The species Brassica rapa includes various vegetable crops. Production of these vegetable crops is usually impaired by heat stress. Some microRNAs (miRNAs) in Arabidopsis have been considered to mediate gene silencing in plant response to abiotic stress. However, it remains unknown whether or what miRNAs play a role in heat resistance of B. rapa. To identify genomewide conserved and novel miRNAs that are responsive to heat stress in B. rapa, we defined temperature thresholds of non-heading Chinese cabbage (B. rapa ssp. chinensis) and constructed small RNA libraries from the seedlings that had been exposed to high temperature (46 °C) for 1 h. By deep sequencing and data analysis, we selected a series of conserved and novel miRNAs that responded to heat stress. In total, Chinese cabbage shares at least 35 conserved miRNA families with Arabidopsis thaliana. Among them, five miRNA families were responsive to heat stress. Northern hybridization and real-time PCR showed that the conserved miRNAs bra-miR398a and bra-miR398b were heat-inhibitive and guided heat response of their target gene, BracCSD1; and bra-miR156h and bra-miR156g were heat-induced and its putative target BracSPL2 was down-regulated. According to the criteria of miRNA and miRNA* that form a duplex, 21 novel miRNAs belonging to 19 miRNA families were predicted. Of these, four were identified to be heat-responsive by Northern blotting and/or expression analysis of the putative targets. The two novel miRNAs bra-miR1885b.3 and bra-miR5718 negatively regulated their putative target genes. 5′-Rapid amplification of cDNA ends PCR indicated that three novel miRNAs cleaved the transcripts of their target genes where their precursors may have evolved from. These results broaden our perspective on the important role of miRNA in plant responses to heat.

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

Significance: Recently N ⁶ -methyladenosine (m ⁶ A) methylation has emerged as a biological process with significant impact on cellular functions. However, almost all the research regarding m ⁶ A methylation has been based on mRNAs. In our research, we focus on how m ⁶ A methylation affects microRNA (miRNA) biogenesis in Arabidopsis . In brief, we show that m ⁶ A methylation is necessary to maintain proper levels of mature miRNAs as well as their precursors. m ⁶ A mark affects pri-miRNA secondary structures and affects the recruitment of the Microprocessor to pri-miRNAs. We also demonstrate the interactions of MTA (m ⁶ A writer) with other proteins involved in miRNA biogenesis, namely RNA Polymerase II and TOUGH. Our study provides evidence of the role played by m ⁶ A in plant miRNA biogenesis.

This study provides evidence of cotranslational RNA decay in a plant transcriptome and reveals a number of surprising features and proteins involved in this pro

Leafy heads of cabbage (Brassica oleracea), Chinese cabbage (Brassica rapa), and lettuce (Lactuca sativa) are composed of extremely incurved leaves. The shape of these heads often dictates the quality, and thus the commercial value, of these crops. Using quantitative trait locus mapping of head traits within a population of 150 recombinant inbred lines of Chinese cabbage, we investigated the relationship between expression levels of microRNA-targeted Brassica rapa ssp. pekinensis TEOSINTE BRANCHED1, cycloidea, and PCF transcription factor4 (BrpTCP4) genes and head shape. Here, we demonstrate that a cylindrical head shape is associated with relatively low BrpTCP4-1 expression, whereas a round head shape is associated with high BrpTCP4-1 expression. In the round-type Chinese cabbage, microRNA319 (miR319) accumulation and BrpTCP4-1 expression decrease from the apical to central regions of leaves. Overexpression of BrpMIR319a2 reduced the expression levels of BrpTCP4 and resulted in an even distribution of BrpTCP4 transcripts within all leaf regions. Changes in temporal and spatial patterns of BrpTCP4 expression appear to be associated with excess growth of both apical and interveinal regions, straightened leaf tips, and a transition from the round to the cylindrical head shape. These results suggest that the miR319a-targeted BrpTCP gene regulates the round shape of leafy heads via differential cell division arrest in leaf regions. Therefore, the manipulation of miR319a and BrpTCP4 genes is a potentially important tool for use in the genetic improvement of head shape in these crops.