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Title: Structural variation within the potato Ve gene locus and correlation with molecular marker analysis

Author
item MEIER, AUSTIN - University Of Wisconsin
item Halterman, Dennis

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/28/2016
Publication Date: 8/18/2016
Publication URL: https://handle.nal.usda.gov/10113/63252
Citation: Meier, A., Halterman, D.A. 2016. Structural variation within the potato Ve gene locus and correlation with molecular marker analysis. Crop Science. 56(6):3133-3142. doi: 10.2135/cropsci2016.02.0137.

Interpretive Summary: Resistance to the potato disease verticillium wilt is conferred by a gene called Ve, which is present in certain wild species relatives of potato. Resistant hybrids have been developed that contain resistance, but genetic markers related to resistance do not work well when crossed with cultivated potato varieties. Using whole-genome sequencing, we have found that the Ve region of the potato genome is dynamic and that duplication or deletion of certain regions within the Ve region could be correlated with resistance and susceptibility. This new information will impact potato breeders and scientists interested in the incorporation of verticllium wilt resistance into new varieties. The sequence information of this region will assist in the development of additional markers that are more useful in detecting resistance in a broad range of potato germplasm.

Technical Abstract: The disconnect between single genotype model systems and plant breeding using wide crosses of diverse germplasm is often too great to affect progress in understanding complex phenotypes. Whole genome sequencing allows researchers and breeders to quickly and inexpensively resequence interesting individuals within a population to identify genetic sequence variation and relate this to observed phenotypic variation. In potato, resistance to Verticillium dahliae, a contributor to potato early dying, can be found in hybrids between wild potato species and this resistance is linked to the Ve locus on chromosome 9. In order to identify sequence variation that might contribute to resistance or susceptibility, the genome of a heterozygous diploid hybrid with resistance to Verticillium wilt was sequenced using the Illumina platform. The resulting reads and a genetic modeling tool known as Pindel were used to show the absence of a previously unannotated putative resistance gene within the Ve locus when compared to sequenced DM1-3 potato genome. Predicted genetic variation was confirmed using PCR primers designed to amplify designated regions shown to be absent in C287. It is hypothesized that this presence/absence variation may play a role in the resistance of potato species to Verticillium wilt. We also evaluated the usefulness of two previously published CAPS markers and found that specificity of these markers can be complicated by the existence of homologous gene sequences.