Genetic diversity and population structure of Turkish European chestnut (Castanea sativa) genotypes assessed using start codon targeted polymorphism (SCoT) markers

Abstract The European chestnut ( Castanea sativa ) is an important nut crop that grows naturally in the Black Sea and Aegean regions of Türkiye. This study examined the genetic diversity and population structure of chestnut genotypes from prominent regions in Türkiye using Start Codon Targeted Polymorphism (SCoT) markers. A total of 44 Turkish chestnut genotypes from the Aegean, Marmara, and Black Sea regions, along with a control group of French variety, were analyzed. The SCoT primers underwent tests to select the most suitable ones, producing 8 selected amplified fragments, 65.34% of which were found to be polymorphic. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCoA) analyses showed clear discrimination between two populations based on their origins, which was supported by the population structure analysis. The analysis of molecular variance (AMOVA) analysis revealed that 3% of the genetic variation was within populations and 97% was among individuals. The out-group (French variety) showed the furthest genetic similarity, and genetic similarity values decreased with increasing geographic distance. The SCoT primers successfully fingerprinted chestnut genotypes and could be used in future research to analyze the phylogeny of chestnuts using genomic DNA.