Identification of both shared and isolate-specific QTL and underlying candidate genes for Vanilla planifolia resistance to Fusarium root and stem rot

Abstract

Vanilla planifolia suffers major losses from root and stem rot (RSR) caused by Fusarium oxysporum f. sp. radicis-vanillae (Forv), amplified by low genetic diversity. We dissected quantitative resistance by phenotyping a selfed population AF_CR0040 (n = 115) inoculated with three Forv isolates (Fo166, Fo254, Fo297). Five traits were scored: symptoms at 5, 10 and 15 days post-inoculation (dpi), the area under the disease progress curve (AUDPC) and the day of mycelium appearance (d.myc). Multiple quantitative trait locus (QTL) mapping (MQM) was realized on a high-density genotyping-by-sequencing (GBS) map. QTL were anchored to the CR0040 genome to identify candidates. We detected 121 QTL across isolates and traits, explaining 2.5 to 21.8% of phenotypic variance, including 39 major loci (≥ 10%). Stable hotspots were shared by several isolates and traits, isolate-specific loci were also identified. Standardizing effects showed 44% of QTL carried favorable alleles (51% among major loci), with frequent dominance, consistent with transgressive segregation. In total, 837 genes lay within QTL windows. Top multi-QTL candidates encoded a calcium-dependent ADP-ribosylation factor GTPase-activating protein (ARF-GAP), three ATP-binding cassette (ABC) transporters, a basic helix-loop-helix (bHLH) transcription factor, a uridine kinase, and a leucine-rich repeat receptor-like kinase (LRR-RLK). These findings reveal coexisting generalist and isolate-specific resistance modules and provide genome-anchored targets for functional validation, gene pyramiding, and marker-assisted selection in vanilla.