The SNPs in the promoter regions of the bovine FADS2 and FABP4 genes are associated with beef quality traits

The Promoter SNPs Were Associated with Both the Contents of Poly-Unsaturated Fatty Acids (PUFAs) and the Expressions of PUFA-Related Genes in Common Carp

The allo-tetraploid common carp encodes two duplicated fads2 genes (fads2a and fads2b) and two duplicated elovl5 genes (elovl5a and elovl5b). The coding SNPs (cSNPs) of these genes were reported to be significantly associated with the PUFA contents. Whether the promoter SNPs (pSNPs) were associated with the PUFA contents has not been reported yet. In this study, after sequencing the promoters of these four genes, we identified six pSNPs associated with the contents of PUFAs in common carp, including one elovl5a pSNP, one elovl5b pSNP, and four fads2b pSNPs. The pSNPs were predicted in the locations of transcriptional factor binding sites. Together with previously identified cSNPs in fads2b and elovl5b, the pSNPs and cSNPs of these two genes had the joint effects on the PUFA contents with higher explained percentage of phenotypic variation of the PUFA contents than single gene. The expression levels of both fads2a and fads2b were significantly positively correlated with the contents of six PUFAs. The fads2b pSNPs corresponding to higher fads2b expression levels were associated with higher PUFA contents. The pSNPs and cSNPs will be useful for the future selection breeding of common carp with higher PUFA contents.

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.

The g.4290 C>G Polymorphism in the FADS2 Gene Modifies the Fatty Acid Profile of the Pectoralis Superficialis Muscle of Ross 308 Broiler Chickens

The effect of the g.4290 C>G substitution in the FADS2 gene and g.285 C>T in the FABP4 gene on carcass quality, meat quality, and fatty acid profile of the pectoralis superficialis muscle of 238 male broiler chickens reared up to 45 days of age was analyzed. A significant influence of g.4290 C>G in the FADS2 gene on the pectoralis superficialis muscle fatty acid profile was demonstrated. Chickens with the GG genotype were characterized by the highest content of conjugated linoleic acid, amino acids, eicosapentaenoic acids, docosapentaenoic acid, docosahexaenoic acids. and the lowest value of the linoleic acid/alpha-linolenic acid ratio. The FABP4 polymorphism determined only the content of C18:1n-9, C18:2n-6 and docosahexaenoic acid. There was no effect of the studied genotypes on final body weight, carcass quality traits, or quality of broiler pectoral muscles.

Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle

Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot.

agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.

Polymorphisms in Fatty Acid Desaturase 2 Gene are Associated with Milk Production Traits in Chinese Holstein Cows

Simple Summary

Searching for causative polymorphisms underlying the variability of milk production traits and then incorporating them into breeding programs are very effective ways to improve the efficiency and reliability of conventional dairy cattle breeding. Fatty acid desaturase 2 (FADS2) plays a pivotal role in the biosynthesis of polyunsaturated fatty acids. Previous studies provided evidence that FADS2 was one of the most downregulated genes during negative energy balance in the liver of postpartum dairy cattle. Genes involved in the energetic pathways may influence other production traits, such as protein, fat and milk yields. Therefore, in the present study, we investigated the common genetic variants of the FADS2 gene in Chinese Holstein cows. Our results provided direct evidence that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis.

Abstract

This study investigated the single nucleotide polymorphisms (SNPs) of Fatty acid desaturase 2 (FADS2) gene and further explored their genetic effects on conventionally collected milk production traits in Chinese Holstein cows using 18,264 test-day records of 841 cows. One missense mutation c. 908 C > T (SNP site in the complementary DNA sequence), which caused an amino acid change from alanine to valine (294Ala > Val), and two 3’ untranslated region (UTR) SNPs, c.1571 G > A and c.2776 A > G were finally identified. The SNP c.908 C > T was significantly associated with test-day milk yield, fat percentage and 305-day milk, fat and protein yield. In particular, the T allele of the SNP c.908 C > T showed a significant association with decreased somatic cell score (SCS) in the investigated population. Significant relationship between the SNP c.1571 G > A and 305-day milk yield showed that genotype GG was linked to the highest milk yield. Substituting the allele G for A at the c.2776 A > G locus resulted in a decrease of protein percentage. Our results demonstrated that FADS2 was an interesting candidate for selection to increase milk production and improve resistance against mastitis.

The effect of polymorphism in the FADS2 gene on the fatty acid composition of bovine milk

Polyunsaturated fatty acids (PUFAs) play a role in a wide variety of physiological processes. They are produced by a series of desaturation and elongation reactions. Δ-6-desaturase is a membrane-bound enzyme that catalyzes the conversion of α-linolenic acid (C18:3n-3) and linoleic acid (C18:2n-6) to stearidonic acid (18:4n-3) and γ-linolenic acid (18:3n-6). It is encoded by the FADS2 gene located on bovine chromosome 29. The aim of this study was to identify a single nucleotide polymorphism in the FADS2 gene and to determine possible associations with milk fatty acid composition in two breeds of dairy cattle, i.e., Jersey and Polish Holstein-Friesian. Direct DNA sequencing revealed the presence of an A-to-G substitution in intron 3 of the FADS2 gene (rs209202414). Both populations were genotyped with an appropriate PCR-RFLP assay. The following genotype distributions were observed: for Jerseys, AA = 0.24, AG = 0.63, and GG = 0.13; for Polish Holstein-Friesians, AA = 0.17, AG = 0.40, and GG = 0.43. In Jerseys, statistically significant relationships were found between the FASD2 genotypes and the following milk fatty acids: lauric (P=0.0486), behenic (P=0.0199), lignoceric (P=0.0209), oleic (P=0.0386), eicosatrienoic (P=0.0113), and docosadienoic (P=0.0181). In Polish Holstein-Friesian cows, significant associations were observed for erucic (P=0.0460) and docosahexaenoic (P=0.0469) acids. The study indicated the A-to-G substitution (rs209202414) in the bovine FADS2 gene as a potential genetic marker for fatty acid composition in cattle milk.

Fatty acid-binding protein 1 increases steer fat deposition by facilitating the synthesis and secretion of triacylglycerol in liver

Castration is an important means of improving the beef quality via increasing fat deposition. However, little is known about the molecular mechanism underlying the fat deposition after castration. Here, the intramuscular fat (IMF) content of the steer group was shown to be much higher than the bull group. To understand transcriptional changes in the genes involved in fat deposition following castration, differential expression patterns of mRNAs in liver tissue were investigated in steers and bulls using RNA sequencing. In total, we obtained 58,282,367-54,918,002 uniquely mapped reads, which covered 90.13% of the currently annotated transcripts; 5,864 novel transcripts and optimized 9,088 known genes were determined. These results indicated that castration could change the expression patterns of mRNAs in liver tissue, and 282 differentially expressed genes (DEGs) were detected between steers and bulls. KEGG pathway analysis showed that the DEGs were mostly enriched in PPAR signaling pathway, steroid biosynthesis, steroid hormone biosynthesis, and biosynthesis of fatty acids. Furthermore, eight DEGs were corroborated via quantitative real-time PCR and we found that FABP1 gene knockdown in bovine hepatocytes prominently reduced intracellular triacylglycerol (TAG) synthesis and very low density lipoprotein (VLDL) secretion in culture medium. In summary, these results indicate that FABP1 may promote fat deposition by promoting the production and secretion of TAG and VLDL in steer liver.

The comprehensive liver transcriptome of two cattle breeds with different intramuscular fat content

Intramuscular fat (IMF) content is an important determinant factor of meat quality in cattle. There is significant difference in IMF content between Jinnan and Simmental cattle. Here, to identify candidate genes and networks associated with IMF deposition, we deeply explored the transcriptome architecture of liver in these two cattle breeds. We sequenced the liver transcriptome of five Jinnan and three Simmental cattle, yielding about 413.9 million sequencing reads. 124 differentially expressed genes (DEGs) were detected, of which 53 were up-regulated and 71 were down-regulated in Jinnan cattle. 1282 potentially novel genes were also identified. Gene ontology analysis revealed these DEGs (including CYP21A2, PC, ACACB, APOA1, and FADS2) were significantly enriched in lipid biosynthetic process, regulation of cholesterol esterification, reverse cholesterol transport, and regulation of lipoprotein lipase activity. Genes involved in pyruvate metabolism pathway were also significantly overrepresented. Moreover, we identified an interaction network which related to lipid metabolism, which might be contributed to the IMF deposition in cattle. We concluded that the DEGs involved in the regulation of lipid metabolism could play an important role in IMF deposition. Overall, we proposed a new panel of candidate genes and interaction networks that can be associated with IMF deposition and used as biomarkers in cattle breeding.