Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.     

Morphogenesis and Gene Mapping of <Emphasis Type="Italic">deformed interior floral organ 1</Emphasis> (<Emphasis Type="Italic">difo1</Emphasis>), a Novel Mutant Associated with Floral Organ Development in Rice

Floral organ identity and specific number directly affect anthesis habits, fertilization and grain yield. Here, we identified a deformed interior floral organ 1 (difo1) mutant from selfing progenies of indica cv. Zhonghui8015 (Zh8015) after ⁶⁰Co γ-ray treatment. Compared with the Zh8015 spikelet, the interior floral organs of the difo1 mutant present various numbers of stamens and stigmas, with no typical filament and no mature pollen grains. Most difo1 flowers exhibited an increased number of stigmas that were attached to the stamens and an intumescent ovule-like cell mass in addition to the ovary. Transverse sections of spikelets and scanning electron microscopy analysis revealed an indeterminate number of interior floral organs and abnormal early spikelet development for the difo1 mutant. Instead of the linear-shaped surface of wild-type stamens, difo1 displayed a glossy stamen surface resulting in immature stamens and complete sterility. In addition, the difo1 mutant exhibited delayed anthesis, rapid anthesis and non-extended stamens compared with wild type. Genetic analysis and gene mapping revealed that difo1 was controlled by a single recessive gene, which was fine-mapped to a 54-kb interval on the short arm of chromosome 4 between markers S22 and RM16439 harboring nine ORFs. Sequence analysis revealed that the mutant carried a single nucleotide deletion in its promoter region, which likely corresponded to the phenotype, in a C₂H₂-type zinc finger protein gene (LOC_Os04g08600). Moreover, qRT-PCR analysis showed a significantly down-regulated expression pattern for DIFO1 and many floral organ identity genes in the interior floral organs of difo1. DIFO1 is therefore an important floral organ development gene in rice, particularly with regard to interior organ meristem identity and floret primordium differentiation.     

Combined Small RNA and Degradome Sequencing Reveals Novel MiRNAs and Their Targets in the High-Yield Mutant Wheat Strain Yunong 3114

Wheat is one of the main food sources worldwide; large amount studies have been conducted to improve wheat production. MicroRNAs (miRNAs) with about 20–30 nucleotide are a class of regulatory small RNAs (sRNAs), which could regulate gene expression through sequence-specific base pairing with target mRNAs, playing important roles in plant growth. An ideal plant architecture (IPA) is crucial to enhance yield in bread wheat. In this study, the high-yield wheat strain Yunong 3114 was EMS-mutagenesis from the wild-type strain Yunong 201, exhibiting a preferable plant structure compared with the wild-type strain. We constructed small RNA and degradome libraries from Yunong 201 and Yunong 3114, and performed small RNA sequencing of these libraries in order identify miRNAs and their targets related to IPA in wheat. Totally, we identified 488 known and 837 novel miRNAs from Yunong 3114 and 391 known and 533 novel miRNAs from Yunong 201. The number of miRNAs in the mutant increased. A total of 37 known and 432 putative novel miRNAs were specifically expressed in the mutant strain; furthermore, 23 known and 159 putative novel miRNAs were specifically expressed in the wild-type strain. A total of 150 known and 100 novel miRNAs were differentially expressed between mutant and wild-type strains. Among these differentially expressed novel miRNAs, 4 and 8 predict novel miRNAs were evidenced by degradome sequencing and showed up-regulated and down-regulated expressions in the mutant strain Yunong 3114, respectively. Targeted gene annotation and previous results indicated that this set of miRNAs is related to plant structure. Our results further suggested that miRNAs may be necessary to obtain an optimal wheat structure.     

Identification of Conserved and Novel microRNAs from Liriodendron chinense Floral Tissues

Background

Liriodendron chinense (L. chinense) is an endangered basal angiosperm plant in China because of its low reproductive efficiency. Recently, miRNAs have obtained great attention because they can play important roles. Through high throughput sequencing technique, large amount of miRNAs were identified from different plant species. But there were few studies about the miRNAs in the basal angiosperms especially in the sexual reproduction process.

Results

Deep sequencing technology was applied to discover miRNAs in L. chinense flowers at different stages. After bioinformatic analysis, 496 putative conserved miRNAs representing 97 families and 2 novel miRNAs were found. Among them, one is previously regarded as gymnosperm specific. Their expressions were further validated by Real-time PCR for 13 selected miRNAs. Putative targeting genes were predicted and categorized with gene ontology (GO) analysis. About ten percents of the targets are involved in the reproduction process. Further expressional analysis showed that many of these miRNAs were highly related to the reproductive growth.

Conclusions

This is the first comprehensive identification of conserved and novel miRNAs in L. chinense. The data presented here might not only help to fill the gap of miRNA registered about basal angiosperm plants but also contribute to understanding the evolution of miRNAs. The differential expression of some of the miRNAs and the prediction of their target genes are also helpful in understanding the regulation of L. chinense sexual reproduction.