Molecular markers, such as Amplified fragment length polymorphisms (AFLP) were used to study genetic diversity in four chilli varieties. Two wild chilli’s (Amashito and Ojo de cangrejo: Capsicum annuum var.glabriusculum) and two growers (Jalapeño and Habanero: C. annuum and Capsicum chinense Jacq.), were used as parents in a diallel cross, with no reciprocal crosses, to produce six F1 hybrid combinations. Crosses between parents were made by hand in the greenhouse at the División Académica de Ciencias Biológicas (DACBiológicas) of the Universidad Juárez Autónoma de Tabasco (UJAT), in Villahermosa, Tabasco, Mexico. The four AFLP markers used amplified 256 bands, of which 62 (24.2%) bands were polymorphic. Dice’s similarity index was used to determine the genetic distances between parents and their offspring. Cluster analyses based on genetic distances separated the parents and crosses belonging of C. annuum from those of Capsicum chinense, confirming the genomic differences between the two species. The cophenetic correlation coefficient (r) value between the similarity matrix and the original matrix to determine if the original data were well represented in the cluster analysis, under 1000 permutations, was 0.87, which is within the range of good. The results of this research are useful for use in a breeding program chilli. It has been shown that the more genetic distance is between the potential parents, the progeny of both present greater heterosis.
Key words: Genetic distances, PCR, Capsicum, diallel crosses, Chilli species.
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