Molecular Breeding

, Volume 25, Issue 3, pp 441–451 | Cite as

High-throughput SNP genotyping with the GoldenGate assay in maize

  • Jianbing Yan
  • Xiaohong Yang
  • Trushar Shah
  • Héctor Sánchez-Villeda
  • Jiansheng Li
  • Marilyn Warburton
  • Yi Zhou
  • Jonathan H. Crouch
  • Yunbi Xu


Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the genomes of most plant species. They have become an ideal marker system for genetic research in many crops. Several high throughput platforms have been developed that allow rapid and simultaneous genotyping of up to a million SNP markers. In this study, a custom GoldenGate assay containing 1,536 SNPs was developed based on public SNP information for maize and used to genotype two recombinant inbred line (RIL) populations (Zong3 x 87-1, and B73 x By804) and a panel of 154 diverse inbred lines. Over 90% of the SNPs were successfully scored in the diversity panel and the two RIL populations, with a genotyping error rate of less than 2%. A total of 975 SNP markers detected polymorphism in at least one of the two mapping populations, with a polymorphic rate of 38.5% in Zong3 x 87-1 and 52.6% in B73 x By804. The polymorphic SNPs in B73 x By804 have been integrated with previously mapped simple sequence repeat markers to construct a high-density linkage map containing 662 markers with a total length of 1,673.7 cM and an average of 2.53 cM between two markers. The minor allelic frequency (MAF) was distributed evenly across 10 continued classes from 0.05 to 0.5, and about 16% of the SNP markers had a MAF below 10% in the diversity panel. Polymorphism rates for individual SNP markers in pair-wise comparisons of genotypes tested ranged from 0.3 to 63.8% with an average of 36.3%. Most SNPs used in this GoldenGate assay appear to be equally useful for diversity analysis, marker-trait association studies, and marker-aided breeding.


Single nucleotide polymorphism Maize Goldengate High-throughput 



Bacteria artificial chromosomes


Doubled haploid


Expression sequence tag


Fingerprinted contigs


Linkage disequilibrium




Marker-assisted recurrent selection


Marker-assisted selection


Nested association mapping


National science foundation


Oligo pool assay


Polymerase chain reaction


Quantitative trait locus


Restriction fragment length polymorphisms


Recombinant inbred lines


Sentrix array matrix


Single nucleotide polymorphism


Simple sequence repeat


Sequence tagged site



We highly appreciate the molecular and functional diversity team of the NSF Maize Genome Project for making available all the SNPs information used in this study. We thank Dr. Ortiz Rodomiro (CIMMYT) for his critical review this manuscript. This research was supported by the National Hi-Tech Research and Development Program of China and the Bill & Melinda Gates Foundation through the Drought Tolerant Maize for Africa project (

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Jianbing Yan
    • 1
    • 2
  • Xiaohong Yang
    • 2
  • Trushar Shah
    • 1
  • Héctor Sánchez-Villeda
    • 1
  • Jiansheng Li
    • 2
  • Marilyn Warburton
    • 3
  • Yi Zhou
    • 2
  • Jonathan H. Crouch
    • 1
  • Yunbi Xu
    • 1
  1. 1.International Maize and Wheat Improvement Center (CIMMYT)México, D.F.Mexico
  2. 2.National Maize Improvement Center of ChinaChina Agricultural UniversityBeijingChina
  3. 3.USDA-ARS Corn Host Plant Resistance Research UnitMississippi StateUSA

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