Journal Article

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

Lv, Qiuyu, Zhu, Liwei, Chen, Qingfu, Li, Hongyou, Meng, Hengling, Deng, Jiao, Shi, Taoxiong, Sun, Xiaoqian

2021

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Annotations / Biological activity / Biomedical and Life Sciences / Biosynthesis / Buckwheat / Cell differentiation / cell growth / Development / Developmental stages / Differentiation (biology) / Elongation / Embryos / Endosperm / Fagopyrum tataricum / Flavonoids / Gene expression / gene expression regulation / Gene sequencing / Genes / Genetic aspects / Genetic regulation / Genomes / Grain size / Hormones / Integrated analysis / Life Sciences / Messenger RNA / MicroRNA / MicroRNAs / miRNA / miRNAs / Organogenesis / Phylogenetics / Phylogeny / Physiological aspects / Plant Sciences / Plants / Polymerase chain reaction / Proteins / quantitative polymerase chain reaction / Regulatory mechanisms (biology) / Research Article / Ribonucleic acid / Rice / RNA / RNA polymerase / Roles / Seed development / Seed size / Seeds / Signal transduction / Target gene / Target recognition / Tartary buckwheat / transcriptome / Transcriptomes / Tree Biology