Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing
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ORIGINAL ARTICLE
Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing Xiaoqian Liu 1 & Shanshan Chu 1 & Chongyuan Sun 1 & Huanqing Xu 1 & Jinyu Zhang 2 & Yongqing Jiao 1 & Dan Zhang 1 Received: 12 April 2020 / Revised: 22 September 2020 / Accepted: 24 September 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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/normalP 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. Keywords Soybean . MiRNA . High-throughput sequencing . Low phosphorus stress
Xiaoqian Liu and Shanshan Chu contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10142-020-00754-9) contains supplementary material, which is available to authorized users. * Dan Zhang [email protected]
Jinyu Zhang [email protected]
Xiaoqian Liu [email protected] Shanshan Chu [email protected] Chongyuan Sun [email protected] Huanqing Xu [email protected]
Yongqing Jiao [email protected] 1
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
2
Henan Institute of Science and Technology, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang 453003, China
Funct Integr Genomics
Introduction Phosphorus (P) is a vital nutrient for plant growth, development and metabolism. However, approximately 40% of the world’s
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