Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing

Abstract

miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna.

Identification and comparative profiling of miRNAs in herbaceous peony (Paeonia lactiflora Pall.) with red/yellow bicoloured flowers

“…The number of sRNAs was far less than the report of miRNAs responsive to Botrytis cinerea in P. lactiflora 21, which demonstrated that the mechanism of colour formation was less complicated compared with the stress response in P. lactiflora . With respect to the length distribution of sRNAs, 21–24 nt sRNAs dominated the sRNA transcriptome in red outer-petal and yellow inner-petal with the 21-nt sRNAs being the most abundant in length, which was in accordance with the reports in P. lactiflora 21, P. persica 17 and C. indica 22, while not in agreement with 24-nt sRNAs being the most abundant in C. tinctorius 16 and D. morifolium 20. This was mainly because of the plant species and the specific enzymes that were used to process the different length of sRNAs40.…”

“…With regard to miRNAs regulating colour formation, only a few studies have been reported to the best of our knowledge. Roy et al 22. used pale yellow and red flowers of C. indica to perform high-throughput sequencing, and found 109 differentially expressed miRNAs, 1,343 corresponding target genes gave 633 GO terms, among them, five miRNA families targeting five genes were involved in phenylpropanoid and pigment metabolic processes.…”

Identification of MicroRNAs and Their Targets Involved in Paeonia rockii Petal Variegation Using High-throughput Sequencing

“…In Arabidopsis thaliana, miRNA156 regulates the squamosal promoter binding protein-like gene (SPL9), which is a negative regulator of anthocyanin accumulation (Gou et al, 2011), and miRNA828 downregulates anthocyanin accumulation through its target genes AtTAS4-siR81(-) and R2R3-MYB TFs (Luo et al, 2012;Nishihara and Nakatsuka, 2011;Tanaka et al, 2008;Yang et al, 2009). Similar results have been reported for Canna indica, tomato (Solanum lycopersicum), and apple (Malus •domestica) exocarp (Jia et al, 2015;Qu et al, 2016;Roy et al, 2016;Xia et al, 2012). For apple, in addition to three predictable MYBs, MdTAS4-siR81(-) also targets a bHLH TF that interacts with MdMYB10 to regulate anthocyanin biosynthesis (Xia et al, 2012).…”

Integrated sRNAome and RNA-Seq Analysis Reveals miRNA Effects on Betalain Biosynthesis in Pitaya

“…In different rose cultivars, miRNAs may negatively regulate target genes to prevent carotenoid accumulation resulting in white owers according to expression analyses of ve miRNAs [9]. miRNAs can also regulate anthocyanin accumulation through their target genes [13][14][15][16][17][18][19][20][21][22][23][24][25].…”