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A Contig-Based Computational Prediction of Conserved miRNAs and Their Probable Role in Regulation of Cuticular Wax Biosynthesis in Banana

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Abstract

Banana has a high leaf area index and shallow root system, hence making it highly susceptible to water stress. One of the adaptive mechanisms is the deposition of cuticular wax on a leaf. Our previous analysis revealed the role of total cuticular wax, carbon chain length of the cuticular wax component, and the role of ester and alcohol wax compounds in maintaining the hydration of banana leaves which was further confirmed by gene expression analysis. To understand the regulatory mechanism of these wax genes in the present study, we have computationally mined and filtered miRNAs whose targets are involved in the wax biosynthetic process using M.balbisiana and M.acuminata transcriptome. Here, we predicted 96 and 62 conserved miRNA families and its targets in M.balbisiana and M.acuminata, respectively. Based on biochemical pathway, we filtered miRNAs and its targets which were involved in the wax biosynthetic process .Here, we report two miRNAs that are MbmiR531 whose target is KCS11 and MbmiR529 whose target is KCS10/FDH. The in silico characterization of MbmiR531 and MbmiR529 revealed that it had a strong, stable secondary structure with MFE of −23.4 and −26.5 kcal/mol, respectively, and MFEI value of −0.70 and −0.66 kcal/mol, respectively. Validation of the computational prediction was carried out on four high wax musa genotypes (990.6–1842.6 μg/dm2) and four low wax musa genotypes (424.1–780.2 μg/dm2) by qRT PCR which further revealed a negative relationship between the target gene and its miRNA thus indicating their role in wax biosynthesis regulation.

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Acknowledgements

We thank the Indian Council of Agricultural Research, New Delhi for financial assistance through the ICAR Network Project on Transgenics in Crops: Functional Genomics-Fusarium wilt and drought tolerance in Banana. M/s Genotypic Pvt. Ltd. Bangalore for sequencing and bioinformatic assistance.

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Authors and Affiliations

  1. Division of Biotechnology, ICAR - Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089, India

    Megha H. Sampangi-Ramaiah & Kundapura V. Ravishankar

  2. Department of Biotechnology, Centre for Post Graduate Studies, Jain University, 9th Main Road, Jaya Nagar East, Bengaluru, 560011, India

    Megha H. Sampangi-Ramaiah

  3. Division of Fruit Crops, ICAR - Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089, India

    Ajitha Rekha

  4. Division of Plant Physiology and Biochemistry, ICAR - Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru, 560089, India

    Kodathalu Seetharamaiah Shivashankara & Laxman R. Hunashikatti

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  1. Megha H. Sampangi-Ramaiah
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Correspondence to Kundapura V. Ravishankar.

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Sampangi-Ramaiah, M.H., Ravishankar, K.V., Rekha, A. et al. A Contig-Based Computational Prediction of Conserved miRNAs and Their Probable Role in Regulation of Cuticular Wax Biosynthesis in Banana. Plant Mol Biol Rep 35, 203–214 (2017). https://doi.org/10.1007/s11105-016-1016-9

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