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Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

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Abstract

Knowledge on structure and conserved domain of Musa chitinase isoforms and their responses to various biotic stresses will give a lead to select the suitable chitinase isoform for developing biotic stress-resistant genotypes. Hence, in this study, chitinase sequences available in the Musa genome hub were analyzed for their gene structure, conserved domain, as well as intron and exon regions. To identify the Musa chitinase isoforms involved in Pratylenchus coffeae (root lesion nematode) and Mycosphaerella eumusae (eumusa leaf spot) resistant mechanisms, differential gene expression analysis was carried out in P. coffeae- and M. eumusae-challenged resistant and susceptible banana genotypes. This study revealed that more number of chitinase isoforms (CIs) were responses upon eumusa leaf spot stress than nematode stress. The nematode challenge studies revealed that class II chitinase (GSMUA_Achr9G16770_001) was significantly overexpressed with 6.75-fold (with high fragments per kilobase of exon per million fragments mapped (FPKM)) in resistant genotype (Karthobiumtham-ABB) than susceptible (Nendran-AAB) genotype, whereas when M. eumusae was challenge inoculated, two class III CIs (GSMUA_Achr9G25580_001 and GSMUA_Achr8G27880_001) were overexpressed in resistant genotype (Manoranjitham-AAA) than the susceptible genotype (Grand Naine-AAA). However, none of the CIs were found to be commonly overexpressed under both stress conditions. This study reiterated that the chitinase genes are responding differently to different biotic stresses in their respective resistant genotypes.

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Acknowledgments

This work was supported by the Indian Council of Agricultural Research (ICAR) Plan fund for the Project No. 2000711005 to S.B. and ICAR grants on Network project on transgenic crops to S.U. We would like to thank the Director, National Research Centre for Banana (NRCB) and ICAR for the facilities provided for the conduct of this study. We immensely thank to Mr. K. Raja and A.S. Saravanakumar for assisting in pathogen inoculation, sample collection, and preparation.

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    1. ICAR-National Research Centre for Banana, Thogmalai Road, Thayanur Post, Trichy, 620102, Tamil Nadu, India

      S. Backiyarani, S. Uma, S. Nithya, A. Chandrasekar, M. S. Saraswathi, R. Thangavelu, M. Mayilvaganan & P. Sundararaju

    2. ICAR-National Research Centre for Plant Biotechnology, New Delhi, India

      N. K. Singh

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    S. Backiyarani and S. Uma contributed equally to this work.

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    Supplementary Table S1

    Details of Illumina sequence reads of NCS, NUS, NCR and NUR (DOCX 14 kb)

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    Backiyarani, S., Uma, S., Nithya, S. et al. Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens. Appl Biochem Biotechnol 175, 3585–3598 (2015). https://doi.org/10.1007/s12010-015-1528-z

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