Genetic determinants of heat content in chile pepper (Capsicum spp.) revealed by multi-locus genome-wide association mapping

Abstract

Capsaicinoids, the bioactive compounds responsible for heat (pungency), are uniquely produced in chile peppers (Capsicum spp.). In addition to providing the characteristic heat, capsaicinoids have health benefits, making them a subject of increasing interest in genetic research. A multi-locus genome-wide association study (GWAS) was performed on 123 pepper genotypes grown in field conditions in Las Cruces, New Mexico, USA, to unravel genetic loci influencing capsaicinoid content. High-performance liquid chromatography analysis was conducted to determine Scoville heat units (SHU). Significant variation among SHU values were observed, where the ‘Superhots’, namely, ‘7 Pot Primo’ and ‘Trinidad Moruga Scorpion’ (C. chinense) showed SHU of 1.45 million and 1.09 million, respectively. After filtering and quality control, 97,395 genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers were used for multi-locus GWAS. A total of 30 GBS-SNP markers distributed across 11 chromosomes were identified for one or more traits from one or multiple GWAS models. SNP markers on chromosome 3 explained the highest phenotypic variation (R2) for capsaicin and dihydrocapsaicin content, respectively: SCM002814.1_54888910 (R2 = 58.71%) and SCM002814.1_54888910 (R2 = 57.05%). Significant differences were observed on the mean total SHU for different alleles for associated SNP markers. Genes including putative acyl-activating enzyme 2, ethylene responsive transcription factor, and histone-lysine N-methyltransferase were identified as candidate genes. Kompetitive Allele Specific PCR (KASP®) markers will be developed to further validate these results for marker-assisted selection for capsaicinoid content in Capsicum.