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A Simple Method for Isolation of Soybean Protoplasts and Application to Transient Gene Expression Analyses
Published on: January 25, 2018
Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput
Xiaoqian Liu1, Shanshan Chu1, Chongyuan Sun1
1Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
Abstract:
MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype), were used for the construction of RNA sequencing (RNA-seq) libraries under low/normal-P treatment by high-throughput sequencing. In total, 603 existing miRNAs and 1699 novel miRNAs belonging to 248 and 1582 families in all samples were identified, respectively. Among these miRNAs, 777 miRNAs were differentially expressed (DE) across different P levels and genotypes. Furthermore, putative targets of DE miRNAs were predicted, and these miRNAs mainly targeted ERF (ethylene responsive factor), auxin response factors (ARF), zinc finger protein, MYB, and NAC domain transcription factors. Gene ontology (GO) analysis showed that targets of DE miRNAs were significantly enriched in binding, metabolic processes, biological regulation, response to stress, and phosphorus metabolic processes. In addition, the expression profiles of chosen P-responsive miRNAs and target genes were validated by quantitative real-time PCR (qRT-PCR). Our study focused on genome-wide miRNA identification in two representative soybean genotypes under low-P stress. Overall, the DE miRNAs across different P levels and genotypes and their putative target genes will provide useful information for further study of miRNAs mediating low-P response and facilitate improvements in soybean breeding.
Insights
Soybean microRNAs (miRNAs) respond to low phosphorus (LP) stress. This study identified novel and existing miRNAs, revealing key targets involved in stress and metabolic processes, aiding soybean breeding for improved phosphorus efficiency.
Area of Science:
- Plant Molecular Biology
- Genomics
- Agricultural Science
Background:
- MicroRNAs (miRNAs) play roles in plant stress responses.
- Limited understanding of miRNA regulation under low phosphorus (LP) stress in soybean.
Purpose of the Study:
- To identify and characterize microRNAs (miRNAs) responsive to low phosphorus (LP) stress in soybean.
- To elucidate the regulatory network of miRNAs and their targets under LP stress.
- To provide insights for breeding soybeans with enhanced LP efficiency.
Main Methods:
- High-throughput RNA sequencing (RNA-seq) of soybean roots under low and normal phosphorus conditions.
- Identification of known and novel miRNAs and prediction of their target genes.
- Differential expression analysis and Gene Ontology (GO) enrichment analysis.
- Validation of miRNA and target gene expression using quantitative real-time PCR (qRT-PCR).
Main Results:
- Identified 603 known and 1699 novel miRNAs across two soybean genotypes.
- 777 differentially expressed miRNAs (DE miRNAs) were found under varying phosphorus levels and genotypes.
- Predicted targets of DE miRNAs include transcription factors like ERF, ARF, MYB, and NAC.
- GO analysis revealed enrichment in binding, metabolic, regulatory, and stress response pathways, including phosphorus metabolism.
Conclusions:
- This genome-wide study provides a comprehensive catalog of miRNAs involved in soybean's low phosphorus (LP) stress response.
- The identified DE miRNAs and their targets offer valuable genetic resources for understanding LP tolerance mechanisms.
- Findings facilitate the development of soybean varieties with improved phosphorus utilization efficiency through breeding programs.
