Identification of cultivars is essential both in breeding and to settle cultivar disputes. The purpose of the study has been to examine cultivar identities based on absorption spectra of plant pigments and to confirm a genetic stability with SCoT and RAPD molecular markers in new Polish lines of Chenopodium quinoa Willd. Spectral analysis of pigments extracted from plant inflorescences in quinoa gives an opportunity to confirm the cultivar identity and identification of ‘Faro’ and ‘Titicaca’ cultivars and their new lines. Spectral analysis is an effective method of confirming cultivar identity and it should be used in practice for the identification of cultivars or cultivars lines in Chenopodium quinoa Willd. Analysis of molecular markers indicated by RAPD as well as SCoT technique revealed a high genetic stability of the derivative lines of ‘Faro’ and ‘Titicaca’, while variation was detected in plants representing original cultivars: banding pattern different than predominant was present in three plants of ‘Titicaca’ (genetic distnaces from 7.5% to 55.9%) and in a single plant of ‘Faro’(genetic distance 61.2% as indicated by SCoT technique).

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