Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay.

Theor Appl Genet 2009 Aug 18;119(3):507-17. Epub 2009 May 18.

Department of Plant Sciences, University of California, Davis, CA 95616, USA.

Single nucleotide polymorphisms (SNPs) are indispensable in such applications as association mapping and construction of high-density genetic maps. These applications usually require genotyping of thousands of SNPs in a large number of individuals. Although a number of SNP genotyping assays are available, most of them are designed for SNP genotyping in diploid individuals. Here, we demonstrate that the Illumina GoldenGate assay could be used for SNP genotyping of homozygous tetraploid and hexaploid wheat lines. Genotyping reactions could be carried out directly on genomic DNA without the necessity of preliminary PCR amplification. A total of 53 tetraploid and 38 hexaploid homozygous wheat lines were genotyped at 96 SNP loci. The genotyping error rate estimated after removal of low-quality data was 0 and 1% for tetraploid and hexaploid wheat, respectively. Developed SNP genotyping assays were shown to be useful for genotyping wheat cultivars. This study demonstrated that the GoldenGate assay is a very efficient tool for high-throughput genotyping of polyploid wheat, opening new possibilities for the analysis of genetic variation in wheat and dissection of genetic basis of complex traits using association mapping approach.

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http://dx.doi.org/10.1007/s00122-009-1059-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715469PMC
August 2009
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