A pot experiment was conducted on two species of chilies C. annuum L. 'Chili-AS Rot' and C. chinense Jacq. 'Naga Morich'. Plants were irrigated at two different irrigation regimes, optimal irrigation or field capacity and deficit irrigation or 50 % field capacity, which can be treated as drought stress. The effects of drought stress on quantity and quality of the yield (primary and secondary metabolites), were studied. Deficit irrigation affected yield quantity, as both chili species had lower yield at deficit irrigation. Species C. chinense 'Naga Morich' under deficit irrigation abscised the flowers, thus no fruits were harvested at the third picking. Concentrations of sugars were lower at both plant species under deficit irrigation. Concentrations of organic acids in fruits of C. annuum 'Chili-AS Rot', such as citric acid, tartaric acid, oxalic acid, fumaric acid, quinic acid were higher at optimal irrigation. Malic acid concentrations were similar at both irrigation treatments. In the fruits of C. chinense Jacq. 'Naga Morich', the concentration of citric acid was higher with optimal irrigation. Concentrations of other organic acids were higher at deficit irrigation. C. annuum 'Chili-AS Rot' had higher concentration of ascorbic acid and total phenolic content at optimal irrigation and higher capsaicin and dihydrocapsaicin concentrations in stressed plants. C. chinense 'Naga Morich' had higher concentrations of ascorbic acid, total phenolic content, capsaicin and dihydrocapsaicin at optimal irrigation regime.
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