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Plant Science Today (PST)

Research Articles

Vol. 13 No. 4 (2026)

Untargeted liquid chromatography–tandem mass spectrometry metabolomics reveals metabolite inheritance, diversity and capsaicinoid variation across successive generations of Capsicum chinense Jacq. (Bhut Jolokia)

DOI
https://doi.org/10.14719/pst.16939
Submitted
22 July 2026
Published
03-10-2026 — Updated on 13-10-2026
Versions

Abstract

The Capsicum chinense Jacq. pepper is known for its exceptional pungency and rich phytochemical composition. Although metabolite diversity in pepper has been extensively investigated, little is known about metabolite variation across successive generations. This study evaluated the untargeted and targeted metabolite profiles of pepper from two lineages (A3 and A4) across three successive generations through liquid chromatography–tandem mass spectrometry (LC–MS/MS) and high-performance liquid chromatography (HPLC), respectively and analysed their diversity and distributions. A total of 103 metabolites were identified, with 77 metabolites detected in the A3 lineage and 46 in the A4 lineage. Both lineages possessed a conserved core metabolome, while numerous lineage- and generation-specific metabolites demonstrated dynamic metabolic variation during successive propagation. The A3 lineage exhibited greater metabolite richness than the A4 lineage, suggesting enhanced biochemical diversity. Multivariate analyses revealed that most metabolites were shared among generations, whereas a smaller proportion represented unique generation-specific compounds. Clustering analysis clearly separated the samples into two distinct clusters, indicating that genotype was the primary determinant of metabolite composition. Capsaicinoid analysis revealed significant variation in pungency across generations, with the second generation exhibiting the highest Scoville heat unit (SHU) values and the third generation showing a marked reduction. Statistical analysis confirmed significant differences in SHU among generations, particularly between the second and third generations. Furthermore, several capsaicinoid-related metabolites, including homocapsaicin, homodihydrocapsaicin and nordihydrocapsaicin, were detected exclusively in the A3 lineage, highlighting lineage-specific regulation of specialised metabolism. These findings provide new insights into metabolic diversity and inheritance in C. chinense and establish a valuable foundation for metabolomics-assisted breeding aimed at improving pungency, nutritional quality and functional phytochemical traits.

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