Two ecotype-related long non-coding RNAs in the environmental control of root growth

Abstract

BackgroundRoot architecture varies widely between species and even between ecotypes of the same species despite the strong conservation of the protein-coding portion of their genomes. In contrast, non-coding RNAs evolved rapidly between ecotypes and may control their differential responses to the environment as several long non-coding RNAs (lncRNAs) can quantitatively regulate gene expression.ResultsRoots from Columbia (Col) and Landsbergerecta(Ler) ecotypes respond differently to phosphate starvation. We compared complete transcriptomes (mRNAs, lncRNAs and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of new lncRNAs categorized as intergenic or antisense RNAs that were largely conserved at DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independently of the phosphate condition. These ecotype-related lncRNAs were characterized by analyzing their sequence variability among plants and their link with siRNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes including specific antisense RNAs targeting key regulators of root growth responses. Mis-regulation of several intergenic lncRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in Col.ConclusionsThe in depth exploration of the non-coding transcriptome of two ecotypes identified thousands of new lncRNAs showing specific expression in root apexes. De-regulation of two ecotype-related lncRNAs revealed a new pathway involved in the regulation of primary root growth. The non-coding genome may reveal novel mechanisms involved in ecotype adaptation of roots to different soil environments.

Lateral root development differs between main and secondary roots and depends on the ecotype

“…9 A second example is the different response to phosphate starvation 10 and the high difference in the root tip transcriptomes of such genotypes including mRNAs, lncRNAs, and small RNAs. 11 Regarding particularly roots, the size of these organs exhibits a natural variation between Col 0 and Ler accessions when plants are subjected to osmotic stress. In such conditions, the total LR number in Ler plants was significantly higher than in Col 0 seedlings.…”

Long noncoding RNAs shape transcription in plants

“…The access to new plant genomes and to transcriptomic datasets coming from tissuespecific samples and under different conditions has revealed the high transcriptional complexity of the genome. Furthermore, the noncoding genome is emerging as a major factor in natural variation [77]. A deeper knowledge about lncRNA activity over protein-coding genes will likely shed light on the adaptation of plants to their environment, allowing new strategies for agriculture.…”