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Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European
C Lepoittevin1,2, C Bodénès1,2, E Chancerel1,2
1UMR 1202 BIOGECO, INRA, Cestas, F-33610, France.
Molecular Ecology Resources
|March 31, 2015
Summary
Developing SNP genotyping arrays for European white oaks revealed significant experimental error rates, with 15-20% of single nucleotide polymorphisms (SNPs) potentially unreliable. This highlights the need for caution when using high-throughput genotyping techniques in Quercus species.
Area of Science:
- Forest Genetics
- Plant Genomics
- Molecular Ecology
Background:
- European white oaks (Quercus spp.) are ecologically and economically important.
- Accurate single nucleotide polymorphism (SNP) genotyping is crucial for understanding oak diversity and evolution.
- Previous SNP discovery methods for oaks have limitations.
Purpose of the Study:
- To construct and evaluate an Illumina Infinium SNP genotyping array for European white oaks.
- To assess genotyping success rates and identify sources of error in mapping and natural populations.
- To provide recommendations for applying high-throughput genotyping in Quercus.
Main Methods:
- SNP discovery using Sanger sequencing and Roche 454 technology across multiple Quercus species.
- Genotyping of 7913 SNPs in parental lines, progenies, and natural populations.
- Analysis of genotyping success rates and identification of genotype cluster compression.
Main Results:
- Genotyping success rates were higher in mapping populations (80.4%) than in natural populations (54.8%).
- Approximately 25% of successfully genotyped SNPs exhibited cluster compression, potentially due to paralogues.
- The Illumina Infinium array showed a high experimental error rate (15-20% of SNPs potentially unreliable).
Conclusions:
- The developed Illumina Infinium array has limitations for Quercus genotyping due to significant error rates.
- Compressed SNP clusters are indicative of unreliable genotypes and should be treated with caution or excluded.
- Recommendations are provided for optimizing high-throughput SNP genotyping in white oaks and related species.
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