Plant Resistance Inducers Suppress Anthracnose on Chili Fruit and Are Associated with Inducer-Specific Transcriptional Responses

Anthracnose caused by Colletotrichum spp. is a major constraint to chili (Capsicum spp.) production in Thailand. We characterized isolates from nine provinces and evaluated five plant resistance inducers (PRIs). Seventy-four isolates were sorted into three morphological groups, and multilocus analysis (ITS, ACT, CHS-1) placed seven representative isolates in the C. gloeosporioides and C. truncatum species complexes. C. truncatum KRI015 and C. gloeosporioides RBR009 were the most aggressive isolates. On the fruit of six genotypes, salicylic acid (SA) and acibenzolar-S-methyl (ASM) significantly reduced anthracnose at 21 days post-inoculation in all five genotype × isolate combinations in which inducers significantly reduced disease (by 27–100%), whereas β-aminobutyric acid (BABA), chitosan (CHI) and Bacillus subtilis B01 were genotype- and application-dependent; the highly susceptible ‘Amphawa Gold’ was only partly protected (27–50%). ASM and foliar B01 increased soluble phenolics at all sampling times. RNA sequencing 24 h after treatment suggested inducer-specific responses: ASM up-regulated putative capsidiol-biosynthesis genes (six 5-epi-aristolochene synthase genes and CYP71D7), WRKY transcription factors and plant–pathogen interaction genes; CHI induced lignin- and cuticle-related genes and protease inhibitors; B01 repressed salicylate carboxymethyltransferase; and BABA-repressed defense genes, compatible with priming. SA and ASM are the most promising candidates for integrated anthracnose management in chili.