Genome-wide profiling of long noncoding RNAs involved in wheat spike development

Pei Cao,Pengjia Li,Wenjuan Fan,Yuxin Hu

doi:10.1186/s12864-021-07851-4

Abstract

BackgroundLong noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear.ResultsHere, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs.ConclusionsThis study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.

Highlights

Long noncoding RNAs have been shown to play important roles in the regulation of plant growth and development
The Long noncoding RNAs (lncRNAs) transcriptomic profiling of developing wheat spike To monitor the dynamic profiling of lncRNAs during wheat spike development, the developing spikes of winter wheat Zhengmai366 were collected at six stages (S1S6) referred as inflorescence meristem (IM) stage (S1), spikelet meristem (SM) stage (S2), glume primordium stage (S3), floral meristem (FM) stage (S4), stamen and pistil primordium stage (S5) and floral organ stage (S6), respectively, according to anatomic and morphological features described previously [8] (Supplementary Fig. S1)
Expression clustering of differentially expressed lncRNAs To explore the possible regulation of lncRNAs during spike development, we focused on the lncRNAs that were differentially expressed among the six developmental stages

Summary

Introduction

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear. The TaTFL12D, an ortholog of Arabidopsis TERMINAL FLOWER 1 (TFL1), regulates wheat spike complexity by altering the number of spikelet, floret, and grain per spike [9], while the VERNALIZATION 1 (VRN1, named as FRUITFULL 1 (FUL1), FUL2 and FUL3 function redundantly in determining SM identity, as the lateral meristems in the vrn ful ful triple mutant are reverted to vegetative meristems to form leaves instead of spikelets [10]. The transcriptome of wheat inflorescence highlighted the gene regulatory networks between miRNAs and their target genes [12], and the gene expression profiles at six developmental stages of wheat spike revealed the expression dynamics of some important genes regulating spike development, including VRN1, Photoperiod-1 (Ppd-1) and Earliness per se 3 (Eps-3) [13]. An associative transcriptome analysis of 90 wheat varieties identified a few of genes related to spike complexity [9]

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Discussion

Conclusion