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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF HARD RED SPRING AND DURUM WHEAT FOR DISEASE RESISTANCE AND QUALITY USING GENETICS AND GENOMICS Title: Use of GoldenGate assay for SNP genotyping in cereal crops

Authors
item Chao, Shiaoman
item Lawley, Cindy -

Submitted to: Methods in Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 21, 2013
Publication Date: N/A

Interpretive Summary: General guidelines and practical procedures for conducting genotyping experiments capable of assaying a large number of DNA markers are described. The GoldenGate assay developed by Illumina is a highly parallel genotyping assay system allowing up to 3,072 genetic variants at single nucleotide positions, known as single nucleotide polymorphisms (SNPs), to be analyzed simultaneously in a single assay. This system has greatly facilitated the use of SNP markers with genome-wide coverage on genetic studies and breeding applications particularly for crops with large and complex genome structures. In this report, we provide step-by-step procedures and offer general guidelines regarding the aspects from preparing DNA samples, developing SNP marker panel, conducting lab assays, to using the software to obtain genotyping results. The information described is comprehensive and will lead the users to obtaining high quality genotype data for downstream applications.

Technical Abstract: The highly parallel genotyping assay, such as the GoldenGate assay developed by Illumina, capable of interrogating up to 3,072 single nucleotide polymorphisms (SNPs) simultaneously, has greatly facilitated the genome-wide studies particularly for crops with large and complex genome structures. In this report, we provide detailed information regarding DNA preparation, SNP assay design, SNP assay protocols, and genotype calling using Illumina's GenomeStudio software.

Last Modified: 12/19/2014
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