In-silico prediction of microRNA targets and finding genes suggesting significant involvement in the development of Glycine max seed

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Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Website:www.vegetosindia.org
Pub Email: contact@vegetosindia.org
Doi: 10.1007/s42535-019-00075-8
First Page: 450
Last Page: 463
Views: 1731


Keywords: miRNAs, Degradome analysis, miRNA target prediction, GO analysis, Expression pattern


Abstract

Glycine max is a worldwide leading economic crop and its seeds are deepening with proteins and oils which supply food and sustenance to all being. Various amounts of alimentary constituents are racked up in the G. max seed in the period of its ontogenesis. Thus, grasping the regulation of biological functions during seed enlargement belong to the basics for crop enhancement. The gene regulatory characteristics of miRNAs in G. max attracted us to focus on its target gene prediction, gene ontology (GO) analysis and expression pattern to their miRNA target genes, which suggest significant involvement in the development of G. max seed. Seven miRNAs have been found from the differential gene expression analysis of development stage 0–4 mm vs. 12–16 mm of G. max seed on the statistical parameter of p value ≤ 0.05 by computational-based microarray data analysis for miRNA target gene prediction. The miRNA target prediction analysis showed total 23 genes that were cleaved from 6 miRNAs, and computationally validated by identifying t-plots of miRNA targets using CleaveLand tool. GO results confirmed that the differentially expressed target genes could be classified into 20 molecular function categories, 73 biological process categories, and 10 cell components categories. On the basis of GO results, two genes were found to be significantly involved in the developmental process of G.max seed. The first miRNA target gene Glyma.01g119500 was predicted to annotate for embryo development ending in seed dormancy, seed dormancy, seed maturation, and seed germination. The second miRNA target gene Glyma.15g005300 was found to be involved in the regulation of seed germination. The Soybean eFP browser analysis suggests that the gene Glyma.01g119500 and Glyma.15g005300 reaches its maximum expression level of 35.88 and 26.6 respectively in the Soybean data source. The present study provides an avenue to explore more genomic and proteomic information about G. max seed developmental stage-specific miRNA target genes.


miRNAs, Degradome analysis, miRNA target prediction, GO analysis, Expression pattern


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Acknowledgements

Authors are grateful to the Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, for providing infrastructure facilities. First author is also thankful to the Ministry of Social Justice and Empowerment, Govt. of India, New Delhi for providing fellowship.


Author Information

Nivedita Yadav
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India

Kavita Goswami
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India


Budhayash Gautam
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India


Pramod Kumar Yadav
Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India

pramod.yadav@shiats.edu.in