Metabolite profiling reveals differential accumulation of secondary metabolites related to flavour and colour across four heirloom chilli landraces

Chillies from Northeast India exhibit wide variability in fruit morphology, pungency, bearing habit and crop duration. An untargeted metabolite profiling using LC-HRMS of four ‘heirloom’ pungent landraces viz. Naga chilli (AL-1), Dalle khursani (AL-2), Sohmynken khnai (AL-3), and J-41(B) was performed and compared with Kashi anmol (KA). While AL-2, J-41(B) and KA belong to C. annuum species, AL-1 is categorised as C. chinense and AL-3 is C. frutescens. A total of 6990 consistent peaks of monoisotopic masses were detected, out of which 2702 metabolites were identified using accurate mass error < 10 ppm. A higher number of differentially accumulated metabolites were seen in J-41(B) versus AL-3 (1376), followed by J-41(B) versus AL-2 (1365), J-41(B) versus AL-1 (1257), KA versus AL-2 (649), AL-3 versus KA (616), KA versus AL-1 (594) and J-41(B) versus KA (413). Variation among species was higher than variation within species. Pathway analysis identified fatty acid, carotenoid, flavonoid and capsaicinoid as key pathways. We identified eight major categories of metabolites, including fatty acids, sterol lipids, and flavonoids, which together account for over 70% of the significantly expressed metabolites across the genotypes. This study explores untargeted metabolites in various chilli species, offering insights into the biochemical and molecular mechanisms which may play a role in governing important fruit traits. Identification of key metabolites and underlying alleles for twenty-one genes across three pathways (flavonoid, capsaicinoid and carotenoid) suggests that the metabolites and associated alleles identified in this study can be used as biomarkers for further characterization of these heirloom chilli and could provide distinct parameter(s) in distinguishing improved cultivars from landraces. This will contribute towards breeding programs in aiding selection of fruits of the desirable traits.