Integrated phenotypic analysis, predictive modeling, and identification of novel trait-associated loci in a diverse Theobroma cacao collection.

Journal: BMC plant biology
Published Date: Aug 9, 2025

Abstract

BACKGROUND: Cacao (Theobroma cacao L.) breeding and improvement rely on understanding germplasm diversity and trait architecture. This study characterized a cacao collection (173 accessions) evaluated in Puerto Rico, examining phenotypic diversity, trait interrelationships, and performing comparative analyses with published Trinidad and Colombia datasets. We also developed machine learning (ML) models for yield prediction and identified yield-associated SNP markers.

Authors

  • Insuck Baek
    Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Powder Mill Road, BARC-East, Bldg 303, Beltsville, MD 20705, USA.
  • Minhyeok Cha
    Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
  • Seunghyun Lim
    Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
  • Brian M Irish
    Plant Germplasm Introduction and Testing Research Unit, Agricultural Research Service, Department of Agriculture, Prosser, WA, 99164, USA.
  • Sookyung Oh
    Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, Department of Agriculture, Beltsville, MD, 20705, USA.
  • Jishnu Bhatt
    Sustainable Perennial Crops Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
  • Rakesh K Upadhyay
    Department of Natural Sciences, College of Arts and Sciences, Bowie State University, 14000 Jericho Park Rd., Bowie, MD, 20715, USA.
  • Moon S Kim
    Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Essen, Germany.
  • Lyndel W Meinhardt
    Sustainable Perennial Crops Laboratory, Agricultural Research Service, Department of Agriculture, Beltsville, MD, 20705, USA.
  • Sunchung Park
    Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA.
  • Ezekiel Ahn
    Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA. Ezekiel.Ahn@usda.gov.

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