| Issue |
BIO Web Conf.
Volume 230, 2026
2026 13th International Conference on Asia Agriculture and Animal (ICAAA 2026)
|
|
|---|---|---|
| Article Number | 01001 | |
| Number of page(s) | 15 | |
| Section | Agricultural Biotechnology and Intelligent Sensing Diagnostics | |
| DOI | https://doi.org/10.1051/bioconf/202623001001 | |
| Published online | 24 March 2026 | |
Genome-wide detection of SH3-associated molecular markers in Coffea cultivars using the Johara R-based bioinformatics pipeline
1 De La Salle University, 2401 Taft Ave, Malate, Manila, 1004 Metro Manila, Philippines
2 Western Michigan University, 1903 W. Michigan Ave, Kalamazoo, Michigan, United States
3 University of Perpetual Help Dalta-System, Alabang-Zapote Rd, Pamplona, 3 Las Pinas City, Philippines
* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.
Abstract
Coffee leaf rust (CLR), caused by Hemileia vastatrix, is a major constraint to global coffee production. This study screened for SH3-linked molecular markers associated with CLR resistance in the genomes of Coffea canephora DH200-94, C. eugenioides Bu-A, and C. arabica ET-39 using a custom R-based workflow (Johara pipeline). Ten molecular markers commonly linked to the SH3 resistance locus were analyzed via exact primer mapping, revealing varying patterns of marker presence across species. C. arabica ET-39 showed the highest number of matches, particularly in the Chromosome 3 regions, suggesting potential SH3-associated resistance, whereas C. eugenioides Bu-A had no detectable markers. This work highlights the utility of computational pipelines for rapid genome-scale detection of resistance-associated loci and provides insights for future breeding programs aimed at enhancing CLR resistance in coffee cultivars.
Key words: Coffea cultivar / genome / SH3 / coffee leaf rust / R software
© The Authors, published by EDP Sciences, 2026
This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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