Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.

The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.

Determination of the effect of functional single-nucleotide polymorphisms associated with glycerolipid synthesis on intramuscular fat deposition in Korean cattle steer.

Intramuscular fat deposition in the longissimus dorsi muscle (LM) of Korean cattle steer is regulated by several genes related to lipid metabolism. One of these genes encodes the enzyme bovine glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), which is located on the mitochondrial outer membrane and catalyzes the initial and committed step of glycerolipid synthesis in lipid metabolism of cattle. Previous studies have shown that the 3 ' -untranslated region (UTR) of the GPAM is quite extended and contains a polyadenylation signal site, erythroid 15-lipoxygenase differentiation control elements (15-LOX-DICEs), and cytoplasmic polyadenylation elements (CPEs) that affect the regulation of triacylglycerol synthesis. Therefore, the aim of this study was to identify single-nucleotide polymorphisms (SNPs) related to the regulation of glycerolipid synthesis in the 3 ' -UTR of GPAM and to verify the function of SNPs affecting the deposition of intramuscular fat in Korean cattle steer. In the present study, 11 SNPs were discovered in the 3 ' -UTR of GPAM. Among these SNPs, g.54853A > G, g.55441A > G, and g.55930C > T were significantly associated with marbling score in a Korean cattle steer population and were strongly correlated with each other within the GPAM gene. Furthermore, based on the results predicted by the RNAhybrid program, four putative microRNAs (miRNAs) were identified, and the above SNPs were found to present in the seed region of these miRNAs. These miRNAs have a differential binding affinity for each allele of SNPs g.54853A > G, g.55441A > G, and g.55930C > T. The in vivo evidence of intramuscular fat deposition in the LM tissue showed that these SNPs affected the regulation of intramuscular fat deposition in Korean cattle steer. Thus, the g.54853A > G, g.55441A > G, and g.55930C > T could be considered as causal mutations regulating intramuscular fat deposition in Korean cattle steer.

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.

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.

Quantitative evaluation of the molecular marker using droplet digital PCR.

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

Beneficial effects of 6-shogaol on hyperglycemia, islet morphology and apoptosis in some tissues of streptozotocin-induced diabetic mice.

BACKGROUND: Diabetes is characterized by hyperglycemia due to impaired insulin secretion and aberrant glucagon secretion resulting from changes in pancreatic islet cell function and/or mass. The aim of the present study was to investigate the effects of ginger on various tissues (i.e., pancreas, kidney, and liver) and insulin resistance in streptozotocin-induced diabetic mice. The pleasant aroma of ginger comes from the constituents present in its volatile oil, while its non-volatile pungent phytochemicals consist of gingerols, shogaols, and paradols. METHODS: This research was conducted to determine the effects of 6-shogaol administration on blood glucose and insulin production in type 1 diabetic mice. Mice were intraperitoneally injected with shogaol at 5 or 10 mg/kg body weight. Untreated mice were injected with an equivalent volume of buffer, three times a week for 2 weeks. The animals were randomly divided into four experimental groups: control group mice (n = 3) were given an intraperitoneal (IP) injection of streptozotocin (STZ) vehicle (1 mL citrate buffer/100 g body weight) at day 1 and received an IP injection of 6-shogaol vehicle [1 mL buffer (0.5% DMSO, 10% Tween 20, and 89.5% PBS)/100 g body weight] every other day for 4 consecutive days. RESULTS: 6-Shogaol exhibited an antidiabetic effect by significantly decreased the level of blood glucose, body weight and attenuated the above pathological changes to the normal levels in the diabetic mice, and has effect against pancreas, kidney, liver damage in the diabetic mice. Since, 6-shogaol prevented the damage for STZ induced stress. CONCLUSION: 6-Shogaol can be used as a therapeutic agent for preventing complications in diabetic patients. Diabetic treatment consider the 6-shogaol as a pharmatheuticals or combination drug with herbal plant or others 6-shogaol may be a good therapeutic drug because it covers not only pancreatic ß-cell but also liver and kidney. Ginger may be ideal because they contain a variety of pharmacological compounds with different known pharmacological actions.

Investigation of Hanwoo-specific structural variations using whole-genome sequencing data.

BACKGROUND: The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies. OBJECTIVE: TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data. RESULTS: We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages. CONCLUSION: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.

Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle.

The fatty acid composition of adipose tissue in livestock has been recognized as an important carcass trait that affects meat quality. To determine the overall positive effect on fatty acid synthesis, we investigated PPARγ, SREBPs, FABP4, SCD, and FASN genes because SNP and/or SNP combinations were strongly affecting each fatty acid synthesis pathway. We screened their SNPs, SNP combinations, and genotype. Furthermore, we studied the economic traits C18:1, monounsaturated fatty acid (MUFA), and marbling score (MS). To enhance the accuracy of the predictive genetic effect, we applied a statistical adjustment model excluding environmental factors. We also selected superior genes, gene combinations, and genotypes for each economic trait by using multifactor dimensionality reduction. Based on the results, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.10153 A>G, g.3977-325 T>C) (AACC, AGCC, GGCC), (g.3690 G>A, g.3977-325 T>C) (GGCC, GACC), (g.3977-325 T>C, g.25670 C>T) (CCCC, CCCT, CCTT) (genotypes of the best SNP combination) was selected as the best gene combination for C18:1 and MUFA. In addition, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.3977-325 T>C, g.6974 G>A) (TTAA, CTAA, CCAA, CCGA, CCGG) as the best SNP combination for MS. We integrated genes that were selected as excellent SNP and SNP combinations affecting two main routes of the fatty acid synthesis pathway and identified the best and final SNP, SNP combination, and superior genotype.

In vivo evidence on the functional variation within fatty acid synthase gene associated with lipid metabolism in bovine longissimus dorsi muscle tissue.

In Korean cattle, intramuscular fat (IMF), or marbling, of the longissimus dorsi muscle (LM) cross section is one of the most important indicators of beef quality and are influenced by environmental and genetic factors. This study was to evaluate the effect of SNPs on the beef quality in Korean cattle for functional studies, such as site-directed mutagenesis based on bovine adipocytes. The fatty acid synthase (FASN) gene plays an important role in lipogenesis. FASN is an essential metabolic and multifunctional enzyme in fatty acid synthesis. Several studies have reported that SNPs g.841G, g.16024A, g.16039T, and g.17924G have a significant impact on marbling scores in Korean cattle and Japanese Black cattle population. These SNPs are located in transcription factor binding sites, the beta-ketoacyl reductase, and thioesterase domains. Our results revealed that the g.17924 A>G SNP is located in the thioesterase domain of the FASN protein, and changes from polar, neutral, and hydrophilic to nonpolar, aliphatic, and hydrophobic, respectively. In in vivo LM tissue of Korean cattle, the g.17924A>G SNP has an effect on increasing fat deposition. Therefore, g.17924A>G SNP could be a causal mutation for increasing fat deposition in Korean cattle LM tissue.

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome.

BACKGROUND: Transposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago. RESULTS: We identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5' and 3' LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker. CONCLUSIONS: GGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification.

Detection of superior genotype of fatty acid synthase in Korean native cattle by an environment-adjusted statistical model.

OBJECTIVE: This study examines the genetic factors influencing the phenotypes (four economic traits:oleic acid [C18:1], monounsaturated fatty acids, carcass weight, and marbling score) of Hanwoo. METHODS: To enhance the accuracy of the genetic analysis, the study proposes a new statistical model that excludes environmental factors. A statistically adjusted, analysis of covariance model of environmental and genetic factors was developed, and estimated environmental effects (covariate effects of age and effects of calving farms) were excluded from the model. RESULTS: The accuracy was compared before and after adjustment. The accuracy of the best single nucleotide polymorphism (SNP) in C18:1 increased from 60.16% to 74.26%, and that of the two-factor interaction increased from 58.69% to 87.19%. Also, superior SNPs and SNP interactions were identified using the multifactor dimensionality reduction method in Table 1 to 4. Finally, high- and low-risk genotypes were compared based on their mean scores for each trait. CONCLUSION: The proposed method significantly improved the analysis accuracy and identified superior gene-gene interactions and genotypes for each of the four economic traits of Hanwoo.

Genetic effects of sterol regulatory element binding proteins and fatty acid-binding protein4 on the fatty acid composition of Korean cattle (Hanwoo).

OBJECTIVE: This study identifies single-nucleotide polymorphisms (SNP) or gene combinations that affect the flavor and quality of Korean cattle (Hanwoo) by using the SNP Harvester method. METHODS: Four economic traits (oleic acid [C18:1], saturated fatty acids), monounsaturated fatty acids, and marbling score) were adjusted for environmental factors in order to focus solely on genetic effects. The SNP Harvester method was used to investigate gene combinations (two-way gene interactions) associated with these economic traits. Further, a multifactor dimensionality reduction method was used to identify superior genotypes in gene combinations. RESULTS: Table 3 to 4 show the analysis results for differences between superior genotypes and others for selected major gene combinations using the multifactor dimensionality reduction method. Environmental factors were adjusted for in order to evaluate only the genetic effect. Table 5 shows the adjustment effect by comparing the accuracy before and after correction in two-way gene interactions. CONCLUSION: The g.3977-325 T>C and (g.2988 A>G, g.3977-325 T>C) combinations of fatty acid-binding protein4 were the superior gene, and the superior genotype combinations across all economic traits were the CC genotype at g.3977-325 T>C and the AACC, GACC, GGCC genotypes of (g.2988 A>G, g.3977-325 T>C).

Whole Genome Re-Sequencing of Three Domesticated Chicken Breeds.

Chicken is one of the most popular domesticated species worldwide, as it can serve an important role in agricultural as well as biomedical research fields. Because it inhabits almost every continent and presents diverse morphology and traits, the need of genetic markers for distinguishing each breed for various purposes has increased. The whole genome sequencing of three different breeds (White Leghorn, Korean domestic, and Araucana) that show similar coloring patterns, with the exception of the White Leghorn breed, have confirmed previously reported genomic alterations and identified many novel variants. Additionally, the Whole Genome Re-Sequencing (WGRS) approach identified an approximately 4 kb insert within SLCO1B3 responsible for blue egg shell color. Targeted investigation of pigment-related genes corroborated previously reported non-synonymous mutations, and provided deeper insight into chicken coloring, where not a single but a combination of non-synonymous mutations in the MC1R gene is likely to be responsible for altered feather coloring.

Relationship between Single Nucleotide Polymorphisms in the Peroxisome Proliferator-Activated Receptor Gamma Gene and Fatty Acid Composition in Korean Native Cattle.

The peroxisome proliferator-activated receptor gamma (PPARγ) gene plays an important role in the biosynthesis process controlled by a number of fatty acid transcription factors. This study investigates the relationships between 130 single-nucleotide polymorphisms (SNPs) in the PPARγ gene and the fatty acid composition of muscle fat in the commercial population of Korean native cattle. We identified 38 SNPs and verified relationships between 3 SNPs (g.1159-71208 A>G, g.42555-29812 G>A, and g.72362 G>T) and the fatty acid composition of commercial Korean native cattle (n = 513). Cattle with the AA genotype of g.1159-71208 A>G and the GG genotype of g.42555-29812 G>A and g.72362 G>T had higher levels of monounsaturated fatty acids and carcass traits (p<0.05). The results revealed that the 3 identified SNPs in the PPARγ gene affected fatty acid composition and carcass traits, suggesting that these 3 SNPs may improve the flavor and quality of beef in commercial Korean native cattle.

Identification of exonic nucleotide variants of the thyroid hormone responsive protein gene associated with carcass traits and Fatty Acid composition in korean cattle.

The thyroid hormone responsive protein (THRSP) gene is a functional gene that can be used to indicate the fatty acid compositions. This study investigates the relationships of exonic single nucleotide polymorphisms (SNPs) in the THRSP gene and fatty acid composition of muscle fat and marbling score in the 612 Korean cattle. The relationships between fatty acid composition and eight SNPs in the THRSP gene (g.78 G>A, g.173 C>T, g.184 C>T, g.190 C>A, g.194 C>T, g.277 C>G, g.283 T>G and g.290 T>G) were investigated, and according to the results, two SNPs (g.78 G>A and g.184 C>T) in exon 1 were associated with fatty acid composition. The GG and CC genotypes of g.78 G>A and g.184 C>T had higher unsaturated fatty acid (UFA) and monounsaturated fatty acid (MUFA) content (p<0.05). In addition, the ht1*ht1 group (Val/Ala haplotype) in a linkage disequilibrium increased MUFAs and marbling scores for carcass traits (p<0.05). As a result, g.78 G>A and g.184 C>T had significantly relationships with UFAs and MUFAs. Two SNPs in the THRSP gene affected fatty acid composition, suggesting that GG and CC genotypes and the ht1*ht1 group (Val/Ala haplotype) can be markers to genetically improve the quality and flavor of beef.

Detection of exonic variants within the melanocortin 1 receptor (MC1R) gene in Black Silky, White Leghorn and Golden duckwing Araucana chicken.

The melanocortin 1 receptor (MC1R) gene can be considered a candidate functional gene for the pigmentation of plumage color. The aim of this study was to investigate the association between the genotype frequencies of g.69 T>C, g.376 G>A and g.427 A>G SNPs within the MC1R gene in Black silky (O), Golden duckwing Araucana (GA) and White Leghorn (W). The CC and AA genotype frequencies of g.69 T>C and g.427 A>G SNPs in White Leghorn (W) were both 1.000, and the TT genotype frequency of the g.69 T>C SNP in Golden duckwing Araucana (GA) was also 1.000. The GG and AA genotype frequencies of g.376 G>A and g.427 A>G SNPs in Black silky (O) were both 0.100. When a haplotype is observed using a combination of markers, a Golden duckwing Araucana (GA) can especially be distinguished when it is a TAG, TGG and TAA type in the SNP combination of the MC1R gene. In case of the CAA types, only White Leghorn (W) could specifically be distinguished. Therefore, three SNPs in MC1R may provide identification in chicken breeds.

Gene-gene interactions of fatty acid synthase (FASN) using multifactor-dimensionality reduction method in Korean cattle.

We examined the gene-gene interactions of five exonic single nucleotide polymorphisms (SNPs) in the gene encoding fatty acid synthase using 513 Korean cattle and using the model free and the non-parametrical multifactor dimensionality reduction method for the analysis. The five SNPs of g.12870 T>C, g.13126 T>C, g.15532 C>A, g.16907 T>C and g.17924 G>A associated with a variety of fatty acid compositions and marbling score were used in this study. The two-factor interaction between g.13126 T>C and g.15532 C>A had the highest training-balanced among the five-factor models and a testing-balanced accuracy at 70.18 % on C18:1 with a cross-validation consistency of 10 out of 10. Also, the two-factor interaction between g.13126 T>C and g.15532 C>A had the highest testing-balanced accuracy at 68.59 % with a 10 out of 10 cross-validation consistency, than any other models on MUFA. In MS, a single SNP g.15532 C>A had the best accuracy at 58.85 % and the two-factor interaction model g.12870 T>C and g.15532 C>A had the highest testing-balanced accuracy at 64.00 %. The three-factor interaction model g.12870 T>C, g.13126 T>C and g.15532 C>A was recorded as having a high testing-balanced accuracy of 63.24 %, but it was lower than the two-factor interaction model. We used likelihood ratio tests for interaction, and Chi square tests to validate our results, with all tests showing statistical significance. We also compared this with mean scores between the high-risk trait group and low-risk trait group. The genotypes of TTCA, TTAA and TCAA at g.15532 and g.13126 on C18:1, genotypes TTCC, TTCA, TTAA, TCAA CCAA at g.15532 and g.13126 on MUFA and genotypes CCCC, TCCA, CCCA, TTAA, TCAA and CCAA at g.15532 and g.12870 on MS were recommended for the genetic improvement of beef quality.

Identification of Single Nucleotide Polymorphisms (SNPs) of the Bovine Growth Hormone (bGH) Gene Associated with Growth and Carcass Traits in Hanwoo.

The purpose of this study was to find any association of the bovine growth hormone (bGH) gene with growth and carcass quality traits in Korean native cattle, Hanwoo. Genomic DNA was extracted from 21 Hanwoo individuals, and the 47 to 2,528 bp region of the bGH 2,856 bp (GenBank accession number M57764) including the promoter and the five exons was sequenced. A total of ten bGH SNPs were confirmed, including four (253 C>T, 303 C>T, 502 C>T, and 559 G>A) in the promoter, one (679 C>T) in exon 1, one (1,692 T>C) in intron 3, and four (2141 C>G, 2258 C>T, 2277 C>T, and 2291 A>C) in exon 5. The ten bGH SNPs were genotyped for a sample of 242 Hanwoo steers and association tests were performed to find any significant SNP that was correlated with growth and carcass quality. Of the SNPs, the 303 C>T SNP in the promoter region was significantly associated with 6-month-old weight, the 559 G>A SNP with longissimus dorsi muscle area, the 2141 C>G SNP in exon 5 with daily weight gain, and the 2258 C>T SNP with daily weight gain and carcass weight (p<0.05). The significant SNPs need to be verified in other Hanwoo populations before considering implementation of marker-assisted selection for genetic improvement of growth and carcass quality in Hanwoo.

Identification of Stearoyl-CoA Desaturase (SCD) Gene Interactions in Korean Native Cattle Based on the Multifactor-dimensionality Reduction Method.

Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase1 (SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.

Novel single nucleotide polymorphisms of bovine SREBP1 gene is association with fatty acid composition and marbling score in commercial Korean cattle (Hanwoo).

The sterol regulatory element binding factor 1 (SREBP1) gene plays an important role in the biosynthesis of fatty acids. The aim of this study was to investigate the association between SNPs within SREBP1 gene and fatty acid composition of muscle fat and marbling score in a commercial population of Korean cattle. Among 10 SNPs in dbSNP of bovine SREBP1 gene, we identified 7 polymorphic SNPs and 84-bp ins/del variation (SREBP1-INT5 SNP) in commercial Korean cattle (n = 513). The SREBP1-9 SNP showed a significant effect on marbling score, monounsaturated fatty acids and C18:1n-9 in the muscle fat of commercial Korean cattle. However, SREBP1-INT5 SNP showed no effect on any fatty acid composition. Therefore, two polymorphisms in SREBP1 may improve flavored beef and meat quality in commercial Korean cattle.

Identification of novel single nucleotide polymorphisms (SNPs) of the lipoprotein lipase (LPL) gene associated with fatty acid composition in Korean cattle.

The lipoprotein lipase (LPL) gene can be considered a functional candidate gene that regulates fatty acid composition. In this study, genetic associations between fatty acid composition and exonic single nucleotide polymorphisms (SNPs) in the LPL gene were examined using 612 Korean cattle. We investigated the relationship between unsaturated fatty acids and five novel SNPs (c.322G>A, c.329A>T, c.527T>G, c.988C>T and c.1591G>A), and confirmed that three polymorphic SNPs (c.322G>A, c.329A>T and c.1591G>A) were associated with fatty acid composition. Korean cattle with an AA genotype of c.322G>A, c.329A>T, and GA genotype of c.1591G>A had higher levels of monounsaturated fatty acids and carcass traits (P < 0.05). Our findings confirmed that three novel SNPs we identified in the LPL gene can affect fatty acid composition and carcass traits. Therefore, selection for AA and GA genotypes should be recommended to genetically improve beef quality and flavor.