From Phenotype to Genome: A Critical Evidence-Based Synthesis of Frosty Pod Rot (Moniliophthora roreri) Resistance in Cacao and a Proposed Evidence-Gated Framework to Support Genetic Gain
- 1Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Agrícolas, Universidad de Córdoba, Montería 230002, Colombia
- 2Facultad de Ciencias Básicas, Universidad de Córdoba, Montería 230002, Colombia
Abstract
Frosty pod rot (FPR), caused by Moniliophthora roreri, severely constrains cacao production in the Neotropics, yet evidence supporting molecular breeding for resistance remains fragmented and is often conflated with findings from witches’ broom disease. We conducted a structured critical review, not a systematic review, and classified each FPR-related claim with an author-developed, multidimensional evidence classification system (E0–E5) separating directness, genetic replication, mechanistic inference and breeding utility. The evidence supports a quantitative, partial and context-dependent architecture of resistance. The strongest QTL have been re-detected only within the Pound 7 × UF273 pedigree (E2a), and no FPR locus replicated in genetically independent material (E2b) was identified in the literature retrieved and verified. Genomic predictive ability reached 0.60–0.67 under random cross-validation within one clonal panel but averaged approximately 0.16 when models were transferred among related populations; these values answer different questions and are not directly comparable. Host and pathogen transcriptomics provide correlative evidence (E3a), and recombinant M. roreri effectors show biological activity in heterologous or cacao tissues (E3b-i), but no stable genetic manipulation altering FPR in a pod-challenge assay (E4) and no documented breeding utility (E5) were identified. We propose a Phenotyping and Reporting Guideline for FPR (PRG-FPR) and MIGGA, a modular, evidence-gated decision framework illustrated with a retrospective worked example; its effect on realised genetic gain remains to be tested.
Related
- An Evidence-Tiered Developmental Framework for Congenital Vertebral Malformations: Spatiotemporal Thresholds in Genotype–Phenotype Interpretation
- Whole-genome sequencing-based characterization of antimicrobial resistance determinants and phenotype–genotype concordance in uropathogenic Escherichia coli isolates from ICU patients in Saudi Arabia
- Genomic and phenotype-based framework for rational design of phage cocktails against Escherichia coli isolates from urinary tract infections
- N-terminal lysine as a critical determinant of odilorhabdin susceptibility to inactivation by the self-resistance acetyltransferase OatA
- RDEmbed: A Sentence-Embedding Framework for Rare Disease Phenotype Representation and Phenotypic Similarity Analysis
BibTeX
@article{pinedarodriguez2026from,
title = {{From Phenotype to Genome: A Critical Evidence-Based Synthesis of Frosty Pod Rot (Moniliophthora roreri) Resistance in Cacao and a Proposed Evidence-Gated Framework to Support Genetic Gain}},
author = {Yirlis Yadeth Pineda-Rodriguez and Juan Jaraba Navas and Alfredo Jarma-Orozco and Luis Eliecer Oviedo-Zumaque and Luis Alfonso Rodríguez-Páez},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27209294},
url = {https://www.mdpi.com/1422-0067/27/20/9294},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - From Phenotype to Genome: A Critical Evidence-Based Synthesis of Frosty Pod Rot (Moniliophthora roreri) Resistance in Cacao and a Proposed Evidence-Gated Framework to Support Genetic Gain
AU - Yirlis Yadeth Pineda-Rodriguez
AU - Juan Jaraba Navas
AU - Alfredo Jarma-Orozco
AU - Luis Eliecer Oviedo-Zumaque
AU - Luis Alfonso Rodríguez-Páez
PY - 2026
DA - 2026/10/01
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27209294
UR - https://www.mdpi.com/1422-0067/27/20/9294
AB - Frosty pod rot (FPR), caused by Moniliophthora roreri, severely constrains cacao production in the Neotropics, yet evidence supporting molecular breeding for resistance remains fragmented and is often conflated with findings from witches’ broom disease. We conducted a structured critical review, not a systematic review, and classified each FPR-related claim with an author-developed, multidimensional evidence classification system (E0–E5) separating directness, genetic replication, mechanistic inference and breeding utility. The evidence supports a quantitative, partial and context-dependent architecture of resistance. The strongest QTL have been re-detected only within the Pound 7 × UF273 pedigree (E2a), and no FPR locus replicated in genetically independent material (E2b) was identified in the literature retrieved and verified. Genomic predictive ability reached 0.60–0.67 under random cross-validation within one clonal panel but averaged approximately 0.16 when models were transferred among related populations; these values answer different questions and are not directly comparable. Host and pathogen transcriptomics provide correlative evidence (E3a), and recombinant M. roreri effectors show biological activity in heterologous or cacao tissues (E3b-i), but no stable genetic manipulation altering FPR in a pod-challenge assay (E4) and no documented breeding utility (E5) were identified. We propose a Phenotyping and Reporting Guideline for FPR (PRG-FPR) and MIGGA, a modular, evidence-gated decision framework illustrated with a retrospective worked example; its effect on realised genetic gain remains to be tested.
SN - 1422-0067
ER -