Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs

Yuliaxis Ramayo-Caldas,Maria Ballester,Olga González-Rodríguez,David Torrallardona,Manuel Revilla,Juan Pablo Sánchez,Klaus Wimmers,Raquel Quintanilla,Henry Reyer

doi:10.1038/s41598-017-19072-5

Abstract

This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co-expressed genes), were significantly associated with FE indicators. Intra-module analyses revealed tissue-specific candidate genes; 12 of these genes were also identified as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, inflammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identified in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues. Our results suggest tissue-specific rather than common transcriptome regulatory processes associated with FE in pigs.

Highlights

Feed efficiency (FE) has a major impact on profitability and in economic sustainability of pig production, where feedstuffs represent the largest expenditure component, accounting for 60% to 70% of production costs[1,2]
Analysed animals were classified in two groups denoted hereafter as HFE and LFE
This result is consistent with the fact that residual intake and body weight gain (RIG) includes the residual gain plus the negative standardized residual feed intake (RFI), so that positive RIG values whereas negative RFI are related to higher feed efficiency (FE)

Summary

Introduction

Feed efficiency (FE) has a major impact on profitability and in economic sustainability of pig production, where feedstuffs represent the largest expenditure component, accounting for 60% to 70% of production costs[1,2]. Improving FE implies a reduction in the amount of minerals, heavy metals and greenhouse gases excreted per kg of meat produced[3], reducing the environmental impact of pig production systems These elements together with the need to optimize the use of feed resources make FE a major economically and socially important trait. In the light of the existing genetic determinism for FE, several genome-wide association (GWAS) and differential expression (DE) analyses have been performed for the aforementioned FE phenotypes, and a number of polymorphisms and genes have been reported to be associated to either RFI, FCR or RIG in livestock, in cattle[8,11,12,13], poultry[14,15] and pigs[16,17,18]. The main goal of this study is to identify candidate genes and pathways associated with FE in pigs through both DE analysis and a network-based approach that combine liver and duodenum transcriptomic data with FE phenotypic information

Objectives

Methods

Results

Conclusion