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

• Published in: Euphytica Vol. 221; no. 7; p. 121
• Main Authors: Khan, Muhammad Ibrar, Lozada, Dennis N., Nankar, Amol N., Khokhar, Ehtisham S., Nourbakhsh, Seyed Shahabeddin
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.07.2025; Springer Nature B.V
• Subjects: Alleles; Bioactive compounds; Biomedical and Life Sciences; Biosynthesis; Biotechnology; Capsaicin; Capsicum; Chromatography; Chromosome 3; Chromosomes; Cultivars; Enthalpy; Gene mapping; Gene polymorphism; Genes; Genetic markers; Genome-wide association studies; Genomes; Genotyping; Germplasm; Heat; High performance liquid chromatography; Histone methyltransferase; Histone-lysine N-methyltransferase; Kinases; Life Sciences; Liquid chromatography; Loam soils; Lysine; Marker-assisted selection; N-Methyltransferase; Nucleotides; Peppers; Phenotypic variations; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Polymorphism; Pungent principles; Quality control; Single-nucleotide polymorphism; Genome-wide association studies; Single nucleotide polymorphisms; Capsaicinoid content; High-performance liquid chromatography; Genotyping-by-sequencing
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-025-03573-w

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 ( R 2 ) for capsaicin and dihydrocapsaicin content, respectively: SCM002814.1_54888910 ( R 2  = 58.71%) and SCM002814.1_54888910 ( R 2  = 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 .