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Poster

Session: Session 2 Presenting Authors at Posters (Odds)

P-023 - Developing an efficient pipeline for sequencing Theobroma cacao amplicons to understand disease resistance to vascular-streak dieback

Wednesday, July 16, 2025
13:30 - 15:15  
Location: Confex Hall 3
Crop resistance genetics and genomics

    Presenting Author(s)

  • JD

    Jacob Downs (he/him/his)

    Postdoctoral Researcher
    University of Sydney
    Camperdown, New South Wales, Australia

    • Author(s)

  • PT

    Peri Tobias

    Dr
    University of Sydney
    Camperdown, NSW, AUSTRALIA

  • SN

    Sylvie Nolf

    University of Sydney
    Camperdown, New South Wales, Australia

  • AP

    Agus Purwantara

    Mars Cocoa Research Station, Pangkep, Indonesia
    Pangkep, Sulawesi Selatan, Indonesia

  • JM

    Junaid Muhammad

    Lecturer
    Cocoa Research Center Faculty of Agriculture, Universitas Hasanuddin, Makassar, Indonesia
    Makassar, Sulawesi Selatan, Indonesia

  • EB

    Eirene Brugman

    Lecturer
    Cocoa Research Center Faculty of Agriculture, Universitas Hasanuddin, Makassar, Indonesia
    Makassar, Sulawesi Selatan, Indonesia

  • DG

    David Guest

    Professor of Plant Pathology
    University of Sydney
    Camperdown, New South Wales, Australia

Theobroma cacao (cocoa) is an economically important crop in Africa, Latin America, Southeast Asia and the Pacific. Ceratobasidium theobromae is an obligate fungal pathogen that causes vascular streak dieback (VSD) of cocoa, leading to significant crop loss in Southeast Asia. Resistance to VSD is highly heritable and durable, therefore breeding resistant cocoa varieties is the most effective solution for disease control. Nucleotide-binding leucine-rich repeat (NLR) genes are a large family of proteins involved in host pathogen resistance. Identifying and characterising putative NLRs will facilitate breeding VSD resistance into agronomically important genotypes. Three quantitative trait loci (QTL) have been mapped to chromosomes 3, 8, and 9. Several NLRs were found to cluster within these QTLs. We developed a pipeline to investigate these NLRs from VSD-phenotyped trees. DNA was extracted and full NLR loci were PCR amplified incorporating barcoded primers. The amplicons were further multiplexed using Oxford Nanopore Technology barcodes and sequenced with a MinION Mk1b. The sequences were processed through our bioinformatic pipeline that bins heterozygous NLR alleles by sequence homology and phenotype. By correlating NLR alleles with phenotypes we aim to identify genetic markers for VSD resistance breeding. This study developed an efficient pipeline for rapid long-read sequencing of multiple samples and builds an understanding of the genetic basis of resistance to VSD.