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Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L.)

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Abstract

Main conclusion

A novel leaf rust responsive ta-siRNA-producing locus was identified in wheat showing similarity to 28S rRNA and generated four differentially expressing ta-siRNAs by phasing which targeted stress responsive genes.

Trans-acting-small interfering RNAs (Ta-siRNAs) are plant specific molecules generally involved in development and are also stress responsive. Ta-siRNAs identified in wheat till date are all responsive to abiotic stress only. Wheat cultivation is severely affected by rusts and leaf rust particularly affects grain filling. This study reports a novel ta-siRNA producing locus (TAS) in wheat which is a segment of 28S ribosomal RNA but shows differential expression during leaf rust infestation. Four small RNA libraries prepared from wheat Near Isogenic Lines were treated with leaf rust pathogen and compared with untreated controls. A TAS with the ability to generate four ta-siRNAs by phasing events was identified along with the microRNA TamiR16 as the phase initiator. The targets of the ta-siRNAs included α-gliadin, leucine rich repeat, trans-membrane proteins, glutathione-S-transferase, and fatty acid desaturase among others, which are either stress responsive genes or are essential for normal growth and development of plants. Expression of the TAS, its generated ta-siRNAs, and their target genes were profiled at five different time points after pathogen inoculation of susceptible and resistant wheat isolines and compared with mock-inoculated controls. Comparative analysis of expression unveiled differential and reciprocal relationship as well as discrete patterns between susceptible and resistant isolines. The expression profiles of the target genes of the identified ta-siRNAs advocate more towards effector triggered susceptibility favouring pathogenesis. The study helps in discerning the functions of wheat genes regulated by ta-siRNAs in response to leaf rust.

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Acknowledgements

The authors are thankful to BTISNet SubDIC (BT/BI/04/065/04) for providing bioinformatics facilities. This work was supported by Centre of Excellence, Technical Education Quality Improvement Program-II (Grant No. NPIU/TEQIP II/FIN/31/158). SD acknowledges Innovation in Science Pursuit for Inspired Research (INSPIRE), Government of India, Ministry of Science and Technology, New Delhi [IF140725], and DK is grateful to the Council of Scientific and Industrial Research [9/554 (0026) 2010-EMR-I] for providing fellowships.

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  1. Dhananjay Kumar

    Present address: Department of Botany, PDM University, Bahadurgarh, Haryana, 124507, India

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

    Summi Dutta, Dhananjay Kumar, Manish Kumar & Kunal Mukhopadhyay

  2. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

    Shailendra Jha & Kumble Vinod Prabhu

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Dutta, S., Kumar, D., Jha, S. et al. Identification and molecular characterization of a trans-acting small interfering RNA producing locus regulating leaf rust responsive gene expression in wheat (Triticum aestivum L.). Planta 246, 939–957 (2017). https://doi.org/10.1007/s00425-017-2744-2

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