Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

Ruihua Wang,Jianbo Wang,Zeyu Li,Mengdi Li,Aqin Cao,Shaoqing Li

doi:10.1186/s12870-020-02508-y

Abstract

BackgroundDistant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported.ResultsHere, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC2F12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies.ConclusionsTaken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.

Highlights

Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice
Overview of the sequencing data To explore the expression characteristics of Long non-coding RNA (lncRNA) and their roles in O. sativa, O. longistaminata and their three backcross introgression lines (BILs) progenies at jointing-booting stage, the strandspecific RNA-seq technology was used in this study
Around 56% clean reads in O. longistaminata and 70% clean reads in three progenies and O. sativa were uniquely mapped to the rice reference genome (Supplementary Table S1) and 66,338 transcripts were identified as known mRNAs

Summary

Introduction

Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. In the past few decades, a lot of backcross introgression lines (BILs) had been constructed to study scientific issues in rice, such as drought resistance [7, 8] genomic structure [3], hybrid sterility [5] and gene, miRNA and metabolic profiling [2, 9]. When lncRNA cis-regulates the target gene, it is encoded from the nucleic acid chain in which their target gene was located. A lncRNA (COLDAIR) cis-regulated the FLOWERING LOCUS C (FLC) gene, which was important in the regulation of flowering time in Arabidopsis; COLDAIR trans-regulated the FLC gene by binding to protein complex PcG [25, 26]. A large number of lncRNAs has been identified in previous studies, the research on their biological functions is still in the initial stage, especially in plants

Methods

Results

Discussion

Conclusion