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Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing

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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.

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Data availability

All relevant data are available in the paper, its Supporting Information files, and from the NCBI BioProject, SRA accession number SRP233151.

Abbreviations

qRT-PCR:

quantitative reverse transcription

TPM:

transcripts per million

ATPase:

ATP synthase

Rfam:

RNA family database

KEGG:

Kyoto encyclopedia of genes and genomes

GO:

gene ontology

sRNAs:

small RNAs

snoRNAs:

small nucleolar RNAs

snRNAs:

small nuclear RNAs

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Funding

This work was supported by the key scientific and technological project of Henan Province (192102110023), the Key Scientific Research Projects of Higher Education Institutions in Henan Province (20A210017), the Henan agricultural university science and technology innovation fund (KJCX2019C02), and the Ministry of Science and Technology of China (2016YFD0100500).

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  1. Xiaoqian Liu and Shanshan Chu contributed equally to this work.

Authors and Affiliations

  1. Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

    Xiaoqian Liu, Shanshan Chu, Chongyuan Sun, Huanqing Xu, Yongqing Jiao & Dan Zhang

  2. Henan Institute of Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, China

    Jinyu Zhang

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  1. Xiaoqian Liu
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  2. Shanshan Chu
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  3. Chongyuan Sun
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  4. Huanqing Xu
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  7. Dan Zhang
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Contributions

Conceptualization: Dan Zhang; methodology: Xiaoqian Liu; formal analysis and investigation: Xiaoqian Liu; writing—original draft preparation: Xiaoqian Liu; writing—review and editing: Dan Zhang, Shanshan Chu; funding acquisition: Dan Zhang; resources: Jinyu Zhang; supervision: Dan Zhang; Data curation: Dan Zhang, Xiaoqian Liu; software: Shanshan Chu; validation: Chongyuan Sun; investigation: Huanqing Xu; visualization: Yongqing Jiao

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Correspondence to Dan Zhang.

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Figure S1.

Functional categorization and distribution of miRNAs targets based on Gene Ontology (GO) classification in Nannong94-156-LP vs Bogao-LP (TIF 146 kb) (PNG 160 kb)

High resolution image (TIF 146 kb)

Figure S2.

Bubble chart of KEGG analysis based on targets of DE miRNAs in Nannong94-156-LP vs Bogao-LP (TIF 185 kb) (PNG 193 kb)

High resolution image (TIF 185 kb)

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Liu, X., Chu, S., Sun, C. et al. Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing. Funct Integr Genomics 20, 825–838 (2020). https://doi.org/10.1007/s10142-020-00754-9

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