Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis

Abstract

We applied whole blood transcriptome analysis and gene set enrichment analysis to identify pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, whole blood samples were collected from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

Dietary fenugreek seed extract improves dry matter intake, apparent total tract nutrient digestibility, and alters whole blood transcriptome of Holstein dairy heifers

“…In order to assess the effects of SAP supplementation on the overall metabolism of the dairy heifers, we analyzed the whole blood transcriptome via GSEA. Gene expression in blood cells reflects physiological changes in the whole body and possibly indicates biological processes related to overall body metabolisms ( Jegou et al, 2016 ; Taiwo et al, 2022b ). The application of pathway analysis based on GSEA provides information and insight into the metabolic processes that are differentially regulated due to dietary supplementation of SAP.…”

“…Erythrocytes contain hemoglobins that are in continuous exposure to high oxygen content which predisposes them to oxidative stress ( Olsson et al, 2007 , Taiwo et al, 2022b ). Oxidative stress, a consequence of an imbalance of pro-oxidants and antioxidants, can lead to cell and tissue damage, resulting in impaired health and performance of animals ( Sordillo and Aitken, 2009 ; Celi and Gabai, 2015 ).…”

“…Analysis of the RNA-seq data has been described in our previous study ( Taiwo et al, 2022b ). Briefly, the removal of low-quality base calls and adapter sequences was performed using Trimmomatic v 0.39 ( Bolger et al, 2014 ), and then the quality-filtered reads were aligned to Bos_taurus .ARS-UCD1.2 reference genome using HISAT2 v 2.2.1 ( Kim et al, 2015 ).…”

“…Many studies have reported the positive effects of fenugreek seed as a source of saponins in humans, rats, and pigs ( Chevallier, 1996 ; Hossain et al, 2015 ), however, its effects on performance, health, and blood transcriptome of ruminants have not been extensively investigated. Transcriptome analysis of biofluids in ruminants provides a robust insight into health and metabolism ( Jiminez et al, 2021 ; Taiwo et al, 2022b ). Therefore, the objective of this study was to determine the effects of dietary supplementation of fenugreek seed extract as a source of saponins on performance, blood metabolites, apparent total tract nutrient digestibility, and whole blood transcriptome of Holstein dairy heifers.…”

Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs

“…Based on the comparison of animals with low or high FCR or RFI, they all concluded to the complex nature of FE since this trait integrates multiple biological pathways orchestrated in and by various tissues [2][3][4]. Among tissues, peripheral blood is a convenient and relatively easy sampling source of biological information that can highlight the variations in tissues metabolism and physiology to understand complex phenotypes [5] and with potential outcomes for applications in diagnostics and selection [6]. In pigs, about one thousand genes were found differentially expressed in the whole blood between two lines of pigs divergently selected for RFI [7,8].…”