1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Comprehensive RNA-Seq Meta-analysis identifies genes/pathways related to fat-tail development of sheep
Paper ID : 1108-ICB10
Authors:
seyedeh fatemeh Hosseini1, Mohammad Reza Bakhtiarizadeh *2, Abdolreza salehi1
1university of tehran
2University of Tehran
Abstract:
Fat-tail content of sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive sheep industry systems, thin-tailed sheep are preferred, because fat deposition requires a greater energy cost than accretion of an equivalent amount of lean tissue. Comparative transcriptome analysis of thin-tailed against fat-tailed breeds can shed light on the genetic mechanisms controlling fat-tail development and improve breeding strategies to modulate fat deposition. Transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on meta-analysis. Here, an RNA-Seq meta-analysis on the transcriptomes of six publicly available datasets was performed. To analyze each study, first, quality control and trimming of the raw reads were done using FastQC and Trimmomatic tools, repectively. Then, the clean reads were aligned against reference sheep genome (V1.0.104). Htseq was employed to quantify the expression levels of the genes and DESeq2 R package was used to identify the genes differentially expressed (DEGs) between fat- and thin-tailed sheep breeds. The output of the DEGs analysis from all studies was further employed for the meta-analysis based on two approaches (fishercomb and invnorm) from metaRNASeq R package. The genes that were identified to be DEGs by both approaches were considered as final DEGs. Totally, 650,605,259 reads related to 6 samples were analyzed. A total of 353 genes (134 upregulated, 219 down-regulated) were identified as DEGs. Some of these genes including SCD, FASN, ACACA, CPT2, ACLY, LPL and DGAT2 confirmed the previous reports of associations with fat-tail development. Functional analysis of DEGs showed 64 KEGG pathways and 2423 GO terms were signiciantly enriched including "fatty acid metabolism pathways", "carbohydrate metabolism" and "steroid biosynthesis” which may contribute to fat storage in sheep tails. Our results highlighted a core set of genes/pathways associated with fat-tail development in sheep.
Keywords:
Sheep, Fat tail, Fat deposition, RNA-seq, Meta-analysis
Status : Paper Accepted (Poster Presentation)