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High-throughput SNP genotyping with the GoldenGate assay in maize

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Abstract

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.

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Abbreviations

BAC:

Bacteria artificial chromosomes

DH:

Doubled haploid

EST:

Expression sequence tag

FPC:

Fingerprinted contigs

LD:

Linkage disequilibrium

LOD:

Logarithm-of-odds

MARS:

Marker-assisted recurrent selection

MAS:

Marker-assisted selection

NAM:

Nested association mapping

NSF:

National science foundation

OPA:

Oligo pool assay

PCR:

Polymerase chain reaction

QTL:

Quantitative trait locus

RFLP:

Restriction fragment length polymorphisms

RIL:

Recombinant inbred lines

SAM:

Sentrix array matrix

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

STS:

Sequence tagged site

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Acknowledgments

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 (http://dtma.cimmyt.org/).

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Authors and Affiliations

  1. International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, México, D.F., Mexico

    Jianbing Yan, Trushar Shah, Héctor Sánchez-Villeda, Jonathan H. Crouch & Yunbi Xu

  2. National Maize Improvement Center of China, China Agricultural University, 100193, Beijing, China

    Jianbing Yan, Xiaohong Yang, Jiansheng Li & Yi Zhou

  3. USDA-ARS Corn Host Plant Resistance Research Unit, Box 9555, Mississippi State, MS, 39762, USA

    Marilyn Warburton

Authors
  1. Jianbing Yan
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  2. Xiaohong Yang
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  3. Trushar Shah
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  4. Héctor Sánchez-Villeda
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  5. Jiansheng Li
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  6. Marilyn Warburton
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  7. Yi Zhou
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  8. Jonathan H. Crouch
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  9. Yunbi Xu
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Correspondence to Jianbing Yan or Yunbi Xu.

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Yan, J., Yang, X., Shah, T. et al. High-throughput SNP genotyping with the GoldenGate assay in maize. Mol Breeding 25, 441–451 (2010). https://doi.org/10.1007/s11032-009-9343-2

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  • DOI: https://doi.org/10.1007/s11032-009-9343-2

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