Structural Variation within the Potato Ve Gene Locus and Correlation with Molecular Marker Analysis

Abstract

Plant breeders rely on molecular markers to guide the selection of traits that are difficult to phenotype or that show wide variation in field trials as they seek to uncover the intricate relationship between an organism's genotype and resulting phenotype. Specificity of molecular markers in wild potato (Solanum spp.) and other less‐adapted germplasm is complicated by the existence of homologous gene clusters. This study examines the consistency and effectiveness of two previously published cleaved amplified polymorphic sequence (CAPS) markers that have been shown to predict Verticillium wilt (VW) resistance. The genome of resistant diploid potato clone C287 was resequenced, and examination of the Ve locus indicated only two homologous regions when compared with the three found in the reference potato genome DM1‐3. The prevalence of each homologous region was examined within a panel of 83 diverse wild potato species. Both structural and genetic sequence variation is predicted to complicate the use of molecular markers developed within specific genetic backgrounds. This study demonstrates that primers designed in the noncoding flanking regions of gene homologs increases specificity and avoids off‐target binding. It is suggested that markers be developed by using more specific primers in these regions coupled with conserved primers within the gene's coding sequence.