Contributions ofFASNandSCDgene polymorphisms on fatty acid composition in muscle from Japanese Black cattle

Lipogenic Gene Single Nucleotide Polymorphic DNA Markers Associated with Intramuscular Fat, Fat Melting Point, and Health-Beneficial Omega-3 Long-Chain Polyunsaturated Fatty Acids in Australian Pasture-Based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu Beef Cattle

This study used targeted sequencing aimed at identifying single nucleotide polymorphisms (SNP) in lipogenic genes and their associations with health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP) of the M. longissimus dorsi muscle in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu cattle. It was hypothesized that SNP encoding for the fatty acid-binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD), and fatty acid synthase (FASN) genes will be significantly associated with health-beneficial n-3 LC-PUFA and the meat eating quality traits of IMF and FMP in an Australian pasture-based beef production system. Two SNP mutations, g.21267406 T>C and g.21271264 C>A, in the SCD gene were significantly (p < 0.05) associated with IMF, FMP, oleic acid (18:1n-9), linoleic acid (LA) 18:2n-6, alpha-linolenic acid (ALA) 18:3n-3, eicosapentaenoic acid (EPA) 20:5n-3, docosahexaenoic acid (DHA) 22:6-n-3, and docosapentaenoic acid (DPA) 22:5n-3. Significant positive correlations (p < 0.05) between FASN SNP g. 50787138 A>G and FMP, 18:1n-9, ALA, EPA, DHA, DPA, and total n-3 LC-PUFA were also detected. An SNP (g.44678794 G>A) in the FABP4 gene was associated with FMP. These results provide significant insights into the contributions of lipogenic genes to intramuscular fat deposition and the biosynthesis of health-beneficial n-3 LC-PUFA. The findings also unravel the potential use of lipogenic gene polymorphisms in marker-assisted selection to improve the content of health-promoting n-3 LC-PUFA and meat eating quality traits in Australian pasture-based Bowen Genetics Forest Pastoral Angus, Hereford, and Wagyu beef cattle.

Towards Sustainable Sources of Omega-3 Long-Chain Polyunsaturated Fatty Acids in Northern Australian Tropical Crossbred Beef Steers through Single Nucleotide Polymorphisms in Lipogenic Genes for Meat Eating Quality

This study aimed to identify single nucleotide polymorphisms (SNP) in lipogenic genes of northern Australian tropically adapted crossbred beef cattle and to evaluate associations with healthy lipid traits of the Longissimus dorsi (loin eye) muscle. The hypothesis tested was that there are significant associations between SNP loci encoding for the fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD) and fatty acid synthase (FASN) genes and human health beneficial omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA) within the loin eye muscle of northern Australian crossbred beef cattle. Brahman, Charbray, and Droughtmaster crossbred steers were fed on Rhodes grass hay augmented with desmanthus, lucerne, or both, for 140 days and the loin eye muscle sampled for intramuscular fat (IMF), fat melting point (FMP), and fatty acid composition. Polymorphisms in FABP4, SCD, and FASN genes with significant effects on lipid traits were identified with next-generation sequencing. The GG genotype at the FABP4 g.44677239C>G locus was associated with higher proportion of linoleic acid than the CC and CG genotypes (p < 0.05). Multiple comparisons of genotypes at the SCD g.21266629G>T locus indicated that the TT genotype had significantly higher eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids than GG genotype (p < 0.05). Significant correlations (p < 0.05) between FASN SNP and IMF, saturated and monounsaturated fatty acids were observed. These results provide insights into the contribution of lipogenic genes to intramuscular fat deposition and SNP marker-assisted selection for improvement of meat-eating quality, with emphasis on alternate and sustainable sources of ω3 LC-PUFA, in northern Australian tropical crossbred beef cattle, hence an acceptance of the tested hypothesis.

Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq

Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.

Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle

Livestock is an important commodity playing a major role in the global economy. Red meat plays an important role in human life, as it is a good source of animal protein and energy. The fatty acid content of beef has been shown to impact the eating experience and nutritional value of beef. Therefore, this study aimed to identify genomic regions which can account for genetic variation in meat fatty acid content. Genotypes imputed to the Illumina BovineHD 770K BeadChip were used in this study. Thirty-six 1-Mb genomic regions with a posterior probability of inclusion (PPI) greater than 0.90 were identified to be associated with variation in the content of at least one fatty acid. The genomic regions (1Mb) which were associated with more than one fatty acid trait with high genetic variance and harbored good candidate genes were on Chromosome (Chr) 6 (fatty acid binding protein 2), Chr 19 (thyroid hormone receptor alpha, fatty acid synthase), Chr 26 (stearoyl-CoA desaturase), and Chr 29 (thyroid hormone responsive, fatty acid desaturase 2, and fatty acid desaturase 3). Further studies are required to identify the causal variants within the identified genomic regions. Findings from the present study will help to increase understanding of the variation in fatty acid content of beef and help to enhance selection for beef with improved fatty acid composition.

Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Background

Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle.

Results

In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B).

Conclusions

Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.

Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array

BACKGROUND

Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying important traits in cattle. In this study, we performed GWAS using high density SNP array to analyze the association between SNPs and fatty acids and evaluated the accuracy of genomic prediction for fatty acids in Chinese Simmental cattle.

RESULTS

Using the BayesB method, we identified 35 and 7 regions in Chinese Simmental cattle that displayed significant associations with individual fatty acids and fatty acid groups, respectively. We further obtained several candidate genes which may be involved in fatty acid biosynthesis including elongation of very long chain fatty acids protein 5 (ELOVL5), fatty acid synthase (FASN), caspase 2 (CASP2) and thyroglobulin (TG). Specifically, we obtained strong evidence of association signals for one SNP located at 51.3 Mb for FASN using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approaches. Also, region-based association test identified multiple SNPs within FASN and ELOVL5 for C14:0. In addition, our result revealed that the effectiveness of genomic prediction for fatty acid composition using BayesB was slightly superior over GBLUP in Chinese Simmental cattle.

CONCLUSIONS

We identified several significantly associated regions and loci which can be considered as potential candidate markers for genomics-assisted breeding programs. Using multiple methods, our results revealed that FASN and ELOVL5 are associated with fatty acids with strong evidence. Our finding also suggested that it is feasible to perform genomic selection for fatty acids in Chinese Simmental cattle.

Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle

BACKGROUND

Identification of genetic variants that are associated with fatty acid composition in beef will enhance our understanding of host genetic influence on the trait and also allow for more effective improvement of beef fatty acid profiles through genomic selection and marker-assisted diet management. In this study, 81 and 83 fatty acid traits were measured in subcutaneous adipose (SQ) and longissimus lumborum muscle (LL), respectively, from 1366 purebred and crossbred beef steers and heifers that were genotyped on the Illumina BovineSNP50 Beadchip. The objective was to conduct genome-wide association studies (GWAS) for the fatty acid traits and to evaluate the accuracy of genomic prediction for fatty acid composition using genomic best linear unbiased prediction (GBLUP) and Bayesian methods.

RESULTS

In total, 302 and 360 significant SNPs spanning all autosomal chromosomes were identified to be associated with fatty acid composition in SQ and LL tissues, respectively. Proportions of total genetic variance explained by individual significant SNPs ranged from 0.03 to 11.06% in SQ, and from 0.005 to 24.28% in the LL muscle. Markers with relatively large effects were located near fatty acid synthase (FASN), stearoyl-CoA desaturase (SCD), and thyroid hormone responsive (THRSP) genes. For the majority of the fatty acid traits studied, the accuracy of genomic prediction was relatively low (<0.40). Relatively high accuracies (> = 0.50) were achieved for 10:0, 12:0, 14:0, 15:0, 16:0, 9c-14:1, 12c-16:1, 13c-18:1, and health index (HI) in LL, and for 12:0, 14:0, 15:0, 10 t,12c-18:2, and 11 t,13c + 11c,13 t-18:2 in SQ. The Bayesian method performed similarly as GBLUP for most of the traits but substantially better for traits that were affected by SNPs of large effects as identified by GWAS.

CONCLUSIONS

Fatty acid composition in beef is influenced by a few host genes with major effects and many genes of smaller effects. With the current training population size and marker density, genomic prediction has the potential to predict the breeding values of fatty acid composition in beef cattle at a moderate to relatively high accuracy for fatty acids that have moderate to high heritability.

Single Nucleotide Polymorphism in the Coding Region of Bovine Chemerin Gene and Their Associations with Carcass Traits in Japanese Black Cattle

Chemerin, highly expressed in adipose and liver tissues, regulates glucose and lipid metabolism and immunity in these tissues in ruminants and mice. Our previous reports showed that chemerin is involved in adipogenesis and lipid metabolism in adipose tissue as an adipokine. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in the coding region of the chemerin gene and to analyze their effects on carcass traits and intramuscular fatty acid compositions in Japanese Black cattle. The SNPs in the bovine chemerin gene were detected in 232 Japanese Black steers (n = 161) and heifers (n = 71) using DNA sequencing. The results revealed five novel silent mutations: NM_001046020: c.12A>G (4aa), c.165G<A (55aa), c.276C>T (92aa), c.321 A>G (107aa), and c.396C>T (132aa). There was no association between 4 of the SNPs (c.12A>G [4aa], c.165G<A [55aa], c.321 A>G [107aa], and c.396C>T) and carcass traits or intramuscular fatty acid compositions. Regarding the remaining SNP, c.276C>T, we found that cattle with genotype CC had a higher beef marbling score than that of cattle with genotype CT, whereas cattle with genotype CT had a higher body condition score (p<0.10). Further, cattle with genotype CC had significantly higher C18:0 content in their intramuscular fat tissue than that of cattle with genotype CT (p<0.05). On the other hand, cattle with genotype CT had significantly higher C14:0 and C16:0 content in their intramuscular fat tissue (p<0.05). Moreover, the number of individuals carrying the minor allele of c.276C>T SNP is small. It is suggested that the c.276C>T SNP of the chemerin gene has potential in cattle breeding using modern methods, such as marker assisted selection. So, further functional and physiological research elucidating the impact of the chemerin gene on bovine lipid metabolism including fatty acid synthesis will help in understanding these results.

Differential Expression of PPARγ, FASN, and ACADM Genes in Various Adipose Tissues and Longissimus dorsi Muscle from Yanbian Yellow Cattle and Yan Yellow Cattle

The objective of this study was to investigate the correlation between cattle breeds and deposit of adipose tissues in different positions and the gene expressions of peroxisome proliferator-activated receptor gamma (PPARγ), fatty acid synthase (FASN), and Acyl-CoA dehydrogenase (ACADM), which are associated with lipid metabolism and are valuable for understanding the physiology in fat depot and meat quality. Yanbian yellow cattle and Yan yellow cattle reared under the same conditions display different fat proportions in the carcass. To understand this difference, the expression of PPARγ, FASN, and ACADM in different adipose tissues and longissimus dorsi muscle (LD) in these two breeds were analyzed using the Real-time quantitative polymerase chain reaction method (qRT-PCR). The result showed that PPARγ gene expression was significantly higher in adipose tissue than in LD in both breeds. PPARγ expression was also higher in abdominal fat, in perirenal fat than in the subcutaneous fat (p<0.05) in Yanbian yellow cattle, and was significantly higher in subcutaneous fat in Yan yellow cattle than that in Yanbian yellow cattle. On the other hand, FASN mRNA expression levels in subcutaneous fat and abdominal fat in Yan yellow cattle were significantly higher than that in Yanbian yellow cattle. Interestingly, ACADM gene shows greater fold changes in LD than in adipose tissues in Yan yellow cattle. Furthermore, the expressions of these three genes in lung, colon, kidney, liver and heart of Yanbian yellow cattle and Yan yellow cattle were also investigated. The results showed that the highest expression levels of PPARγ and FASN genes were detected in the lung in both breeds. The expression of ACADM gene in kidney and liver were higher than that in other organs in Yanbian yellow cattle, the comparison was not statistically significant in Yan yellow cattle.

Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle

BACKGROUND

As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this study was to determine the extent to which molecular markers could account for variation in fatty acid composition of skeletal muscle and identify genomic regions that harbor genetic variation.

RESULTS

Subsets of markers on the Illumina 54K bovine SNPchip were able to account for up to 57% of the variance observed in fatty acid composition. In addition, these markers could be used to calculate a direct genomic breeding values (DGV) for a given fatty acids with an accuracy (measured as simple correlations between DGV and phenotype) ranging from -0.06 to 0.57. Furthermore, 57 1-Mb regions were identified that were associated with at least one fatty acid with a posterior probability of inclusion greater than 0.90. 1-Mb regions on BTA19, BTA26 and BTA29, which harbored fatty acid synthase, Sterol-CoA desaturase and thyroid hormone responsive candidate genes, respectively, explained a high percentage of genetic variance in more than one fatty acid. It was also observed that the correlation between DGV for different fatty acids at a given 1-Mb window ranged from almost 1 to -1.

CONCLUSIONS

Further investigations are needed to identify the causal variants harbored within the identified 1-Mb windows. For the first time, Angus breeders have a tool whereby they could select for altered fatty acid composition. Furthermore, these reported results could improve our understanding of the biology of fatty acid metabolism and deposition.

Estimates of genetic parameters for fatty acids in brisket adipose tissue of Canadian commercial crossbred beef steers

Heritability and genetic and phenotypic correlations between 15 individuals and 10 groups of fatty acids with a concentration greater than 0.5% in the brisket adipose tissue of 223 Angus and Charolais based crossbred commercial steers were estimated using univariate and bivariate animal models. Individual saturated fatty acids were low to moderately heritable, with heritability estimates ranging from 0.05 (C16:0) to 0.31 (C15:0). Individual monounsaturated fatty acids were low to moderately highly heritable ranging from 0.04 (9c C17:1 and 11c C18:1) to 0.51 (9c C14:1). Polyunsaturated fatty acid C18:2n-6 was moderately heritable (0.17). Among groups of fatty acids, heritability estimates ranged from 0.03 for branched chain fatty acid (BCFA) and n-6/n-3 to 0.16 for n-6 and Health Index. A range of low (0.00) to high (1.00) phenotypic and genetic correlations was observed among the 25 fatty acids considered in this study. In general, fatty acids such as conjugated linoleic acid (CLA) and 11t C18:1, with potential health benefits, showed significant antagonistic correlations with unhealthy fatty acids such as C14:0 and C16:0. The results from this study provide insight into the direct genetic control of host genes on fatty acid composition of beef tissues and will facilitate designs of genetic selection and/or genetic based diet management to improve fatty acid composition in beef cattle.