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.
Highlights
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality
The IMF content was significantly higher in the HIMF group than in the LIMF group (P = 0.006)
The results indicated that the differentially expressed genes (DEGs) identified by RNA-Seq and the differentially abundant proteins (DAPs) identified by tandem mass tags-based (TMT)-based proteomics were reliable and efficient
Summary
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. We used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that regulate subcutaneous fat and IMF deposition in Dingyuan pigs. China’s pig breeds are rich in genetic resources and have good meat quality They suffer from problems such as a slow growth rate, high fat deposits, and low lean meat p ercentages[1]. The Dingyuan pig is an indigenous pig breed distributed in Dingyuan County, Anhui Province, China It has the advantages of high intramuscular fat, and good meat quality, and has a low lean meat percentage and relatively slow growth rate. We believe that this population may harbor key genes that regulate subcutaneous and intramuscular fat deposition, providing a good study system to investigate the molecular mechanisms regulating tissue-level differences in fat deposition. Dingyuan pig is an excellent indigenous pig breed, but there is no relevant report yet
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