High throughput deep sequencing elucidates the important role of lncRNAs in Foxtail millet response to herbicides

Genomics. 2020 Nov;112(6):4463-4473. doi: 10.1016/j.ygeno.2020.07.045. Epub 2020 Aug 5.

Abstract

Long non-coding RNAs (lncRNAs) play an important function in plant growth and development as well as response to stresses. However, little information was known in foxtail millet; no study was reported on lncRNAs in plant response to herbicide treatment. In this study, by using deep sequencing and advanced bioinformatic analysis, a total of 2547 lncRNAs were identified, including 787 known and 1760 novel lncRNAs. These lncRNAs are distributed across all 9 chromosomes, and the majority were located in the intergenic region with 1-2 exons. These lncRNAs were differentially expressed between different genotypes under different herbicide treatments. lncRNAs regulate plant growth and development as well as response to herbicide treatments through targeting protein-coding genes that directly relate to chemical metabolism and defense system. Multiple potential target genes and lncRNA-mRNA-miRNA gene networks were discovered. These results elucidate the potential roles of lncRNAs in plant response to herbicides.

Keywords: Deep sequencing; Foxtail millet; Gene network; Herbicide stress; LncRNAs; Transcriptional profiling.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Gene Expression Regulation, Plant*
  • Herbicides / toxicity*
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / metabolism
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism*
  • RNA, Long Noncoding / physiology
  • RNA-Seq
  • Setaria Plant / drug effects*
  • Setaria Plant / genetics*
  • Setaria Plant / growth & development
  • Setaria Plant / metabolism

Substances

  • Herbicides
  • MicroRNAs
  • RNA, Long Noncoding