Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

Tianqing Huang,Wei Gu,Enhui Liu,Xiulan Shi,Bingqian Wang,Wenhua Wu,Fulin Dong,Gefeng Xu

doi:10.1016/j.ygeno.2021.08.018

Abstract

Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for searching of a underlying mechanism of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood. By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at three different developmental stages between the diploid (XX) and triploid (XXX) female rainbow trout. These stages were gonads before differentiation (65 days post fertilisation, dpf), at the beginning of morphological differences (180 dpf) and showing clear difference between diploids and triploids (600 dpf), respectively. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R + 1, and 6 targeted DE lncRNAs were identified. Also, qRT-PCR was performed to validate the credibility of the network. Overall, this study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. The mRNA, lncRNA and miRNA screened in this study may be helpful to identify the functional elements regulating fertility of rainbow trout, which may provide reference for character improvement in aquaculture.

Highlights

Chromosomal ploidy manipulation is one of the means to create excellent germplasm
This study explored the potential interplay between coding and noncoding Ribonucleic acid (RNA) during the gonadal development of polyploid fish
It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction

Summary

Introduction

Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The artificial induction of polyploidy is of great significance to aquaculture production, which could provide research models for studying the genome diversity and adaptation (Francesc et al.,2009). Most triploid fish has been reported to be sterile because of the imbalance of nuclear-cytoplasmic ratio, the disorders of homologous chromosome pairing during meiosis or the epigenetic instability (Comai, 2005), which would lead to produce abnormal gametes and the cessation of gonad development (Benfey, 1999; Tiwary et al, 2004). All-female triploid rainbow trout were focused in this study

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