Metabolomic profiling of pepper germplasm resources and its correlation with color, shape, and pungency traits

Peppers exhibit a diverse array of germplasm resources with variations in fruit color, pungency degree, and shape. Various phenotypes and associated target compounds are often the primary targets in breeding programs. This study employed liquid chromatography high-resolution tandem-mass spectrometry (LC-HR-MS) to construct a spectral tag library, which enabled the identification of chemical compounds in the pepper fruits from eighty distinct germplasm sources. For the first time, differential secondary metabolites were correlated with the fruit shape. Alkaloids represented the largest proportion, underscoring their dominant role in shaping the relationship between secondary metabolites and pepper fruit morphology. 6′′,7′′-Dihydro-5′,5′′′-dicapsaicin was the primary contributor to notable variations in pungency levels and morphology. The concentrations of flavonoids, phenolic acids, and alkaloids demonstrated significant associations with fruit color. This study improves the comprehension of pepper germplasm resources and offers significant insights for the selection and breeding of novel pepper varieties. • Germplasm-rich peppers exhibit diverse colors, degrees of pungency, and shapes. • Differential compounds were screened in 80 pepper fruits with varying traits. • Four compounds were identified as common differential metabolite across all traits. • Alkaloids were the major contributors to both the pungency and shape of fruits. • 6′′,7′′-Dihydro-5′,5′′′-dicapsaicin contributed most in pungency degree and shape.