ISSR-PCR markers for assessment of genetic diversity in some Iranian and foreign grape cultivars ( <i>Vitis vinifera</i> L.)

Abstract With the rise in planting new grape varieties, accurate identification and ensuring plant authenticity are crucial, as mistakes can cause significant financial losses in wine and table grape production. However, traditional morphological methods are often unreliable because they are strongly influenced by environmental conditions, creating a need for robust molecular approaches. Inter-simple sequence repeat (ISSR) markers represent a powerful DNA-based system for diversity analysis and accurate identification of grape varieties. Iran, as a centre of grape domestication, hosts a rich diversity of grape ( Vitis vinifera L.) cultivars. This study aimed to assess the genetic relationships among 20 Iranian and foreign grape cultivars cultivated in Iran using seven ISSR primers. A total of 31 bands were produced, of which 23 (74.19%) were polymorphic. The effective number of alleles (Ae) ranged from 1.22 to 1.70, and the polymorphic information content varied from 0.18 to 0.40. The highest Shannon’s index (0.84) was obtained for the UBC848 primer, indicating strong discriminatory ability. Cluster analysis and principal component analysis (PCA) classified the cultivars into three main groups, regardless of geographic origin. Cultivars from Japan, the USA and Iran showed close genetic relationships, suggesting historical germplasm exchange through human or natural-mediated gene flow. The observed moderate genetic differentiation (Fst = 0.236) and limited gene flow (Nm = 0.81) highlight the impact of geographical and anthropogenic barriers on cultivar divergence. The results also indicated that genetically distant Iranian cultivars, such as ‘Bidaneh Ghermez’ and ‘Dizmari’, offer promising material for breeding programmes aimed at maximizing heterosis. Overall, ISSR markers proved effective in detecting polymorphism and assessing genetic diversity in grape cultivars. Future work should expand the analysis to a broader set of Iranian and international germplasm using complementary molecular markers to strengthen breeding strategies and improve adaptability under climate change. Significance of the study What is already known on this subject? Research has shown that grape cultivars from different geographical origins can exhibit genetic similarities, likely due to historical germplasm exchange facilitated by environmental factors or human activities such as trade and farming. What are the new findings? The greatest genetic distance (0.589) was observed between the Iranian Bidaneh Ghermez and the Uzbek Black Seedless, suggesting limited gene flow between these populations. This finding highlights unique genetic reservoirs that could be valuable for breeding programmes. What are the expected impacts on horticulture? This study’s findings are expected to strengthen grape breeding, conservation, and commercial production by: (1) Enabling targeted cross-breeding for better cultivars; (2) Supporting genetic preservation of rare Iranian varieties; (3) Improving vineyard management through DNA-based identification; and (4) Promoting sustainable viticulture by leveraging natural genetic diversity. ltimately, these impacts will contribute to more resilient, productive, and economically viable grape cultivation systems, benefiting farmers, researchers, and the horticulture industry.