A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity (Record no. 68735)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 04318nab|a22004817a|4500 |
| 001 - CONTROL NUMBER | |
| control field | 68735 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MX-TxCIM |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20250512165418.0 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 20254s2025||||mx |||p|op||||00||0|eng|d |
| 022 ## - INTERNATIONAL STANDARD SERIAL NUMBER | |
| International Standard Serial Number | 1471-2164 |
| 024 8# - OTHER STANDARD IDENTIFIER | |
| Standard number or code | https://doi.org/10.1186/s12864-025-11428-w |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | MX-TxCIM |
| 041 ## - LANGUAGE CODE | |
| Language code of text/sound track or separate title | eng |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Savva, L. |
| 9 (RLIN) | 38726 |
| 245 12 - TITLE STATEMENT | |
| Title | A portable, nanopore-based genotyping platform for near real-time detection of Puccinia graminis f. sp. tritici lineages and fungicide sensitivity |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT) | |
| Place of publication, distribution, etc. | London (United Kingdom) : |
| Name of publisher, distributor, etc. | BioMed Central Ltd., |
| Date of publication, distribution, etc. | 2025. |
| 500 ## - GENERAL NOTE | |
| General note | Peer review |
| 500 ## - GENERAL NOTE | |
| General note | Open Access |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc. | Background: Fungal plant disease outbreaks are increasing in both scale and frequency, posing severe threats to agroecosystem stability, native biodiversity and food security. Among these, the notorious wheat stem rust fungus, Puccinia graminis f.sp. tritici (Pgt), has threatened wheat production since the earliest days of agriculture. New Pgt strains continue to emerge and quickly spread over vast distances through the airborne dispersal of asexual urediniospores, triggering extensive disease outbreaks as these exotic Pgt strains often overcome resistance in dominant crop varieties of newly affected regions. This highlights the urgent need for a point-of-care, real-time Pgt genotyping platform to facilitate early detection of emerging Pgt strains. Results: In this study, we developed a simple amplicon-based re-sequencing platform for rapid genotyping of Pgt isolates. This system is built around a core set of 276 Pgt genes that we found are highly polymorphic between Pgt isolates and showed that the sequence of these genes alone could be used to accurately type Pgt strains to particular lineages. We also developed a simplistic DNA preparation method and an automated bioinformatic pipeline, to enable these Pgt gene markers to be sequenced and analysed rapidly using the MinION nanopore sequencing device. This approach successfully enabled the typing of Pgt strains within approximately 48 h of collecting Pgt-infected wheat samples, even in resource-limited locations in Kenya and Ethiopia. In addition, we incorporated monitoring capabilities for sequence variations in Pgt genes that encode targets of the azole and succinate dehydrogenase inhibitor fungicides, enabling real-time tracking of potential shifts in fungicide sensitivity. Conclusion: The newly developed Pgt Mobile And Real-time, PLant disEase (MARPLE) diagnostics platform we established, now allows precise typing of individual Pgt strains while simultaneously tracking changes in fungicide sensitivity, providing an early warning system for potential indicators of changes in the Pgt population and emerging fungicide resistance. Further integration of this Pgt MARPLE diagnostics platform into national surveillance programmes will support more informed management decisions and timely responses to Pgt disease outbreaks, helping reduce the devastating crop losses currently caused by this 'cereal killer'. |
| 546 ## - LANGUAGE NOTE | |
| Language note | Text in English |
| 597 ## - CGIAR Initiative | |
| Donor or Funder | United States Agency for International Development (USAID) |
| -- | Biotechnology and Biological Sciences Research Council (BBSRC) |
| -- | John Innes Foundation |
| -- | Bill & Melinda Gates Foundation (BMGF) |
| -- | Foreign, Commonwealth & Development Office (FCDO) |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Puccinia graminis |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 2130 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Wheat |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 1310 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Rusts |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 1251 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Diseases |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 5952 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Nanopore sequencing |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 38727 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Fungicides |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 8809 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Bryan, A. |
| 9 (RLIN) | 38728 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Vinopal, D. |
| 9 (RLIN) | 38729 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Gonzalez-Navarro, O.E. |
| 9 (RLIN) | 4136 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Kosgey, Z.C. |
| 9 (RLIN) | 18082 |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Kimani Cyrus Ndung’u |
| 9 (RLIN) | 38730 |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Jemal Tola Horo |
| 9 (RLIN) | 38731 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Danu, K.G. |
| 9 (RLIN) | 23313 |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Messele Molla |
| 9 (RLIN) | 38732 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Alemayehu, Y. |
| 9 (RLIN) | 1359 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Hodson, D.P. |
| Miscellaneous information | Sustainable Agrifood Systems |
| Field link and sequence number | INT2550 |
| 9 (RLIN) | 843 |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Saunders, D.G.O. |
| 9 (RLIN) | 6079 |
| 773 0# - HOST ITEM ENTRY | |
| Title | BMC Genomics |
| Related parts | v. 26, no. 1, art. 327 |
| Place, publisher, and date of publication | London (United Kingdom) : BioMed Central Ltd, 2025. |
| International Standard Serial Number | 1471-2164 |
| Record control number | 56896 |
| 856 4# - ELECTRONIC LOCATION AND ACCESS | |
| Link text | Open Access through DSpace |
| Uniform Resource Identifier | https://hdl.handle.net/10883/35627 |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Koha item type | Article |
| Suppress in OPAC | No |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Date last seen | Total Checkouts | Price effective from | Koha item type | Lost status | Source of classification or shelving scheme | Damaged status | Not for loan | Collection code | Withdrawn status | Home library | Current library | Date acquired |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 04/12/2025 | 04/12/2025 | Article | Not Lost | Dewey Decimal Classification | CIMMYT Staff Publications Collection | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Knowledge Center: John Woolston Library | 04/12/2025 |