Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing.

Jing-Yao Yu,Hong-Wei Jiang,Qing-Shan Chen,Zhen-Gong Yin,Ze-Xin Zhang,Hong-Tao Qin,Shan-Shan Liu,Hui-Dong Qi,Wen-Jing Pan,Zhen-Bang Hu,Zhao-Ming Qi,Da-Wei Xin,Xin-Yu Wang,Shi-Yu Huang,Ke-Xin Qu,Zhan-Guo Zhang,Xue Han,Chun-Yan Liu,Xiao-Xia Wu

doi:10.3390/genes10060408

Jing-Yao Yu, Hong-Wei Jiang + Show 17 more

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https://doi.org/10.3390/genes10060408

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Abstract

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

Highlights

MicroRNAs are a class of endogenous small RNAs that are single-stranded RNA molecules composed of approximately 22 nucleotides [1]
High protein high oil (HPHO), low protein low oil (LPLO), low protein high oil (LPHO), and high protein low oil (HPLO), with the phenotypes of protein and oil content in the top 10% and the bottom 10% of the chromosome segment substitution line (CSSL) population distribution in 2014–2016 were selected, and there was no significant difference in other traits from SN14, as illustrated in Figure 1a by Qi et al
Glyma.04G178400 was annotated with sugar and the results showed that the gene expression pattern was not consistent with the four extreme materials in Real-time Quantitative PCR (RT-qPCR)

Summary

Introduction

MicroRNAs (miRNAs) are a class of endogenous small RNAs that are single-stranded RNA molecules composed of approximately 22 nucleotides [1]. Most miRNAs exist in the genome as single copies, multiple copies or clusters of genes [2]. Together with short interfering RNAs (siRNAs), Genes 2019, 10, 408; doi:10.3390/genes10060408 www.mdpi.com/journal/genes miRNAs are a key part of the evolutionarily conserved system of RNA genes and play an important regulatory role in plants and animals [3]. MicroRNA database (MiRBase) (http://www.mirbase.org/) is a searchable database of published miRNA sequences and annotations, containing miRNA information for a variety of plants and animals [4]. The platform manages and integrates genomics, transcriptomics, proteomics and metabolomics data and analyzes gene function and annotation of biological pathways, including four entities, genes, microRNAs, metabolism and single nucleotide polymorphisms (SNPs) [5]. Studies have shown that miRNAs negatively regulate their target genes

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