Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

Abstract

Background Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored. Results In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5′ cDNA ends (5′-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development. Conclusions Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

In Vitro Effects of Tartary Buckwheat-Derived Nanovesicles on Gut Microbiota

“…The total number of known miRNAs for all sample comparisons was 129, and the newly predicted miRNAs were 11 in total, as shown in Table . 101 known miRNAs and 129 newly predicted miRNAs in buckwheat seeds were found in Li’s study . Among them, TBDNs and seeds share 16 miRNA families.…”

“…101 known miRNAs and 129 newly predicted miRNAs in buckwheat seeds were found in Li's study. 48 Among them, TBDNs and seeds share 16 miRNA families. In addition, TBDNs have 29 unique miRNA families and 11 new miRNAs.…”

“…There are large differences in miRNA between different varieties, and seeds are abundant in nucleic acids, as organs for storing reproductive organs and primary nutrients of crops. 48 Therefore, there are more types of miRNAs in the seed than TBDNs, indicating that only part of miRNAs can be encapsulated in vesicles to form exosomes. The sequence lengths were mostly distributed between 18 and 28 nt.…”

Cytological, physiological and transcriptomic analysis of variegated Leaves in Primulina pungentisepala offspring

“…qRT‒PCR was carried out with a TAKARA PrimeScript™ RT reagent Kit with gDNA Eraser and TB Green® Premix Ex Taq™ II [ 51 ]. Expression levels were calculated by the 2 −ΔΔCt method [ 52 ] and normalized to the level of the reference gene Actin7 .…”

Identification of Nitrogen Starvation-Responsive miRNAs to Reveal the miRNA-Mediated Regulatory Network in Betula luminifera

“…In recent years, the widespread high-throughput sequencing strategy was used for sRNAome ( Wen et al, 2022 ). The ability to detect low-expressed miRNAs contributes to the tremendous progress of miRNAs, especially in non-model plant species ( Dos Santos et al, 2019 ; Li H. et al, 2021 ). Furthermore, the combination of sRNA sequencing and degradome sequencing promotes the identification of miRNA target genes ( Charles Addo-Quaye, 2008 ).…”