Molecular Breeding

, Volume 25, Issue 3, pp 441–451

High-throughput SNP genotyping with the GoldenGate assay in maize

Authors

    • International Maize and Wheat Improvement Center (CIMMYT)
    • National Maize Improvement Center of ChinaChina Agricultural University
  • Xiaohong Yang
    • National Maize Improvement Center of ChinaChina Agricultural University
  • Trushar Shah
    • International Maize and Wheat Improvement Center (CIMMYT)
  • Héctor Sánchez-Villeda
    • International Maize and Wheat Improvement Center (CIMMYT)
  • Jiansheng Li
    • National Maize Improvement Center of ChinaChina Agricultural University
  • Marilyn Warburton
    • USDA-ARS Corn Host Plant Resistance Research Unit
  • Yi Zhou
    • National Maize Improvement Center of ChinaChina Agricultural University
  • Jonathan H. Crouch
    • International Maize and Wheat Improvement Center (CIMMYT)
    • International Maize and Wheat Improvement Center (CIMMYT)
Article

DOI: 10.1007/s11032-009-9343-2

Cite this article as:
Yan, J., Yang, X., Shah, T. et al. Mol Breeding (2010) 25: 441. doi:10.1007/s11032-009-9343-2

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.

Keywords

Single nucleotide polymorphismMaizeGoldengateHigh-throughput

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

Supplementary material

11032_2009_9343_MOESM1_ESM.doc (402 kb)
Supplementary material 1 (DOC 402 kb)
11032_2009_9343_MOESM2_ESM.xlsx (13 kb)
Supplementary material 2 (XLSX 13 kb)
11032_2009_9343_MOESM3_ESM.xlsx (124 kb)
Supplementary material 3 (XLSX 124 kb)
11032_2009_9343_MOESM4_ESM.xlsx (51 kb)
Supplementary material 4 (XLSX 51 kb)
11032_2009_9343_MOESM5_ESM.xlsx (36 kb)
Supplementary material 5 (XLSX 35 kb)

Copyright information

© Springer Science+Business Media B.V. 2009