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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #283902
Title: Use of the Illumina GoldenGate assay for single nucleotide polymorphism (SNP) genotyping in cereal crops

Author
item Chao, Shiaoman
item LAWLEY, CINDY - Illumina, Inc

Submitted to: Methods in Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2013
Publication Date: 6/1/2015
Citation: Chao, S., Lawley, C. 2015. Use of the Illumina GoldenGate assay for single nucleotide polymorphism (SNP) genotyping in cereal crops. In: Batley, J., editor. Plant Genotyping: Methods and Protocols, Methods in Molecular Biology. Volume 1245. New York, NY: Springer Science+Business Media. p. 299-312. doi: 10.1007/978-1-4939-1966-6.

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.