Black corn is a native variety of this crop, present in the Andean Highlands of Ecuador. Despite its importance as a functional food, due to its anthocyanin content with antioxidant and anti-carcinogenetic properties, its usage has tended to be reduced because of a widespread preference in farmers and consumers for the improved yellow corn varieties. In this research, twenty four S2 lines of black corn were morphologically and molecularly evaluated to determine their diversity level and thus their potential as a source of parents for future breeding programs, especially aimed to developing varieties with high anthocyanin content. For the molecular evaluation, a set of ten SSR primer pairs, one per chromosome, was used to amplify microsatellite regions from the corn genome. For the morphological analysis, seven traits were measured in two vegetative cycles of self-pollination. A total of 43 alleles were revealed for the 10 SSR loci. The number of alleles per locus ranged from 2 to 8, with an average of 4.3 ± 2.06. The genetic distances ranged from 0.29 to 0.95. UPGMA analysis grouped the S2 lines in six groups with one predominant group. The morphological data showed variation especially in plant height, ear insertion height and leaf length. Endogamy depression was evidenced mainly for plant height and ear insertion height. A morphological dendrogram also grouped the 24 S2 lines of black corn in six groups, although they were not the same as in the molecular dendrogram. It is concluded that a moderate variability level exists in this collection and therefore a potential for the development of new varieties.
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