Analysis of liver proteome and identification of critical proteins affecting milk fat, protein and lactose metabolism in dariy cattle with iTRAQ.

In this study, we investigated the proteomes of liver tissues in three periods of the lactation cycle of Holstein cows by using isobaric tag for relative and absolute quantification (iTRAQ) technique to obtain liver proteome and identify functional proteins/genes involved with milk synthesis in dairy cattle. Based on iTRAQ analysis, we detected 3,252 proteins in the liver tissues (false discovery rate (FDR) ≤ 0.01). We identified 32 differently expressed proteins (DEPs) among the three periods by p-value < 0.05 and Fold change (FC) ≥ 2 or ≤ 0.5, and 183 DEPs based on p-value < 0.05 and FC ≥ 1.5 or ≤ 0.67. In addition, we obtained 905 DEPs across the three periods by p-value < 0.05 and FC ≥ 1.2 or ≤ 0.83, and the subsequent GO and KEGG pathway functional analysis indicated that 73 DEPs were significantly enriched into the metabolic terms and pathways involved with milk synthesis such as citrate cycle, fatty acid, starch and sucrose metabolism, mTOR and PPAR signaling pathways. Further, 41 out of 73 DEPs were identified near to both the peak locations of the reported quantitative trait locus (QTLs) and significant single nucleotide polymorphisms (SNPs) that associated with milk yield and composition traits. In addition, we analyzed the 41 DEPs with the previous liver transcriptome data that used the same samples as this study, and considered nine proteins/genes, ALDH18A1, APOA4, CYP7A1, HADHB, PRKACA, IDH2, LDHA, LDHB, and MAT2A, to be the promising candidates for milk fat, protein and lactose synthesis in dairy cattle. This study provided a new vision for identifying the potential critical genes associated with milk synthesis of dairy cattle. This article is protected by copyright. All rights reserved.