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

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.