Meta data for RNA-seq and RT-qPCR assays. (XLSX 20 kb

Dekkers, Jack

Liu, Haibo

Nettleton, Dan

Nguyen, Yet

Tuggle, Christopher

BMC Genomics

PubMed

Background: Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired. In this study, we aimed to explore whether differences exist in the global gene expression profiles of peripheral blood of 35 to 42 day-old pigs with extremely low (more efficient) and high RFI (less efficient) values from two lines that were divergently selected for RFI during the grow-finish phase, to use such information to explore the potential molecular basis of RFI differences, and to initiate development of predictive biomarkers for RFI.
Results: We identified 1972 differentially expressed genes (DEGs) (q ≤ 0.15) between the low (n = 15) and high (n = 16) RFI groups of animals by using RNA sequencing technology. We validated 24 of 37 selected DEGs by reverse transcription-quantitative PCR (RT-qPCR) in a joint analysis of 24 (12 per line) of the 31 samples already used for RNA-seq plus 24 (12 per line) novel samples from the same contemporary group of pigs. Using an analysis of the 24 novel samples alone, only nine of the 37 selected DEGs were validated. Genes involved in small molecule biosynthetic process, antigen processing and presentation of peptide antigen via major histocompatibility complex (MHC) class I, and steroid biosynthetic process were overrepresented among DEGs that had higher expression in the low versus high RFI animals. Genes known to function in the proteasome complex or mitochondrion were also significantly enriched among genes with higher expression in the low versus high RFI animals. Alternatively, genes involved in signal transduction, bone mineralization and regulation of phosphorylation were overrepresented among DEGs with lower expression in the low versus high RFI animals. The DEGs significantly overlapped with genes associated with disease, including hyperphagia, eating disorders and mitochondrial diseases (q 
Conclusions: The post-weaning blood transcriptome was clearly different between the low and high RFI groups. The identified DEGs suggested potential differences in mitochondrial and proteasomal activities, small molecule biosynthetic process, and signal transduction between the two RFI groups and provided potential new insights into the molecular basis of RFI in pigs, although the observed relationship between the post-weaning blood gene expression and RFI phenotype measured during the grow-finish phase was not strong. DEGs and representative genes in co-expression modules that were associated with RFI phenotype provide a preliminary list for developing predictive biomarkers for RFI in pigs.This article is published as Liu, Haibo, Yet T. Nguyen, Dan Nettleton, Jack CM Dekkers, and Christopher K. Tuggle. "Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake." BMC genomics 17 (2016): 73. doi: 10.1186/s12864-016-2395-x.</p

Digital Repository @ Iowa State University (ISU)

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Haibo Liu

Yet T. Nguyen

Dan Nettleton

Jack C. M. Dekkers

Christopher K. Tuggle

Crossref

Summary of IPAD-based pathway and disease enrichment analyses. (XLSX 59 kb

Haibo Liu (171264)

Yet Nguyen (3439898)

Dan Nettleton (6085)

Jack Dekkers (3439892)

Christopher Tuggle (3439895)

The Francis Crick Institute

Additional file 8: Table S6. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Association of gene expression with RFI phenotype. (XLSX 12 kb

Additional file 10: Table S8. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Subnetwork consisting of differentially expressed genes regulated by the inferred upstream regulator IL-15. Nodes were colored based on the log ratio of averaged expression levels of genes between groups, with up-regulated genes in red and down-regulated genes in green. (PDF 86 kb

Additional file 7: Figure S2. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Association of module eigengenes with RFI phenotype. (XLSX 10 kb

Additional file 13: Table S11. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Validation of differentially expressed genes by RT-qPCR assays. (XLSX 18 kb

Additional file 9: Table S7. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Differentially expressed genes identified by RNA-seq. (XLSX 5306 kb

Additional file 4: Table S4. of Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

https://figshare.com/articles/Additional_file_5_Figure_S1_of_Post-weaning_blood_transcriptomic_differences_between_Yorkshire_pigs_divergently_selected_for_residual_feed_intake/4346630

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

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