Ability to use ITS and rbcL sequencing for determination of the genetic diversity and relationships among olive (Olea europaea L.) genotypes.

Olives are of considerable economic and commercial importance and are mostly used in both daily life and industries. The DNA barcode method has a lot of potential for reviving the science of arithmetics and traditional biodiversity studies, so it has been widely used on plants and for classification and arithmetic purposes. In this study, we sequenced seven different olive genotypes (Olea europaea cv. Olive yellow, O. europaea cv. Oliy, O. europaea cv. Roodbar Oily, O. europaea cv. Mari, O. europaea cv. Fishemi, O. europaea cv. Manzanila, O. europaea cv. Koroneiki) to study their diversity and evolution. The data were analyzed using Clustalw2 and BioEdit software. The homology rate of rbcL and ITS sequences was all in the range of 97-100%. It was identified, for ITS, 1,059 genetic luci (580 luci without deletion and addition and 479 luci with deletion and addition (328 luci polymorphs, 151 monomorphs), 217 singletons, and for rbcL, 565 genetic luci with ( 60 luci without deletion and addition and 505 luci with deletion and addition (2 luci with polymorphs, 503 monomorphs), 1 singleton. It was determined that the number of four haplotypes (haplotype diversity index = 0.80) was determined for ITS and three haplotypes (haplotype diversity index = 0.71) for RBCL. The results indicated that in the nucleotide sequence of the ITS gene among olive varieties, guanine was the most abundant base at 28.7%, while adenine had the lowest abundance at 5%. In contrast, the rbcL gene showed that thymine was the most abundant base at 29.8%, with cytosine being the least abundant at 20.6%. Estimates of nucleotide transitions in the ITS gene revealed a high frequency of pyrimidine transitions, with a thymine-to-cytosine transition rate of 16.84% and a cytosine-to-thymine transition rate of 11.63%. The ITS primer successfully identified and separated only six genotypes, whereas rbcL identified all seven genotypes. Although the success rates of 60-70% for both ITS and rbcL may not seem particularly high, they still significantly contribute to large-scale biodiversity inventories, especially for olive species.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04336-z.