Genotyping microarrays are widely used for genetic mapping, but in high-diversity organisms, the quality of SNP calls can be diminished by genetic variation near the assayed nucleotide. To address this limitation in grapevine, we developed a simple heuristic that uses hybridization intensity to genetically map phenotypes without the need to distinguish between polymorphic states. We applied this approach to the mapping of three previously mapped traits, each controlled by single major effect loci—color, flower sex, and powdery mildew resistance—and confirmed that intensity values outperform SNP calls in all cases. Further, because per sample cost is a major limitation to the adoption of genotyping microarrays in applied genetic research and plant breeding, we tested how many samples were required to map a Mendelian trait in an F1 grape population and found that we could identify the correct genomic region with as few as 12 samples. For high-diversity species for which genotyping arrays are available or under development, our findings suggest a powerful and cost-effective approach to identify large-effect QTL when faced with poor SNP quality.
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