Knowledge of genetic diversity is one of the important tools used for genetic management of quinoa accessions for plant breeding. This research aimed to molecularly characterize five quinoa genotypes using ISSR markers to reveal genetic polymorphism and identify unique markers for each genotype. Analysis of inter-simple sequence repeats (ISSR) revealed that 10 ISSR primers produced 53 amplicons, out of them 33 were polymorphic and the average percentage of polymorphism was 61.83%. The number of amplicons per primer ranged from 3 (HB-13, HB-10, HB-8 and 17898A) to 10 (HB-15) with an average of 5.3 fragments/primer across the different quinoa genotypes. Data showed a total number of unique ISSR markers of 24; eleven of them were positive and 13 were negative. Using ISSR analysis, we were able to identify some unique bands associated with quinoa genotypes. The genetic similarity ranged from 49% (between Ollague and each of QL-3 and Chipaya) to 76% (between CICA-17 and CO-407). The results indicated that all the five quinoa genotypes differ from each other at the DNA level where the average of genetic similarity (GS) between them was about 59%. The dendrogram separated the quinoa genotypes into two clusters; the first cluster included two genotypes (QL-3 and Chipaya). The second cluster was divided into two groups; the first group included two genotypes (CICA-17 and CO-407) and the second group included only one genotype (Ollague). Our results indicated that ISSR technique is useful in the establishment of the genetic fingerprinting and estimation of genetic relationships among quinoa genotypes. Also, this technique could detect enough polymorphism in the studied quinoa genotypes to distinguish each genotype from the others. Furthermore, the use of these results in the future is important for quinoa germplasm management and improvement as well as for the selection strategies of parental lines that facilitate the prediction of crosses in order to produce hybrids with higher performance. Using ISSR analysis, we were able to identify unique bands associated with quinoa genotypes. These bands might also be used in breeding programs for differentiating among Chinopodium quinoa varieties.
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