Experimental Validation and Characterization of Sugarcane Genome-Encoded MicroRNAs and Their Targets Using PCR-Based Expressional Methodology

Document Type : Original Research

Authors
A. Baqi 1
Samiullah 2
M. Z. Saleem 3
M. Ayub 4
H. Habibullah 1
1 Colleges, Higher and Technical Education Department, Balochistan, Quetta, Pakistan.
2 Department of Chemistry, University of Balochistan, Quetta 87300, Pakistan.
3 Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
4 University of Balochistan
10.22034/JAST.26.5.1057
Abstract
MicroRNAs (miRNAs) are typically small, endogenous, non-coding RNAs molecules that regulate gene expression at post-transcriptional level by mRNA degradation or translational repression. They are composed of 18-26 nucleotides and are conserved during evolution for the development of new miRNAs in a variety of plants. Sugarcane (Saccharum officinarum) is generally a valuable food and forage crop grown all over the world. Until now, different sugarcane miRNAs have been characterized for plant development and stress responses. In this research, 50 unique conserved sugarcane miRNAs from 44 different miRNA families have been predicted using a variety of genomics-based tools. The predicted sugarcane miRNAs were validated using a set of 15 randomly chosen primers and RT-PCR. Stem loop secondary structures are created using MFOLD tool. The psRNA-Target algorithm identified 7,976 various protein targets of sof-miRNAs including 55 specific GO terms. They have significant targets in biological, cellular, and molecular functions. Moreover, the sof-miR5205a regulates sulfur compound biosynthetic process and 9653a directs ubiquitin-dependent protein catabolic process. Consequently, the RNA binding and thylakoid membrane are controlled by sof-miR9657b and 2091, respectively. As a result, the outcomes of the novel sugarcane miRNAs target a variety of substantial genes that aid in controlling the environment for sugarcane to produce a higher quality crop.

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Subjects

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Journal of Agricultural Science and Technology
Volume 26, Issue 5
September and October 2024
Pages 1057-1071