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

  • Nivedita Yadav
  • Kavita Goswami
  • Budhayash Gautam
  • Pramod Kumar YadavEmail author
Research Articles


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 



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.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

42535_2019_75_MOESM1_ESM.xlsx (21 kb)
Supplementary material 1 (XLSX 21 kb)
42535_2019_75_MOESM2_ESM.xlsx (23 kb)
Supplementary material 2 (XLSX 22 kb)


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Copyright information

© Society for Plant Research 2019

Authors and Affiliations

  • Nivedita Yadav
    • 1
  • Kavita Goswami
    • 1
  • Budhayash Gautam
    • 1
  • Pramod Kumar Yadav
    • 1
    Email author
  1. 1.Jacob Institute of Biotechnology and Bioengineering, Department of Computational Biology and BioinformaticsSam Higginbottom University of Agriculture, Technology and SciencesPrayagrajIndia

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