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
Article

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 polymorphism Maize Goldengate High-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

Notes

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/).

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)

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664CrossRefGoogle Scholar
  3. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678CrossRefPubMedGoogle Scholar
  4. Buckler ES, Stevens NM (2005) Maize Origins, Domestication, and selection. In: Motley TJ, Zerega N, Cross H (eds) Darwin’s harvest. Columbia University Press, New York, pp 67–90Google Scholar
  5. Chander S, Guo YQ, Yang XH et al (2008) Using molecular markers to identify two major loci controlling carotenoid contents in maize grain. Theor Appl Genet 116:223–233CrossRefPubMedGoogle Scholar
  6. Fan JB, Chee MS, Gunderson KL (2006a) Highly parallel genomic assays. Nat Rev Genet 7:632–644CrossRefPubMedGoogle Scholar
  7. Fan JB, Gunderson KL, Bibikova M et al (2006b) Illumina universal bead arrays. Methods Enzymol 410:57–73CrossRefPubMedGoogle Scholar
  8. Gao SB, Martinez C, Skinner DJ et al (2008) Development of a seed DNA-based genotyping system for marker-assisted selection in maize. Mol Breeding 22:477–494CrossRefGoogle Scholar
  9. Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18CrossRefPubMedGoogle Scholar
  10. Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE 2:e1367CrossRefPubMedGoogle Scholar
  11. Helentjaris T, Slocum M, Wright S et al (1986) Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet 72:761–769CrossRefGoogle Scholar
  12. Helentjaris T, Weber D, Wright S (1988) Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118:353–363PubMedGoogle Scholar
  13. Hyten DL, Song Q, Choi IY et al (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945–952CrossRefPubMedGoogle Scholar
  14. Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, Whitehead Institute, CambridgeGoogle Scholar
  15. Liu K, Goodman MM, Muse S et al (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128PubMedGoogle Scholar
  16. Lu H, Bernardo R (2001) Molecular diversity among current and historical maize inbreds. Theor Appl Genet 103:613–617CrossRefGoogle Scholar
  17. Ma XQ, Tang JH, Teng WT et al (2007) Epistatic interaction is an important genetic basis of grain yield and its components in maize. Mol Breeding 20:41–51CrossRefGoogle Scholar
  18. McMullen MM, Kresovich S, Villeda HS et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740CrossRefPubMedGoogle Scholar
  19. Rostoks N, Ramsay L, MacKenzie K et al (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661CrossRefPubMedGoogle Scholar
  20. Saghai Maroof MA, Soliman KM, Jorgensen RA et al (1984) Ribosomal DNA spacer length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018CrossRefPubMedGoogle Scholar
  21. Senior L, Lynn M, Heun M (1993) Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36:884–889CrossRefPubMedGoogle Scholar
  22. Song XF, Song TM, Dai JR et al (2004) QTL mapping of kernel oil concentration with high-oil maize by SSR markers. Maydica 49:41–48Google Scholar
  23. Teng WT, Can JS, Chen YH et al (2004) Analysis of maize heterotic groups and patterns during past decade in China. Sci Agric Sin 37:1804–1811Google Scholar
  24. Yu JM, Holland JB, McMullen MD et al (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551CrossRefPubMedGoogle Scholar

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

Personalised recommendations