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

Abstract

Abstract Grape is one of the most produced horticultural crops, being one of the oldest domesticated plants that undergo genetic differentiation due to the natural crossing, bud mutations, and the effect of the continuously changing demand for wine types and table grapes. Recognition and discrimination of autochthonous varieties are the first steps for breeding studies. In this study, an autochthonous grapevine population was recognized by iPBS (Inter primer binding sites) retrotransposon markers and the genetic relationships with some other varieties from Turkey and Europe. The trait-associated loci were determined by GLM (general linear model) and MLM (mixed linear model) analysis. Eight iPBS markers generated 136 loci, of which 106 were polymorphic. The neighbor-joining method clustered the genotypes and standard varieties into three main and seven subclusters. Structure analysis also grouped the grapes into seven populations. Molecular variance analysis showed that the variability occurred mainly among individuals. In the association mapping, 36 loci were correlated with quantitative traits in GLM, whereas 21 loci were correlated in MLM. A remarkable diversity among the autochthonous grape population, even among the same-named individuals, was determined by diversity assessments. Distinct genotypes with desired characteristics will be valuable in breeding studies. The loci determined by both mapping approaches might help to create functional markers to select genotypes with the desired traits.