Elucidation of miRNAs-Mediated Responses to Low Nitrogen Stress by Deep Sequencing of Two Soybean Genotypes

Autor: Qinnan Hao, Aihua Sha, Yejian Wang, Xinan Zhou, Chanjuan Zhang, Longping Yuan, Rong Zhou
Rok vydání: 2013
Předmět:
Gene regulatory network
lcsh:Medicine
Plant Science
Plant Genetics
Biochemistry
Plant Roots
MiRBase
RNA interference
Gene Expression Regulation
Plant
Molecular Cell Biology
Plant Genomics
Genomic library
Genome Sequencing
lcsh:Science
Flowering Plants
Cellular Stress Responses
Genetics
Regulation of gene expression
Multidisciplinary
Reverse Transcriptase Polymerase Chain Reaction
High-Throughput Nucleotide Sequencing
Agriculture
Genomics
Exons
Plants
Up-Regulation
Nucleic acids
Plant Shoots
Research Article
Evolutionary Processes
Nitrogen
Sequence analysis
Molecular Sequence Data
Down-Regulation
Crops
Protein degradation
Biology
Deep sequencing
Molecular Genetics
Open Reading Frames
Stress
Physiological
microRNA
Genome-Wide Association Studies
Gene Regulation
Adaptation
Gene Library
Crop Genetics
Evolutionary Biology
Base Sequence
Sequence Analysis
RNA
lcsh:R
Reproducibility of Results
Molecular Sequence Annotation
Introns
MicroRNAs
Small Molecules
RNA
lcsh:Q
Soybeans
Genome Expression Analysis
Zdroj: PLoS ONE, Vol 8, Iss 7, p e67423 (2013)
PLoS ONE
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0067423
Popis: Nitrogen (N) is a major limiting factor in crop production, and plant adaptive responses to low N are involved in many post-transcriptional regulation. Recent studies indicate that miRNAs play important roles in adaptive responses. However, miRNAs in soybean adaptive responses to N limitation have been not reported. We constructed sixteen libraries to identify low N-responsive miRNAs on a genome-wide scale using samples from 2 different genotypes (low N sensitive and low N tolerant) subjected to various periods of low nitrogen stress. Using high-throughput sequencing technology (Illumina-Solexa), we identified 362 known miRNAs variants belonging to 158 families and 90 new miRNAs belonging to 55 families. Among these known miRNAs variants, almost 50% were not different from annotated miRNAs in miRBase. Analyses of their expression patterns showed 150 known miRNAs variants as well as 2 novel miRNAs with differential expressions. These differentially expressed miRNAs between the two soybean genotypes were compared and classified into three groups based on their expression patterns. Predicted targets of these miRNAs were involved in various metabolic and regulatory pathways such as protein degradation, carbohydrate metabolism, hormone signaling pathway, and cellular transport. These findings suggest that miRNAs play important roles in soybean response to low N and contribute to the understanding of the genetic basis of differences in adaptive responses to N limitation between the two soybean genotypes. Our study provides basis for expounding the complex gene regulatory network of these miRNAs.
Databáze: OpenAIRE
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