Proteomics Analysis and Identification of Critical Proteins and Network Interactions that Regulate the Specific Deposition of IMF of Jingyuan Chicken

Abstract Background: Improving broiler production efficiency and delivering good quality chicken has become an exciting area of research. Many factors affect the quality of chicken, and the IMF content is one of the critical factors determining the quality of chicken. At present, there are many reports on the molecular mechanism of IMF-specific deposition in chicken; however, only a few reports discuss the specific deposition of IMF in different parts of a chicken.Methods: In order to analyze the molecular mechanism of IMF specific deposition in different parts of chickens, the present study has selected 180-days old Jingyuan chicken breast and leg muscles as the research materials, using proteomics technology and screening of PRM protein quantitative detection methods, identification and quantitative verification of proteins that control the IMF-specific deposition in the leg muscles and breast muscles of Jingyuan chickens. The protein was analyzed by advanced bioinformatics using GO, KEGG, R language, Gallus_gallus_UniPort, and other biological software, including tools and related databases for screening and identification.Results: By screening and identifying LC-MS/MS mass spectrometry data and comparing it with the Gallus_gallus_UniPort database, a total of 1940.0 proteins were screened and identified, of which 1317.0 proteins were quantified. Compared with the breast muscles, there are 190 differentially expressed proteins between leg and breast muscles. In the leg muscles, 121 proteins are up-regulated, whereas 69 are down-regulated. Gene Ontology (GO) function annotation and enrichment analysis were done for 190 differential proteins. These proteins participate in a biological process (BP), cellular component (CC), and molecular function (MF) pathways. However, a total of 286 signaling pathways involved 190 differential proteins using a KEGG pathway. Significantly different proteins between the leg and breast muscles were primarily enriched with gga00500Starchandsucrosemetabolism, gga00071 Fattyaciddegradation, gga01212Fattyacidmetabolism, gga03320PPAR signaling pathway. PRM was used to confirm and identify the differential proteins by screening quantitatively; 10 of them are related to fat deposition, namely E1BTT4, E1C0Q5 (ACAT1), F1NC38 (ACADL), Q5F420 (ACSL1), A0A1D5P3S9 (ECI1), Q5ZL56 (ACADS), F1NUQ3 (FABP3), A0A1D5PL36 (ACAA2), F1NR44 (ECHS1), Q5ZIR7 (FABP5) using STRING and Cytoscape software to analyze the network interactions of 10 differentially expressed proteins, resulting in 19 network interaction paths.Conclusion: We used modern omics technology, omics software, and related databases to screen and identify 3 key signal pathways, including 10 key functional proteins that control IMF-specific deposition in different parts of chickens. At the same time, the present results can be used for different parts of the chicken. Specifically, the molecular mechanism of IMF-specific deposition has been explained, and a key regulatory role is played by the network interaction analysis of proteins that control IMF-specific deposition in different parts of chickens. The results have a scientific value and theoretical significance for improving chicken quality and molecular breeding of high-quality local chicken breeds.