Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs

Abstract

Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.

Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs

“…Many genes regulate lipid droplet size and deposition. Forty candidate genes that may regulate fat deposition in subcutaneous and intramuscular fat were identified using transcriptomics in Ding Yuan pigs ( Zhang et al, 2022a ). In addition, based on transcriptomes of different breeds (Landrace pigs, Tibetan pigs, and Rongchang pigs) and tissues (SAT and VAT), Zhou et al (2013) suggested that subcutaneous adipose tissue differs from visceral and intermuscular adipose tissues due to lipid metabolism regulation ( Zhou et al, 2013 ).…”

“…FASN is associated with fat deposition in pigs and sheep ( Xing et al, 2021 ; Zhang et al, 2019 ; Zhao et al, 2022 ). Zhang et al (2022a) considered FASN a candidate gene for fat deposition. Another study showed a strong correlation between FASN and intramuscular fat ( Wang et al, 2020 ), and FASN determined lipid deposition using transcriptome and proteome data ( Wang et al, 2021 ).…”

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

“…Comparing gene expression between individuals with divergent traits in the same population can reduce noise owing to different genetic backgrounds [ 12 ]. In the present study, all pigs were selected based on the same breed, sex, and weight to allow candidate genes to be more dependable, thereby excluding unreliable factors identified owing to different breeds or different feed conditions.…”

“…As a polygenic trait, IMF is a complex metabolic process determined by the hyperplasia and hypertrophy of adipocytes and involves many biological processes and pathways, which are regulated by various molecules, such as hormones, transcription factors, protein-coding genes, and non-coding RNAs [ 10 , 11 , 12 ]. However, when compared with other traits, dissecting the genetic basis of IMF content is still limited, owing to its complexity.…”

“…Pig breeds in China have high contents of subcutaneous and intramuscular fat and good meat quality [ 18 ]. However, commercial pig breeds, such as Duroc, Landrace, and Yorkshire, are selected for better lean muscle growth, leading to a decrease in the deposition of fat, including IMF, resulting in reduced meat palatability [ 12 ]. Studies have also shown that IMF varies considerably among pure commercial breeds [ 7 , 11 , 16 ].…”