition, another study reported 16 polymorphisms, six of which were nonsynonymous mutations in the FASN coding regions in Hanwoo cattle [47]. Furthermore, two GWAS studies identified that this gene was significantly associated with C14:0 [48] and marbling score [41]. A positional candidate gene on bovine chromosome 14 is DGAT1 (diacylglycerol O-acyltransferase 1), a microsomal enzyme that catalyzes the final step of triglyceride synthesis [49]. Substitution of lysine for alanine in exon 8 region 232 (K232A) of this gene has been proposed to be associated with fat content and composition [50,51], marbling score [52], intramuscular fat content [53,54,55], and subcutaneous fat thickness [56] in different cattle breeds. This gene is related to transferase activity, transferring phosphorus-containing groups, and 2-acylglycerol O-acyltransferase activity, according to gene ontology (GO) terms, and it is involved in different pathways, including metabolic pathways, fat digestion and absorption, and glycerolipid metabolism. Regarding fatty acid biosynthesis in cattle, the SCD (stearoyl-CoA desaturase) gene encodes an enzyme that catalyzes the conversion of saturated fatty acid (SFA) to monounsaturated fatty acid (MUFA), primarily the synthesis of oleic acid in adipose tissue [57]. The bovine SCD gene is mapped on chromosome 26 with six exons, and plays an essential role in regulating the expression of genes that are involved in lipogenesis as well as regulating mitochondrial fatty acid oxidation and body energy homeostasis. Candidate gene studies in Hanwoo cattle have reported that polymorphisms in the SCD gene have important effects on marbling score, meat texture, and grade of meat quality [41,58,59,60,61,62]. The STAT6 (signal transducer and activator of transcription 6) gene, located on chromosome 5 and identified to be linked to back fat thickness, was previously shown to be associated with carcass weight, calculated yield grade, cutability, back fat rate, dry matter intake, days on feed, and average daily gain in different beef cattle breeds [63]. This gene acts both as a mediator of leptin signaling and as a transcription factor, playing an essential role in the regulation of body weight by signaling the size of adipose tissue mass [64,65]. In addition to the above-discussed genes, ANGPTL3, LPL, and MAP2K6 genes were also found to be involved in regulating the lipid metabolism signaling pathway (Figure 1). ANGPTL3 (angiopoietin-like 3) gene is a member of the ANGPTL family that plays a crucial role in lipid metabolism by enhancing high-density lipoprotein cholesterol and plasma lipids [66], and free fatty acids (FFA) transport in adipose tissue [67]. The bovine LPL (lipoprotein lipase) gene, located on chromosome 8 with ten exons, encodes a key enzyme in triglyceride metabolism and has the dual functions of triglyceride hydrolase and ligand/bridging factor for receptor-mediated lipoprotein uptake [68,69]. Previous studies reported that the MAP2K6 gene was associated with marbling score and back fat thickness in Hanwoo cattle [11,70] and fatty acid profile in Nellore cattle [71]. This gene is a member of the dual-specificity protein kinase family that plays a role in regulating the mitogen-activated protein kinase pathway.

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