Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

Abstract

Background Long noncoding RNAs (lncRNAs) are emerging as the important regulators involving in growth and development as well as stress response in plants. However, current lncRNA studies were mainly performed at the individual level and the significance of it is not well understood in wheat. Results In this study, the lncRNA landscape of wheat spike was characterized through analysing a total of 186 spike RNA-seq datasets from 93 wheat genotypes. A total of 35,913 lncRNAs as well as 1,619 lncRNA-mRNA pairs comprised of 443 lncRNAs and 464 mRNAs were obtained. Compared to coding genes, these lncRNAs displayed rather low conservation among wheat and other gramineous species. Based on re-sequencing data, the genetic variations of these lncRNA were investigated and obvious genetic bottleneck were found on them during wheat domestication process. Furthermore, 122 lncRNAs were found to act as ceRNA to regulate endogenous competition. Finally, association and co-localization analysis of the candidate lncRNA-mRNA pairs identified 170 lncRNAs and 167 target mRNAs significantly associated with spike-related traits, including lncRNA.127690.1/TraesCS2A02G518500.1 (PMEI) and lncRNA.104854.1/TraesCS6A02G050300.1 (ATG5) associated with heading date and spike length, respectively. Conclusions This study reported the lncRNA landscape of wheat spike through the population transcriptome analysis, which not only contribute to better understand the wheat evolution from the perspective of lncRNA, but also lay the foundation for revealing roles of lncRNA playing in spike development.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

“…However, this finding was limited to a single wheat genotype, leaving the genetic variations and evolutionary characteristics of wheat lncRNAs largely unexplored. Yang et al [139] addressed this gap by conducting a comprehensive study involving 93 wheat genotypes to unveil the lncRNA landscape associated with wheat spikes. The analysis yielded a total of 35,913 lncRNAs, along with 1619 lncRNA-mRNA pairs.…”

Transcriptomic analysis reveals the regulatory mechanisms of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in response to waterlogging stress in rye (Secale cereale L.)

“…They can affect the regulation of other genes in a cis or trans manner and various processes such as alternative splicing, translation, and posttranscriptional gene epigenetic regulation [ 11 ]. Several lncRNAs have been identified in various plant species, including maize [ 12 ], barley [ 13 ], rice [ 14 ], and wheat [ 15 ]. The advent of high-throughput RNA sequencing (RNA-Seq) technology has facilitated the discovery of lncRNAs involved in biotic and abiotic stress responses in plants.…”

Plant long non-coding RNAs: identification and analysis to unveil their physiological functions

“…and less on plants (Zhao et al, 2021;. In the case of plants, lncRNAs have been reported on Arabidopsis and crop plants such as cotton, wheat, rice, and maize (Chekanova, 2015;Bai et al, 2019;Yang G. et al, 2022;Yang X. et al, 2022;Zhang et al, 2022). In plants, lncRNAs are transcribed mainly by the RNA polymerases I, II, and III.…”