Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genomewide association study

Abstract Background Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici . Multi-locus genomewide association study (GWAS) was conducted to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a diversity panel consisting of 157 Capsicum spp. genotypes. Individual plants were inoculated with P. capsici isolates, ‘PWB-185’, ‘PWB-186’, and ‘6347’ separately at the 4–8 leaf stage and were scored for disease symptoms up to 14 days post-inoculation. Disease scores were used to calculate disease parameters including disease severity index percentage, percent of resistant plants, the area under disease progress curve, and estimated marginal means for each genotype. Results Most of the genotypes displayed root rot symptoms, whereas five accessions were completely resistant to all the isolates and displayed no symptoms of infection. A total of 55,117 single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) were used to perform multi-locus GWAS which identified 330 significant SNP markers associated with disease resistance. Of these, 56 SNP markers distributed across all chromosomes were common across the isolates, indicating association with more durable resistance. Candidate genes including nucleotide-binding site leucine-rich repeat (NBS-LRR), systemic acquired resistance (SAR8.2), and receptor-like kinase (RLKs), were identified within 0.5Mb of the associated markers. Conclusions These genomic loci can be targeted for improving P. capsici root rot resistance using molecular methods. Results will be used to improve resistance to Phytophthora root rot in chile peppers by the development of Kompetitive allele-specific markers (KASP®) for marker validation, genomewide selection, and marker-assisted breeding.