Identification and characterization of circular RNAs in association with the feed efficiency in Hu lambs

Abstract

Background Circular RNA (circRNA), as a new members of noncoding RNA family, have vital functions in many biological processes by as microRNA sponges or competing endogenous RNAs (ceRNAs). However, little has been reported about the genetic mechanism of circRNAs regulation of feed efficiency in sheep. Results This study aimed to explore the expression of circRNAs in the liver of Hu sheep with High-RFI (High residual feed intake) and Low-RFI (Low residual feed intake) using transcriptome sequencing. A total of 20,729 circRNAs were identified in two groups, in which 219 circRNAs were found as significantly differentially expressed. Several circRNAs were validated by using RT-PCR, sanger sequencing and RT-qPCR methods. These results demonstrated that the RNA-seq result and expression level of circRNAs identified are reliable. Subsequently, GO and KEGG enrichment analysis of the parental genes of the differentially expressed (DE) circRNAs were mainly involved in immunity response and metabolic process. Finally, the ceRNA regulatory networks analysis showed that the target binding sites for miRNA such as novel_41, novel_115, novel_171 and oar-miR-485-3p in the identified DE cirRNAs. Importantly, two metabolic (SHISA3 and PLEKHH2) and four (RTP4, CD274, OAS1, and RFC3) immune-related target mRNAs were identified from 4 miRNAs. Association analysis showed that the polymorphism (RTP4 c.399 A > G) in the target gene RTP4 were significantly associated with RFI (P < 0.05). Conclusions Analysis of sequencing data showed some candidate ceRNAs that may play key roles in the feed efficiency in sheep by regulating animal immune and metabolic. These results provide the basis data for further study of the biological functions of circRNAs in regulating sheep feed efficiency.

Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves

“…Fueling immune response is an energetically expensive process [55]. The transfer of nutrients from growth-to immune-related processes may increase maintenance requirements in animals during the immune response [12,56]. Therefore, the results of GO enrichment of these DEGs led to speculation that feeding calves with different feed types might result in less energy being consumed for combating systemic inflammation, and hence more efficient utilization of nutrients for growth and protein accretion.…”

“…A high proportion of concentrated feed can improve ruminal starch digestibility, lower rumen pH and reduce the activity of the rumen papillae needed to absorb VFA [6][7][8]. The inclusion of dietary fiber through forage supplementation provides more physical stimulation, thereby enhancing the rumen volume, wall muscle content, motility and weight [9][10][11][12]. Therefore, with the rapid development of animal husbandry, determining whether different types of solid feed (including feed and concentrate) can provide certain nutrients for rumen growth and development is an urgent problem.…”

“…It can regulate cell development, proliferation and differentiation by adsorbing miRNA and alleviating its inhibitory effect on mRNA in cells and tissues [20,21]. Zhang et al showed that some candidate ceRNAs (cir_41, cir_115 and cir_171) might play key roles in immune and metabolic status in sheep [12].…”

Polymorphisms in SHISA3 and RFC3 genes and their association with feed conversion ratio in Hu sheep

“…Many relevant candidate genes and quantitative trait loci associated to feed efficiency were screened using sequencing technology, which may be used for marker-assisted selection (MAS) to enhance FE and lower production costs ( 15 – 21 ). In Hu sheep, it was discovered that ME1 gene polymorphism was significantly associated with FCR and RFI ( P < 0.05), whereas CA1 gene polymorphism was significantly associated with FCR ( P < 0.05) and the polymorphism in gene RTP4 were significantly associated with RFI ( P < 0.05) ( 17 , 22 ). According to methodological research using genome-wide association analysis, the genes CREB1, STEAP4, CTBP1, RIP140, SMURF2, FBF1, DTNBP1, SETD7 , and RBM11 may be candidates for fat deposition in sheep tails ( 23 , 24 ).…”

“…In this work, we selected two candidate genes, SHISA3 and RFC3 , which showed differential expression in previous studies on residual feed intake ( 21 ), while circulating RNAs associated with lamb feed efficiency were identified as miRNA target genes in studies ( 22 ). SHISA family member 3 ( SHISA3 ) is a gene that codes for proteins.…”