Genetic diversity and population structure of quinoa (Chenopodium Quinoa Willd.) Using iPBS- retrotransposons markers

Abstract

Quinoa (Chenopodium quinoa Willd.) is a nutritionally important plant with a good protein quality and a high concentration of vitamins and minerals. It has been cultured for several thousand years in South America. In this study, we investigated the use of inter-primer binding site (iPBS) for the molecular characterization of 17 quinoa genotypes (Chenopodium quinoa Willd.) cultivated in Turkey. For this purpose, 25 iPBS markers were employed, and six primers provided sufficient polymorphic data generating a total of 19 alleles with an average of 2.83 bands/primer. The number of iPBS bands per individual was calculated as 1.12. The rate of polymorphism information content ranged from 0.02 to 0.49 with an average of 0.20. Genetic associations were assessed using the Dice dissimilarity coefficient between different pairs of accessions and revealed an average value of 0.84 for the French population and Q-52 genotypes. Cluster analysis on the unweighted pair-group mean average divided the 17 quinoa genotypes into two major clusters. The results of the principal component analysis were in agreement with those of the cluster analysis. The highest number of alleles, Nei’s genetic diversity, and Shannon’s information index were obtained from the French Vanilla genotype at 1.99, 0.50 and 0.69, respectively, whereas the lowest values were observed in the Q-52 genotype at 1.10, 0.09 and 0.20, respectively. The expected heterozygosity ranged from 0.398 in the first sub-population to 0.140 in the second sub- population with an average of 0.269. The mean population differentiation measurement (F st) values of the sub-populations were 0.048 and 0.676 for the first and second sub-populations, respectively. The results of this study provide useful information for the management of the quinoa germplasm and contribute to the improvement of existing breeding approaches. They also presented the iPBS marker system as a suitable tool for identification and genetic diversity analysis of quinoa genotypes.