Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

Abstract

Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

Identification of Long Non-Coding RNAs Involved in Fat Deposition in Pigs Using Two High-Throughput Sequencing Methods

“…The KEGG results showed that the meaningful pathways were mostly concentrated on glucose metabolism. Some of these pathways, such as 'Glycolysis / Gluconeogenesis,' were also found in a previous study by our team [44] . Although they are not directly related to lipid synthesis and metabolism, glucose and lipids can change into each other and participate together in the tricarboxylic acid cycle.…”

Deletion of Trim28 in committed adipocytes promotes obesity but preserves glucose tolerance

“…Two genes substantially influenced by Trim28 adi-KO were Olr1 (oxidized low density lipoprotein receptor 1) and Klf14 , both of which have been previously implicated in adipocyte function 18 – 25 . We demonstrated a 30–40-fold increase in Olr1 gene expression in both male and female adi-KO mice (Fig.…”

“…Indeed, studies from Olr1-KO mice have demonstrated inhibition of de novo lipogenesis via reductions in expression of fatty acid synthase ( Fasn ), stearoyl-CoA desaturase ( Scd1 ), and ELOVL family member 6 ( Elovl6 ) 21 . Moreover, other studies have implicated Olr1 as a gene that regulates FM in several mammalian models 22 , 25 , and that its’ expression is regulated by PPARγ to control adipocyte cholesterol levels 20 . Thus, the substantial upregulation of Olr1 in adipose tissue of Trim28 adi-KO mice, could explain several aspects of the observed phenotype, particularly those related to alterations in the abundance of specific lipid species.…”

Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review

“…Insulin is stimulating ECM development [87] and the genes involved in ECM were enriched in Duroc than Iberian pigs [86]. In addition, genes involved in insulin signaling pathway and insulin resistance were upregulated in local Songliao pigs compared to in the Landrace pig breed [88]. Functional analysis of differentially expressed genes in the subcutaneous adipose tissue indicated upregulation of lipogenic and adipogenic processes, while processes associated with lipid mobilization and expenditure were downregulated in local breeds compared to modern breeds.…”