Candidate gene expression affects intramuscular fat content and fatty acid composition in pigs

The objective of this study was to correlate the expression pattern of candidate genes with the intramuscular fat (IMF) content and fatty acid composition of the Longissimus dorsi muscle of Duroc × Shanzhu commercial crossbred pigs. Animals of both sexes were slaughtered at a body weight of about 90 kg. The IMF content and fatty acid composition of the Longissimus dorsi muscle were measured and correlated with candidate genes mRNA expression (AdPLA, ADRB3, LEPR, MC4R, PPARγ, PPARα, LPL, PEPCK, and SCD). Females presented higher IMF content (p < 0.05) than males. The total saturated fatty acid (SFA) in males was greater (p < 0.01), whereas the total monounsaturated fatty acid (MUFA) (p < 0.01) and polyunsaturated fatty acid (PUFA) (p < 0.05) were lower than in females. The expressions of AdPLA, MC4R, PEPCK, and SCD correlated with the IMF content (p < 0.05). AdPLA showed a positive association with MUFA and a negative association with SFA (p < 0.05). LEPR and MC4R were both positively and significantly associated with C18:3 and C20:0 (p < 0.05). PPARα and PPARγ were negatively correlated with SFA, and PPARγ was positively associated with MUFA (p < 0.05). LPL was positively associated with MUFA and negatively associated with SFA (p < 0.05). PEPCK was negatively correlated with PUFA (p < 0.05). SCD was positively associated with MUFA (p < 0.05). The revealed correlations may confirm that these candidate genes are important for fat deposition and fatty acid composition in pigs, and the evaluation and use of these genes may be useful for improving porcine meat quality.     

猪PID1基因CDS区的克隆及其mRNA表达与肌内脂肪沉积关系

为了探索PID1(Phosphotyrosine interaction domain containing1)基因的表达与脂肪沉积的关系,文章利用兼并引物进行RT-PCR从猪脂肪和肌肉组织中克隆PID1基因CDS(Coding region)区全序列,并采用荧光定量PCR方法对大白猪、鲁莱黑猪、莱芜猪3个猪品种的肝脏、脂肪和肌肉组织PID1基因mRNA表达进行了相对定量分析。结果表明:经克隆、测序,得到了猪PID1基因654bp全编码区序列,通过Blast比对,与人、大鼠、牛有93.88%、66.94%、88.07%的同源性。PID1基因在同一个品种猪中mRNA表达水平总体表现为:肝脏脂肪肌肉。在不同品种3种组织中PID1基因mRNA表达水平总体表现为:莱芜猪鲁莱黑猪大白猪,其中肝脏中差异显著(P0.05),但是在脂肪和肌肉组织中莱芜猪与鲁莱黑猪差异不显著(P0.05)。对于高肌内脂肪(LWH)、中等肌内脂肪(LWI)和低肌内脂肪(LWL)沉积的3组莱芜猪,PID1基因在肝脏组织中的表达水平是LWH显著高于LWL(P0.05),在肌肉组织中则是LWH显著高于LWI和LWL(P0.05)。PID1基因在莱芜猪品种内3个组织中mRNA表达量与IMF含量相关均不显著,而在品种间3个组织中mRNA表达量与IMF含量呈显著正相关(P0.05)。结果提示:PID1的表达可能与脂肪沉积性状存在一定的关系。     

Investigation of porcine FABP3 and LEPR gene polymorphisms and mRNA expression for variation in intramuscular fat content

Porcine chromosome 6 (SSC6) has been reported to have QTL affecting intramuscular fat content (IMF) in multiple populations. The objective of this study was to investigate the effect of FABP3 and LEPR genetic variations as well as their mRNA expression on the IMF trait in a three-generation of Korean native pig and Yorkshire crossed animals. Several polymorphisms of the FABP3 (HinfI, HaeIII and HinfI*) were significantly associated with moisture, tenderness and flavor score (P < 0.05), and were used to construct haploytpes: haplotype 1 (-TCT-) increased the marbling and intramuscular fat content, however, haplotype 2 (-CCT-) decreased tenderness. The LEPR AvaII polymorphism showed significant association with moisture, intramuscular fat, cholesterol and flavor score (P < 0.05). The linkage analyses with six microsatellites mapped FABP3 gene in the interval between the markers Sw1129 and S0228 (Sw1129—11.7 cM—FABP3—9.1 cM—S0228), and the LEPR gene between the markers S0121 and Sw322 (S0121—7.5 cM—LEPR—28.5 cM—Sw322). QTL mapping suggested a significant QTL affecting Moisture (83 cM) and IMF (84 cM) located close to marker S0228. The gene expression results showed that in the loin muscle, both of the FABP3 and LEPR genes showed significantly higher expression in pigs with higher IMF%, however, in the backfat, only FABP3 showed differential expression between these two groups of pigs (significantly higher expression in pigs with lower IMF%) (P < 0.05). In the liver, both of these two genes did not show any difference between the high and low IMF% groups.     

Developmental changes of the content of acetyl-CoA carboxylase mRNA in chicken liver

Utilizing RNA blot hybridization and immunoblotting techniques, the changes of the hepatic contents of acetyl-CoA carboxylase mRNA and of the enzyme protein in growing chicks have been investigated. In the post-hatching period, the hepatic mRNA level markedly increased at least 70-fold when compared to that before hatching. This increase was not observed in chicks receiving no diet. These changes were closely paralleled with the rise of the hepatic content of acetyl-CoA carboxylase protein in chicks up to 10 days old. Neither the acetyl-CoA carboxylase mRNA level nor the enzyme quantity significantly changed in heart. It is concluded from these results that the developmental regulation of acetyl-CoA carboxylase in the post-hatching period of chicks is tissue specific and occurs primarily at a pretranslational step. The content of acetyl-CoA carboxylase mRNA in adult chicken liver was low, which is comparable to those in embryos at 3 days before hatching and chicks at hatching day. Although acetyl-CoA carboxylase mRNA was detected in adult chicken brain, heart, lung, kidney, uropygial gland, spleen, testis, and chest muscle as well as liver, the mRNA level in these tissues was much lower than that in liver of growing chicks.     

Exploration of genes showing intramuscular fat deposition-associated expression changes in musculus longissimus muscle

Marbling, as defined by the amount of intramuscular fat, is an economically important trait in beef cattle. Intramuscular fat deposition is postulated to arise mainly from a series of adipogenic events in intramuscular adipocyte-lineage cells and in the physiological or anatomical milieux surrounding them. This study was designed to investigate gene-expression patterns associated with fat deposition in musculus longissimus muscle, including adipocyte-lineage cells and part of the milieux. Differential-display PCR (ddPCR) was used to examine expression differences between low-marbled and high-marbled steer groups at 8, 10, 12 and 14 months of age, encompassing the time that marbling starts to appear. Seventy-four of 2114 total bands on ddPCR gel-bands were significant (P < 0.05) for the group effect, the interaction effect between group and age, or both the group and the interaction effects. Sequence analysis of 72 of these bands revealed 77 genes, including 35 annotated genes and 42 novel sequences. Among the 35 annotated genes, 6 (BTG2, PDHB, SORBS1, TRDN, TTN and MGP) have been related to changes in intramuscular fat deposition, possibly by exerting effects on adipocyte-lineage cells or on the milieux surrounding them.     

Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa).

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 619 F(2) animals and their parents were typed for molecular markers covering the entire porcine genome. Associations were studied between these markers and two fatness traits: intramuscular fat content and backfat thickness. Association analyses were performed using interval mapping by regression under two genetic models: (1) an outbred line-cross model where the founder lines were assumed to be fixed for different QTL alleles; and (2) a half-sib model where a unique allele substitution effect was fitted within each of the 19 half-sib families. Both approaches revealed for backfat thickness a highly significant QTL on chromosome 7 and suggestive evidence for a QTL at chromosome 2. Furthermore, suggestive QTL affecting backfat thickness were detected on chromosomes 1 and 6 under the line-cross model. For intramuscular fat content the line-cross approach showed suggestive evidence for QTL on chromosomes 2, 4, and 6, whereas the half-sib analysis showed suggestive linkage for chromosomes 4 and 7. The nature of the QTL effects and assumptions underlying both models could explain discrepancies between the findings under the two models. It is concluded that both approaches can complement each other in the analysis of data from outbred line crosses.     

A study of associations of the H-FABP genotypes with fat and meat production of pigs

Although the content of intramuscular fat (IMF) influences significantly meat quality, it can be estimated only after the slaughter of animals. Variants of the H-FABP gene were suggested as candidate genes influencing the variability of IMF. The effect of H-FABP - HinfI polymorphism on the content of IMF, backfat thickness, the weight and percentages of major meat parts and of the leg in carcass weight was studied in a group of 97 pigs (46 gilts and 51 barrows) of Large White and Landrace breeds using the test of fattening capacity and carcass value. In the set of experimental animals, the frequencies of genes were H = 0.75 +/- 0.03 and h = 0.25 +/- 0.03. Biometric analyses did not corroborate differences among different H-FABP - HinfI genotypes and all the traits under study. Only in genotypes HH and Hh the differences between least-square means of phenotypic IMF values under study were close to the limit of significance (P = 0.06).     

Associations of A-FABP and H-FABP Markers with the Content of Intramuscular Fat in Beijing-You Chicken

This study has assessed the association of single nucleotide polymorphisms (SNP) identified in the adipocyte fatty acid binding protein (A-FABP) and heart-type fatty acid binding protein (H-FABP) genes with the content of intramuscular fat (IMF) in a population of male Beijing-You chickens. A previously described SNP in the chicken A-FABP gene had a significant (P < 0.05) effect on IMF content. Chickens inheriting the homozygous BB genotype at A-FABP had a significantly higher content of IMF in thigh muscles and breast muscles than did those inheriting the AA and AB genotypes. A novel SNP, identified here, in the H-FABP gene was also significantly (P < 0.05) associated with IMF content in thigh and breast muscle. Chickens inheriting the genotypes of DD and CD had much higher content of IMF than those inheriting the homozygous genotype of CC. Markers at the A-FABP and H-FABP genes were associated with IMF content in the studied population. Chickens inheriting the BB genotype at A-FABP, along with the CD genotype at H-FABP, produced muscles with a much higher content of IMF when compared with all other genotypes. A weak interaction between A-FABP and H-FABP was detected (P < 0.09) for IMF content in the tested population. The statistical significance of interaction is tentative because of the limited number of observations for some genotypic combinations. Markers identified within the A-FABP and H-FABP genes are suitable for future use in identifying chickens with the genetic potential to produce more desirable muscle with higher IMF content, at least in the population of Beijing-You male chickens.     

Genome-wide association study reveals a quantitative trait locus and two candidate genes on Sus scrofa chromosome 5 affecting intramuscular fat content in Suhuai pigs

Intramuscular fat content (IFC) is an essential quantitative trait of meat, affecting multiple meat quality indicators. A certain amount of IFC could not only improve the sensory score of pork but also increase the flavour, tenderness, juiciness and shelf-life. To dissect the genetic determinants of IFC, two methods, including genome-wide efficient mixed-model analysis (GEMMA) and linkage disequilibrium adjusted kinships (LDAKs), were used to carry out genome-wide association studies for IFC in Suhuai pig population. A total of 14 and 18 significant single nucleotide polymorphisms (SNPs) were identified by GEMMA and LDAK, respectively. The results of these two methods were highly consistent and all 14 significant SNPs in GEMMA were detected by LDAK. Seven of the 18 SNPs reached the genome-wide significance level (P < 9.85E−07) while 11 cases reached the suggestive significance level (P < 1.77E−05). These significant SNPs were mainly distributed on Sus scrofa chromosome (SSC) 5, 3, and 7. Moreover, one locus resides in a 2.27 Mb (71.37–73.64 Mb) region on SSC5 harbouring 13 significant SNPs associated with IFC, and the lead SNP (rs81302978) also locates in this region. Linkage disequilibrium (LD) analysis showed that there were four pairs of complete LD (r² = 1) among these 13 SNPs, and the remaining 9 SNPs with incomplete LD (r² ≠ 1) were selected for subsequent analyses of IFC. Association analyses showed that 7 out of 9 SNPs were significantly associated with IFC (P < 0.05) in 330 Suhuai pigs, and the other 2 SNPs tended to reach a significant association level with IFC (P < 0.1). The phenotypic variance explained (PVE) range of these 9 SNPs was 0.92–3.55%. Meanwhile, the lead SNP was also significantly associated (rs81302978) with IFC (P < 0.05) in 378 commercial hybrid pigs (Pietrain × Duroc) × (Landrace × Yorkshire) (PDLY), and the PVE was 1.38%. Besides, two lipid metabolism-relevant candidate genes, the leucine rich repeat kinase 2 (LRRK2) and PDZ domain containing ring finger 4 (PDZRN4) were identified in the 2.27 Mb region on SSC5. In conclusion, our results may provide a set of markers useful for genetic improvement of IFC in pigs and will advance the genome selection process of IFC on pig breeding programmes.     

Relationships between hepatic stearoyl-CoA desaturase-1 activity and mRNA expression with liver fat content in humans

Stearoyl-CoA desaturase-1 (SCD1) has gained much interest as a future drug target to treat fatty liver and its consequences. However, there are few and inconsistent human data about expression and activity of this important enzyme. We investigated activity and expression of SCD1 and their relationships with liver fat (LF) content in human liver samples. Fifty subjects undergoing liver surgery were studied. SCD1 activity was estimated from the ratio of oleate (C18:1) to stearate (C18:0) within lipid subfractions. Furthermore, SCD1 mRNA expression and LF content were measured. Similarly to previous studies, we observed a strong positive correlation between LF content and the C18:1/C18:0 ratio in the combined fatty acid (FA) fractions (r = 0.96, P < 0.0001), which could be interpreted as higher SCD1 activity with increasing LF. However, hepatic SCD1 mRNA expression did not correlate with LF (r = 0.16, P = 0.13). To solve these conflicting data, we analyzed the FA composition of hepatic lipid subfractions. With increasing LF content the amount of FAs from the triglyceride (TG) fraction increased (r = 0.96, P < 0.0001), whereas the FAs from the phospholipid (PL) fraction remained unchanged (r = -0.17, P = 0.19). Of these two major lipid fractions, the C18:1/C18:0 ratio in TG was 16-fold higher than in PL. Supporting the SCD1 mRNA expression data, the C18:1/C18:0 ratio of the TG or PL fraction did not correlate with LF (r = 0.26, P = 0.12 and r = 0.08, P = 0.29). We provide novel information that SCD1 activity and mRNA expression appear not to be elevated in subjects with high LF content. We suggest that the FA composition of lipid subclasses, rather than of mixed lipids, should be analyzed to estimate SCD1 activity.     

Integrating genome-wide association study with RNA-seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.     

The correlation of intramuscular fat content between muscles of the lamb carcass and the use of computed tomography to predict intramuscular fat percentage in lambs

Intramuscular fat (IMF) % contributes positively to the juiciness and flavour of lamb and is therefore a useful indicator of eating quality. A rapid, non-destructive method of IMF determination like computed tomography (CT) would enable pre-sorting of carcasses based on IMF% and potential eating quality. Given the loin muscle (longissimus lumborum) is easy to sample, a single measurement at this site would be useful, providing is correlates well to other muscles. To determine the ability of CT to predict IMF%, this study used 400 animals and examined 5 muscles from three sections of the carcass: from the fore-section the m. supraspinatus and m. infraspinatus, from the saddle-section the m. longissimus lumborum and from the hind-section the m. semimembranosus and m. semitendinosus. The average CT pixel density of muscle was negatively associated with IMF% and can be used to predict IMF% although precision in this study was poor. The ability of CT to predict IMF% was greatest in the m. longissimus lumborum (slope −0.07) and smallest in the m. infraspinatus (slope −0.02). The correlation coefficients of IMF% between the five muscles were variable, with the highest correlation coefficients evident between muscles of the fore section (0.67 between the m. supraspinatus and the m. infraspinatus) and the weakest correlations were between the muscle of the fore and hind section. The correlation between the m. longissimus lumborum to the other muscles was fairly consistent with values ranging between 0.34 and 0.40 (partial correlation coefficient). The correlation between the proportion of carcass fat and the IMF% of the five muscles varied and was greatest in the m. longissimus lumborum (0.41).     

Developmental changes in fat body and midgut chromosomes of Drosophila auraria

Changes in puffing activity of fat body (FB) and midgut (MG) chromosomes of Drosophila auraria during late larval and white prepupal development as well as after in vitro culture with or without ecdysterone were studied and compared with those of the salivary gland (SG). The Balbiani Rings characteristic of the SG chromosomes of D. auraria, are not formed in FB and MG. Most of the inverted tandem chromosomal duplications that have been found to be common to all three tissues showed differentiation of puffing activity of the bands considered to be homologous. The major early ecdysone puffs 73A and 73B (considered to be homologues of D. melanogaster puffs 74EF and 75B, respectively), together with other early ecdysone puffs were present in all three tissues. Clear intermoult and postintermoult puffs were not evident in FB and MG chromosomes. However, a small set of late ecdysone puffs could be scored in FB, while no late ecdysone puffs were abserved in MG. Other tissue-specific puffs were identified, but a very small number of them were limited to MG.by W. Beermann