Genetic mapping in grapevine using SNP microarray intensity values

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 gene...

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Bibliographic Details
Published in:Molecular breeding 2015-03, Vol.35 (3), p.1-12, Article 88
Main Authors: Myles, Sean, Mahanil, Siraprapa, Harriman, James, Gardner, Kyle M., Franklin, Jeffrey L., Reisch, Bruce I., Ramming, David W., Owens, Christopher L., Li, Lin, Buckler, Edward S., Cadle-Davidson, Lance
Format: Article
Language:English
Subjects:
Airborne microorganisms
Biodiversity
Biomedical and Life Sciences
Biotechnology
Gene mapping
Genetic diversity
Genotyping
Grapevines
Hybridization
Life Sciences
Mapping
Molecular biology
Nucleotides
Phenotypes
Plant biology
Plant breeding
Plant Genetics and Genomics
Plant Pathology
Plant Physiology
Plant Sciences
Powdery mildew
Quantitative trait loci
Single-nucleotide polymorphism
Species diversity
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Summary: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.
ISSN:1380-3743
1572-9788
DOI:10.1007/s11032-015-0288-3