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Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection

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Abstract

Key message

NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions.

Abstract

Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.

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Abbreviations

NB-ARC:

Nucleotide-binding adaptor shared by APAF-1, R proteins and CED-4

HMM:

Hidden Markov model

NBS-LRR:

Nucleotide-binding site-leucine-rich repeat

CDD:

Conserved domain database

CD-HIT:

Cluster database at high identity with tolerance

PRGdb:

Plant resistance gene database

Pfam:

Protein families

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Acknowledgements

The authors are thankful to BTISNet SubDIC (BT/BI/04/065/04) for providing facilities for bioinformatics analyses. This work was supported by Department of Biotechnology, Government of India (Grant Nos. BT/PR6037/AGR/02/308/05 and BT/PR3925/BID/7/384/2011) and Centre of Excellence, Technical Education Quality Improvement Program-II (Grant No. NPIU/TEQIP II/FIN/31/158).

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  1. Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India

    Saket Chandra, Andaleeb Z. Kazmi, Zainab Ahmed, Gargi Roychowdhury, Veena Kumari, Manish Kumar & Kunal Mukhopadhyay

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  1. Saket Chandra
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Chandra, S., Kazmi, A.Z., Ahmed, Z. et al. Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. Plant Cell Rep 36, 1097–1112 (2017). https://doi.org/10.1007/s00299-017-2141-0

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