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RESEARCH ARTICLE (Open Access)
Contents Vol 75(6)

A novel Leifsonia xyli subsp. xyli quantitative LAMP-based diagnostic correlated with sugarcane ratoon stunting disease rating

Moutoshi Chakraborty https://orcid.org/0000-0002-2699-9284 A B * , Shamsul A. Bhuiyan https://orcid.org/0000-0001-7245-670X C D , Simon Strachan https://orcid.org/0000-0001-8498-4331 B C , Sithi Saha D , Rabbee G. Mahmudunnabi https://orcid.org/0000-0002-3720-4264 B C , Nam-Trung Nguyen https://orcid.org/0000-0003-3626-5361 C , Muhammad J. A. Shiddiky https://orcid.org/0000-0003-4526-4109 B C E and Rebecca Ford https://orcid.org/0000-0002-4192-0706 A B
+ Author Affiliations
- Author Affiliations

A Centre for Planetary Health and Food Security (CPHFS), Nathan Campus, Griffith University (GU), Nathan, Qld 4111, Australia.

B School of Environment and Science (ESC), Nathan Campus, Griffith University, Nathan, Qld 4111, Australia.

C Queensland Micro and Nanotechnology Centre (QMNC), Nathan Campus, Griffith University, Nathan, Qld 4111, Australia.

D Sugar Research Australia (SRA), 90 Old Cove Road, Woodford, Qld 4514, Australia.

E Rural Health Research Institute (RHRI), Charles Sturt University, Orange, NSW 2800, Australia.

* Correspondence to: moutoshi.chakraborty@griffithuni.edu.au

Handling Editor: Enrico Francia

Crop & Pasture Science 75, CP24053 https://doi.org/10.1071/CP24053
Submitted: 29 February 2024  Accepted: 28 May 2024  Published: 19 June 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

Context

Ratoon stunting disease (RSD), caused by Leifsonia xyli subsp. xyli (Lxx), poses a significant economic threat to sugarcane (Saccharum hybrid) worldwide. RSD is hard to manage due to its elusive visible symptomology and disease rating of cultivars is subjective.

Aims

We aimed to develop a sensitive, rapid, and quantitative Lxx diagnostic method able to correlate Lxx titre and disease resistance rating of sugarcane cultivars.

Methods

A Lxx diagnostic method was developed using heat lysis-based reagent-free DNA isolation from xylem sap followed by loop-mediated isothermal amplification (LAMP)-based colorimetric and fluorescence quantification within a single microcentrifuge tube. Bacterial titre was then statistically correlated with industry-agreed disease resistance ratings for key sugarcane cultivars.

Key results

The diagnostic was highly sensitive (1 cell/μL) and reproducible (%s.d. = <5%, for n = 3), and showed excellent linear dynamic range (i.e. 10 pM−1 aM or 107−100 copies/μL, r = 0.99) for quantitative Lxx detection. LAMP quantifications were completely concordant with quantitative polymerase chain reaction quantification from the same samples. Additionally, a strong correlation was determined between the detected quantitative bacterial titres and known cultivar disease resistance ratings (r = 0.82, n = 10, P < 0.001).

Conclusion

The novel LAMP-based Lxx diagnostic was validated as a fast, simple, and relatively cost-effective means of RSD resistance rating, making it a reliable contribution towards RSD management.

Implications

The development of this diagnostic tool provides a practical solution for accurately measuring Lxx titre and assessing disease resistance in sugarcane plants, aiding in effective risk management of RSD spread, and mitigating its economic impact on sugarcane crops worldwide.

Keywords: diagnostic method, disease resistance ratings, isothermal amplification, nucleic acid isolation, quantitative detection, ratoon stunting disease, screening for disease resistance, sugarcane.

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