MicroRNA and Putative Target Discoveries in Chrysanthemum Polyploidy Breeding

Abstract

MicroRNAs (miRNAs), around 22 nucleotides (nt) in length, are a class of endogenous and noncoding RNA molecule that play an essential role in plant development, either by suppressing the transcription of target genes at a transcriptional level or inhibiting translation at a posttranscriptional level. To understand the roles of miRNAs and their target genes in chrysanthemum polyploidy breeding, three sRNA libraries of normal and abnormal embryos after hybridization were performed by RNA-Seq. As a result, a total of 170 miRNAs were identified and there are 41 special miRNAs in cross of paternal chromosome doubling, such as miR169b, miR440, and miR528-5p. miR164c and miR159a were highly expressed in a normal embryo at 18 days after pollination, suggesting the regulatory role at the late stage of embryonic development. miR172c was only detected in the normal embryo at 18 days after pollination, which means that miR172c mainly mediates gene expression in postembryonic development and these genes may promote embryo maturation. Other miRNAs, including miR414, miR2661, and miR5021, may regulate the genes participated in pathways of auxin response and energy metabolism; then they regulate the complex embryonic development together.

Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

“…Although 16 homologue miRNAs were found in all 2x and 4x, two of them (miR482 and miR2916) significantly changed their expression, being either induced or repressed in 4x vs. 2x. MiR482 is known to be active in response to the inoculum of viruses, Verticillium dahliae , soybean cyst nematodes, and Ralstonia solanacearum [ 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 ]. In particular, it is a negative regulator of tolerance to pathogens by targeting conserved sequences encoding the P-loop of NBS–LRR resistance proteins.…”

“…Interestingly, we found that miR414 primarily targets transcriptional regulators belonging to MYB , B3 , AP2/ERF, and bZIP families. All of them were described as playing a key role in plant growth and development, physiological adjustments and morphological changes, secondary metabolism, and defense against stressors [ 44 , 45 ]. Since little is known about the transcriptional regulators active during polyploidization, the transcription factors identified in this survey represent promising candidates for being experimentally validated.…”

Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development

“…Modulation of the miR414 micro RNA (miRNA) level in response to nad9 knockdown was also in line. miR414 was proposed earlier to be involved in the regulation of the genes participating in auxin response pathways and energy metabolism during plant embryonic development [63] and a number of its target genes were reported to play an important role in hormone signal transduction, especially in the auxin and ethylene pathways [64]. miR164 is a further miRNA highlighted in previous mitochondrion-nucleus communication analyses [61].…”

High-throughput identification of chrysanthemum gene function and expression: An overview and an effective proposition

“…Based on the use of 454 sequencing platform, the C. indicum completed chloroplast genome was achieved with 150,972 bp in length including inverted repeats (IR; 24,956 bp), large single copy (LSC; 82,741 bp), and small single (SSC; 18,319 bp) regions (Xia et al 2016). miRNAs target genes were studied on the normal and abnormal embryos within three sRNA libraries by RNA-Seq to identify 170 miRNAs with 41 special miRNAs in the paternal chromosome doubling cross including miR169b, miR440, and miR528-5p (Zhang et al 2017). For floral traits of chrysanthemum, the 454-pyrosequencing technology was used to construct normalized cDNA libraries in chrysanthemum.…”