Plant Genotyping pp 299-312 | Cite as
Use of the Illumina GoldenGate Assay for Single Nucleotide Polymorphism (SNP) Genotyping in Cereal Crops
Abstract
Highly parallel genotyping assays, such as the GoldenGate assay developed by Illumina, capable of interrogating up to 3,072 single nucleotide polymorphisms (SNPs) simultaneously, have greatly facilitated genome-wide studies, particularly for crops with large and complex genome structures. In this report, we provide detailed information and guidelines regarding genomic DNA preparation, SNP assay design, SNP assay protocols, and genotype calling using Illumina’s GenomeStudio software.
Key words
DNA marker High-throughput genotyping Oligo pool assay OPA Single nucleotide polymorphism SNPNotes
Acknowledgements and Disclaimer
This work was supported by USDA-NIFA Grant No. 2009-85606-05701 (“Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement”); USDA-NIFA Grant No. 2009-65300-05638 (“Single Nucleotide Polymorphism (SNP) Markers for High-Throughput Genotyping to Advance Genomic, Genetic, and Breeding Research in Wheat”); USDA-NIFA Grant No. 2009-65300-05707 (“Oat SNP Development and Identification of Loci Affecting Key Traits in North American Oat Germplasm using Association Mapping”); General Mills, Inc.; and USDA CRIS Project No. 5442-22000-033-00D (“Improvement of Hard Red Spring and Durum Wheat for Disease Resistance and Quality using Genetics and Genomics”). Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.
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