Genetic structure analysis and genetic finger printing of sweet orange cultivars (Citrus sinensis (L.) Osbeck) by using SCoT molecular markers

Citrus plant species are among the most important and consumed fruit plants throughout the world. In general, genetic diversity investigations in all Citrus species and varieties are in hand in order to add to the knowledge of these important plant species. The sweet orange cultivars (Citrus sinensis), are among the most wanted among Citrus species. Various genetic diversity investigations by using different molecular markers have been performed in different regions of the world. We investigated 23 cultivars of sweet oranges available in Iran and two out-group cultivars produced by crossing Lemon and Kumquat. We used Start Codon Targeted (SCoT) molecular markers for genetic study. The studied cultivars produce 64 SCoT loci or bands. In total each cultivar studied contained 8–29 SCoT bands and six cultivars had 1–2 private/specific bands due to their peculiar genetic structure. Genetic diversity parameters were determined in these cultivars and revealed that the genetic polymorphism varied from 6.15% into 44% in the Studied sweet orange trees. We identified many loci with high discrimination power (> 0.80) in SCoT marker. Analysis of molecular variance (AMOVA) revealed significant genetic difference among these cultivars, and pair-wise AMOVA identified those sweet oranges which differed genetically from each other. Unweighted pair group method with arithmetic mean dendrogram of the studied samples separated most of the cultivars and their replicates in distinct clusters. STRUCTURE analysis revealed genetic structure of sweet oranges, showing their genetic similarities versus genetic uniqueness. We could differentiate some of Thompson cultivars, coming with different origins or locality. It held true for red blood and Jaffa oranges too. We identified few potential hybrids in the country. These findings will be used in future sweet orange conservation and breeding.