Candidate gene marker associations with fatty acid profiles in heavy pigs

Characterization and Function Analysis of miRNA Editing during Fat Deposition in Chinese Indigenous Ningxiang Pigs

This study aimed to identify active miRNA editing sites during adipose development in Ningxiang pigs and analyze their characteristics and functions. Based on small RNA-seq data from the subcutaneous adipose tissues of Ningxiang pigs at four stages-30 days (piglet), 90 days (nursery), 150 days (early fattening), and 210 days (late fattening)-we constructed a developmental map of miRNA editing in the adipose tissues of Ningxiang pigs. A total of 505 miRNA editing sites were identified using the revised pipeline, with C-to-U editing types being the most prevalent, followed by U-to-C, A-to-G, and G-to-U. Importantly, these four types of miRNA editing exhibited base preferences. The number of editing sites showed obvious differences among age groups, with the highest occurrence of miRNA editing events observed at 90 days of age and the lowest at 150 days of age. A total of nine miRNA editing sites were identified in the miRNA seed region, with significant differences in editing levels (p < 0.05) located in ssc-miR-23a, ssc-miR-27a, ssc-miR-30b-5p, ssc-miR-15a, ssc-miR-497, ssc-miR-15b, and ssc-miR-425-5p, respectively. Target gene prediction and KEGG enrichment analyses indicated that the editing of miR-497 might potentially regulate fat deposition by inhibiting adipose synthesis via influencing target binding. These results provide new insights into the regulatory mechanism of pig fat deposition.

Fatty Acid Composition of M. Biceps Femoris of Edible Dormouse (Glis glis L.)

This study aimed to investigate the fatty acid (FA) composition of edible dormouse m. biceps femoris in both sexes. More than 20 FA were identified in the muscle, with the 18:1cis-9 (oleic acid) being the most abundant in both sexes, comprising more than 50% of total FA in muscle. The most dominated FA were monounsaturated (MUFA), followed by saturated FA (SFA) and polyunsaturated FA (PUFA), reaching 54.8%, 25.43% and 19.8% of total FA, respectively. Sums of PUFA and n-3 PUFA tended (p > 0.05) to be higher in males than in females. There were no significant differences between sexes on the FA composition. Nevertheless, the 18:2n-6 tended to differ between sexes (p = 0.063). Several long-chain PUFA (LC-PUFA) were detected in dormouse muscle, with the 20:4 n-6 (arachidonic acid, AA) and the 22:6 n-3 (docosahexaenoic acid, DHA) being the most abundant in both sexes. The relatively high stearoyl-CoA desaturase (SCD) indexes and the large concentration of 18:1cis-9 in dormouse muscle tissues might point to a low mobilization of the SCD products. Furthermore, finding the unusual FA 20:3 ∆5,∆11,∆14, suggests feeding on leaf and wood lipids of Coniferophytes. We demonstrated sexual size monomorphism in edible dormouse. The literature regarding the composition of dormouse meat is scarce and no studies reported the FA composition of muscle, thus, this work can contribute to increasing the knowledge on edible dormouse physiology and nutritional traits.

Impact of Arachidonic and Docosahexaenoic Acid Supplementation on Neural and Immune Development in the Young Pig

Background: Human milk contains both arachidonic acid (ARA) and docosahexaenoic acid (DHA). Supplementation of infant formula with ARA and DHA results in fatty acid (FA) profiles, neurodevelopmental outcomes, and immune responses in formula-fed infants that are more like those observed in breastfed infants. Consequently, ARA and DHA have been historically added together to infant formula. This study investigated the impact of ARA or DHA supplementation alone or in combination on tissue FA incorporation, immune responses, and neurodevelopment in the young pig.

Methods: Male pigs (N = 48 total) received one of four dietary treatments from postnatal day (PND) 2–30. Treatments targeted the following ARA/DHA levels (% of total FA): CON (0.00/0.00), ARA (0.80/0.00), DHA (0.00/0.80), and ARA+DHA (0.80/0.80). Plasma, red blood cells (RBC), and prefrontal cortex (PFC) were collected for FA analysis. Blood was collected for T cell immunophenotyping and to quantify a panel of immune outcomes. Myelin thickness in the corpus callosum was measured by transmission electron microscopy and pig movement was measured by actigraphy.

Results: There were no differences in formula intake or growth between dietary groups. DHA supplementation increased brain DHA, but decreased ARA, compared with all other groups. ARA supplementation increased brain ARA compared with all other groups but did not affect brain DHA. Combined supplementation increased brain DHA levels but did not affect brain ARA levels compared with the control. Pigs fed ARA or ARA+DHA exhibited more activity than those fed CON or DHA. Diet-dependent differences in activity suggested pigs fed ARA had the lowest percent time asleep, while those fed DHA had the highest. No differences were observed for immune or myelination outcomes.

Conclusion: Supplementation with ARA and DHA did not differentially affect immune responses, but ARA levels in RBC and PFC were reduced when DHA was provided without ARA. Supplementation of either ARA or DHA alone induced differences in time spent asleep, and ARA inclusion increased general activity. Therefore, the current data support the combined supplementation with both ARA and DHA in infant formula and raise questions regarding the safety and nutritional suitability of ARA or DHA supplementation individually.

Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig

Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.

An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat-related traits in pigs

Meat quality improvement is of great interest to researchers in pig breeding and many researchers have identified abundant associated quantitative trait loci, genes and polymorphisms (QTXs) for fat-related traits. However, it is challenging to determine credible candidate genes from a mass of associations. The efficiency of identification of credible candidate genes in these QTXs is restricted by limited integration analyses of data from multiple omics. In this study, we constructed a 'candidate gene map' of fat-related traits in pigs based on published literature and the latest genome. In total, 6,861 QTXs, which covered 9,323 genes on the pig genome, were used. Combining the QTX hotspots and pathway analysis, we identified 180 candidate genes that may regulate the fat-related traits, and choose PNPLA2, PPARG, SREBF1, ACACA, PPARD and PPARA as credible candidate genes. In addition, we discussed the importance of incorporating transcriptome data and genomic data in causal gene identification, and the multi-omics information can effectively improve the credibility of identified candidate genes.

Gene Expression and Fatty Acid Profiling in Longissimus thoracis Muscle, Subcutaneous Fat, and Liver of Light Lambs in Response to Concentrate or Alfalfa Grazing

A better understanding of gene expression and metabolic pathways in response to a feeding system is critical for identifying key physiological processes and genes associated with polyunsaturated fatty acid (PUFA) content in lamb meat. The main objective of this study was to investigate transcriptional changes in L. thoracis (LT) muscle, liver, and subcutaneous fat (SF) of lambs that grazed alfalfa (ALF) and concentrate-fed (CON) slaughtered at 23 kg and using the Affymetrix Ovine Gene 1.1 ST whole-genome array. The study also evaluated the relationship between meat traits in LT muscle, including color, pigments and lipid oxidation during 7 days of display, α-tocopherol content, intramuscular fat (IMF) content and the fatty acid (FA) profile. Lambs that grazed on alfalfa had a greater α-tocopherol concentration in plasma than CON lambs (P < 0.05). The treatment did not affect the IMF content, meat color or pigments (P > 0.05). Grazing increased the α-tocopherol content (P < 0.001) and decreased lipid oxidation on day 7 of display (P < 0.05) in LT muscle. The ALF group contained a greater amount of conjugated linoleic acid (CLA), C18:3 n−3, C20:5 n−3, C22:5 n−3, and C22:6 n−3 than did the CON group (P < 0.05). We identified 41, 96 and four genes differentially expressed in LT muscle, liver, and subcutaneous fat, respectively. The most enriched biological processes in LT muscle were skeletal muscle tissue development, being the genes related to catabolic and lipid processes downregulated, except for CPT1B, which was upregulated in the ALF lambs. Animals grazing alfalfa had lower expression of desaturase enzymes in the liver (FADS1 and FADS2), which regulate unsaturation of fatty acids and are directly involved in the metabolism of n−3 PUFA series. The results found in the current study showed that ingesting diets richer in n−3 PUFA might have negative effects on the de novo synthesis of n−3 PUFA by downregulating the FADS1 and FADS2 expression. However, feeding diets poorer in n−3 PUFA can promote fatty acid desaturation, which makes these two genes attractive candidates for altering the content of PUFAs in meat.

A polymorphism in the fatty acid desaturase-2 gene is associated with the arachidonic acid metabolism in pigs

Arachidonic acid (C20:4) is related to a wide range of biological effects including lipid homeostasis. The fatty acid desaturase-2 (FADS2) gene encodes for the delta-6-desaturase, which is involved in the biosynthesis of C20:4 from linoleic acid (C18:2). The purpose of this study was to characterise mutations in the promoter of the porcine FADS2, evaluating in particular the effect of one haplotype tagging polymorphism (rs321384923A > G) on the biosynthesis pathway of C20:4. A total of 1,192 Duroc barrows with records on fatty acid composition in muscle and subcutaneous fat were genotyped. Pigs carrying the A allele showed, irrespective of fat content, both enhanced FADS2 expression and higher C20:4 in muscle and exhibited increased ratios of C20:4 to C18:2 and of C20:4 to eicosadienoic acid (C20:2) in both muscle and adipose tissue. Despite the inverse relationship observed between C20:4 and fat content, the rs321384923 polymorphism had no impact on lean weight. It is concluded that the haplotype encompassing the rs321384923 polymorphism at the porcine FADS2 affects the n-6 fatty acid profile by specifically modifying the desaturation efficiency of C18:2 to C20:4 rather than by concomitant variations in C18:2 following changes in fat content.

Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition

Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play an important role in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), and short-chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle. To further identify the candidate genes and pathways responsible for these phenotypic differences, the transcriptome of LD muscle from the two breeds were measured using RNA-seq. A total of 1347 differentially expressed genes were identified. The major metabolic pathways that were differentially modulated were lipolysis and glycometabolism. Yunling cattle showed a higher expression of lipolysis genes (ALDH9A1, ACSL5, ACADM, ACAT2, ACOT2) and a lower expression of genes related to glycometabolism (PGM1, GALM, PGM1, GPI, LDHA). This research identified candidate genes and pathways for IMF content and FA composition in the LD muscle of beef cattle, which may facilitate the design of new selection strategies to improve meat quality.

Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition

BACKGROUND

The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed.

RESULTS

Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM-receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated.

CONCLUSIONS

This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep.

Association of single nucleotide polymorphisms in fat metabolism candidate genes with fatty acid profiles of muscle and subcutaneous fat in heavy pigs

Dietary and organoleptic qualities of pork products are largely influenced by the profiles of fatty acids (FAs) of meat and fat. The objective of this work was to investigate the potential associations between FA profile in subcutaneous adipose (back fat and leg fat) and muscular (longissimus dorsi and biceps femoris) tissues in heavy pigs (n = 129, 9-month-old) with single nucleotide polymorphisms (SNPs) in six candidate genes involved in fat metabolism: Stearoyl-CoA desaturase (SCD), Diacylglycerol acyltransferase 1 and 2 (DGAT1 &DGAT2), Microsomal Triglyceride Transfer Protein (MTTP), Fatty Acid Synthase (FASN) and Heart- fatty acid binding protein (H-FABP). Preliminary results suggest a putative association between MTTP, DGAT2 and FASN and the FA content in both fat and meat, whereas between DGAT1, SCD and H-FABP the association was found in adipose tissue only. However, the effect of the analyzed genes, needs to be verified in a larger and better characterized pig population to support the hypothesized associations with FA content.

Activity, Expression, and Substrate Preference of the Δ(6)-Desaturase in Slow- or Fast-Growing Rabbit Genotypes

In the present paper liver fatty acid Δ(6) desaturation (fads2) activity was analyzed in two rabbit strains with slow- (S, 27.5 g/day) or fast-growing (F, 48.5 g/day) rate. The fatty acid profile of the liver showed a different PUFA profile in the two strains with a lower n-6/n-3 ratio in the S rabbits. The expression of fads2 was 2-fold higher in S than in F rabbits, whereas enzyme activity was higher in F and more oriented toward the desaturation of linoleic acid (90%). In contrast, S showed a higher preference for linolenic acid (38.9 vs 10%). This study identified a single difference in the fads2 amino acid sequence between these two strains. Such a difference consists in the substitution of Gly104 to Ser104 in the sequence of F fads2. These results indicate for the first time that genetic selection for performance may affect the preference for PUFA toward desaturation of linoleic/linolenic acid.

Polymorphism of fat metabolism genes as candidate markers for meat quality and production traits in heavy pigs

High meat quality is required for dry-cured ham production, which quality depends on meat fat quantity and composition. The aim was to study the polymorphisms of six genes involved in fat metabolism, namely, Stearoyl-CoA desaturase (SCD), Diacylglycerol acyltransferase 1 and 2 (DGAT1 &DGAT2), Microsomal triglyceride transfer protein (MTTP), Fatty acid synthase (FASN) and Heart fatty acid binding protein (H-FABP) in two traditional (Large White or Duroc × (Landrace × Large White)) and two industrial hybrids (Goland and Danbred), which are used for dry-cured ham production. Significant associations of SCD and MTTP were found with carcass weight. DGAT2 was associated with back fat thickness and L* fat colour (objective white colour score). Several genes (DGAT2, MTTP &FASN) were associated with weight loss during salting, first step in dry-cured ham production, affecting final yield. Finally, MTTP was associated with shear force. Our findings suggest that the SCD, DGAT2, MTTP and FASN polymorphisms are associated with quality of heavy pig meat products.

Differences in muscle transcriptome among pigs phenotypically extreme for fatty acid composition

BACKGROUND

Besides having an impact on human health, the porcine muscle fatty acid profile determines meat quality and taste. The RNA-Seq technologies allowed us to explore the pig muscle transcriptome with an unprecedented detail. The aim of this study was to identify differentially-expressed genes between two groups of 6 sows belonging to an Iberian × Landrace backcross with extreme phenotypes according to FA profile.

RESULTS

We sequenced the muscle transcriptome acquiring 787.5 M of 75 bp paired-end reads. About 85.1% of reads were mapped to the reference genome. Of the total reads, 79.1% were located in exons, 6.0% in introns and 14.9% in intergenic regions, indicating expressed regions not annotated in the reference genome. We identified a 34.5% of the intergenic regions as interspersed repetitive regions. We predicted a total of 2,372 putative proteins. Pathway analysis with 131 differentially-expressed genes revealed that the most statistically-significant metabolic pathways were related with lipid metabolism. Moreover, 18 of the differentially-expressed genes were located in genomic regions associated with IMF composition in an independent GWAS study in the same genetic background. Thus, our results indicate that the lipid metabolism of FAs is differently modulated when the FA composition in muscle differs. For instance, a high content of PUFA may reduce FA and glucose uptake resulting in an inhibition of the lipogenesis. These results are consistent with previous studies of our group analysing the liver and the adipose tissue transcriptomes providing a view of each of the main organs involved in lipid metabolism.

CONCLUSIONS

The results obtained in the muscle transcriptome analysis increase the knowledge of the gene regulation of IMF deposition, FA profile and meat quality, in terms of taste and nutritional value. Besides, our results may be important in terms of human health.

A functional variant in the stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork

There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18 ∶ 1) by desaturating stearic acid (18 ∶ 0). Here we describe a total of 18 mutations in the promoter and 3' non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18 ∶ 1/18 ∶ 0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18 ∶ 0+18 ∶ 1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18 ∶ 1/18 ∶ 0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18 ∶ 1/18 ∶ 0 and, consequently, the proportion of monounsaturated to saturated fat.

Fatty acid desaturase 2 (FADS2) insertion/deletion polymorphism impact on muscle fatty acid profile in European grayling (Thymallus thymallus)

An insertion (In)/deletion (Del) polymorphism in the fatty acid desaturase 2 (FADS2) gene, which codes for Δ6-desaturase, was for the first time observed in fish. The polymorphism is located in the seventh intron of FADS2 and the insertion consists of eleven repeats of CTGT (44 bp) with an allelic frequency, for the insertion, of 39 %. The polymorphism was associated with a modulation in Δ6-desaturase activity as significant effects on the ratio of EPA or DHA to their precursors were found (P< 0·001). A different distribution of SFA, MUFA and PUFA among the In/In, In/Del and Del/Del groups was also detected in fish fillet. The results suggest that genetic selection for this marker might improve the ability of European grayling to utilise dietary n-3 long-chain PUFA precursors, as Δ6-desaturase is the rate-limiting enzyme in the production of EPA and DHA from α-linolenic acid.