Diversity and association mapping assessment of an untouched native grapevine genetic resource by iPBS retrotransposon markers

Grapes are among the most widely cultivated horticultural crops and have a long history of domestication. They exhibit genetic variation due to natural crossbreeding, bud mutations, and the changing demand for different types of wine and table grapes. Identifying and distinguishing autochthonous grape cultivars is an essential first step in breeding. In this research, an autochthonous grapevine (Vitis vinifera L.) population was identified using retrotransposon markers called iPBS (Inter primer binding sites), and genetic relationships with other cultivars from Turkiye and Europe were examined. The association between loci and specific traits was determined using GLM (general linear model) and MLM (mixed linear model) analyses. A total of 136 loci were generated by eight iPBS markers, of which 106 were polymorphic. Genotypes and standard cultivars were clustered into three main groups and seven subclusters by the neighbor-joining method. Structure analysis further classified the genotypes and cultivars into seven populations. Molecular variance analysis revealed that most of the variability occurred among individuals. In the association mapping, 36 loci were correlated with quantitative traits in GLM, while 21 were in MLM. The diversity assessments uncovered significant diversity within the autochthonous grape population, even among individuals with the same name. This diversity retains value for breeding research as it allows identifying distinct genotypes with desirable characteristics. The loci identified through both mapping approaches have the potential to serve as functional markers for selecting genotypes with desired traits.