Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis.

Jie Wu,Rongrong Ding,Ting Gu,Zheng Xu,Xingwang Wang,Zhenfang Wu,Jie Yang,Enqin Zheng,Yong Ye,Ming Yang,Gengyuan Cai,Jianping Quan

doi:10.3390/ani10020189

Abstract

Simple SummaryFeed efficiency is one of the most valuable economic traits in the pig industry. The small intestine is the site where most of the nutrients are absorbed from ingested food. Here, we studied the relationship between small intestinal proteomics and feed efficiency in Duroc × (Landrace × Yorkshire) pigs, which is the most popular commercial pig in the Chinese pork market. Exploring the molecular mechanisms of feed efficiency will create great value for the pig industry. Our research provided a reference for further understanding of the key proteins that affect small intestinal microvilli formation and the important pathways related to feed efficiency in pigs.Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; p ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs.

Highlights

Feed cost accounts for 60–70% of total pig production costs [1]
Many omics methods have been used to study feed efficiency traits, very limited amounts of research have used the isobaric tag for relative and absolute quantification (iTRAQ) method to study this trait in DLY pigs at the protein level
Our results provided a new perspective for exploring candidate genes that affect feed efficiency (FE) traits in DLY commercial pigs

Summary

Introduction

Feed cost accounts for 60–70% of total pig production costs [1]. Feed efficiency (FE) is one of the most important economic traits of pig breeding. Animals 2020, 10, 189 feed intake (RFI) traits are often used to measure FE traits [2]. The heritabilities of RFI and FCR traits range from 0.14–0.40 and 0.30–0.47, respectively [3,4,5]. Low FCR and RFI ratios correspond to high FE [7]. Part of the explanation for this phenomenon may be due to the stronger intestinal endotoxin detoxification ability, increased intestinal lactobacillus, and higher antibacterial enzyme activity of low-RFI pigs [8,9]. Duroc × (Landrace × Yorkshire) (DLY) hybrid pigs have the largest sales share in the Chinese pork market due to their fast growth and good meat quality [10]

Objectives

Methods

Results

Conclusion