Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep.

Xu Feng,Fengzhe Li,Tingting Zhang,Caifang Ren,Jing Pang,Ziyu Wang,Guomin Zhang,Feng Wang,Yanli Zhang,Hua Yang

doi:10.1042/bsr20171350

Abstract

Reproductive ability, especially prolificacy, impacts sheep profitability. Hu sheep, a unique Chinese breed, is recognized for its high prolificacy (HP), early sexual maturity, and year-round estrus. However, little is known about the molecular mechanisms underlying HP in Hu sheep. To explore the potential mRNAs and long non-coding RNAs (lncRNAs) involved in Hu sheep prolificacy, we performed an ovarian genome-wide analysis of mRNAs and lncRNAs during the follicular stage using Hu sheep of HP (litter size = 3; three consecutive lambings) and low prolificacy (LP, litter size = 1; three consecutive lambings). Plasma luteinizing hormone (LH) concentration was higher in the HP group than in the LP group (P<0.05) during the follicular stage. Subsequently, 76 differentially expressed mRNAs (DE-mRNAs) and five differentially expressed lncRNAs (DE-lncRNAs) were identified by pairwise comparison; quantitative real-time PCR (qRT-PCR) analysis of ten randomly selected DE genes (mRNA and lncRNA) were consistent with the sequencing results. Gene Ontology (GO) analysis of DE-mRNAs revealed significant enrichment in immune response components, actin filament severing and phagocytosis. Pathway enrichment analysis of DE-mRNAs indicated a predominance of immune function pathways, including phagosomes, lysosomes, and antigen processing. We constructed a co-expression network of DE-mRNAs and mRNA-lncRNAs, with C1qA, CD53, cathepsin B (CTSB), CTSS, TYROBP, and AIF1 as the hub genes. Finally, the expression of lysosomal protease cathepsin genes, CTSB and cathepsin D (CTSD), were significantly up-regulated in sheep ovaries in the HP group compared with the LP group (P<0.05). These differential mRNAs and lncRNAs may provide information on the molecular mechanisms underlying sheep prolificacy.

Highlights

Reproductive ability has important impacts on the profitability of sheep production
Many studies have associated the dysregulation of long non-coding RNA (lncRNA) with reproduction, including germ cell formation, early embryo implantation and development, and reproductive hormone regulation
The present study examined the expression profile of mRNAs and lncRNAs in sheep ovaries associated with prolificacy, and found that mRNAs and lncRNAs were differentially expressed in the different groups analyzed

Summary

Introduction

Reproductive ability has important impacts on the profitability of sheep production. Reproduction is a complex process, and traits such as ovulation rate and litter size are genetically affected by causative mutations in some minor and major genes [1,2]. Mutations in bone morphogenetic protein 15 (BMP15), growth differentiation factor 9 (GDF9), and bone morphogenetic protein receptor, type 1B (BMPR-1B) have been identified in some sheep breeds as fecundity genes that affect follicular development and ovulation [4]. Mutations in these fecundity genes have different effects on ovulation rate and litter size. A recent study showed that the differential regulation of miRNAs and lncRNAs might be related to fecundity in Small Tail Han sheep and Dorset sheep [20] Despite these findings, research on prolificacy-associated lncRNA in Hu sheep and its target mRNA, especially their interaction networks, remains limited. We further constructed mRNA–mRNA and lncRNA–mRNA regulatory networks associated with sheep prolificacy

Materials and methods

Result

Findings

Discussion