Theoretical and Applied Genetics

, Volume 116, Issue 7, pp 945–952

High-throughput genotyping with the GoldenGate assay in the complex genome of soybean

  • David L. Hyten
  • Qijian Song
  • Ik-Young Choi
  • Mun-Sup Yoon
  • James E. Specht
  • Lakshmi K. Matukumalli
  • Randall L. Nelson
  • Randy C. Shoemaker
  • Nevin D. Young
  • Perry B. Cregan
Original Paper

DOI: 10.1007/s00122-008-0726-2

Cite this article as:
Hyten, D.L., Song, Q., Choi, IY. et al. Theor Appl Genet (2008) 116: 945. doi:10.1007/s00122-008-0726-2

Abstract

Large numbers of single nucleotide polymorphism (SNP) markers are now available for a number of crop species. However, the high-throughput methods for multiplexing SNP assays are untested in complex genomes, such as soybean, that have a high proportion of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a 3-day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A custom 384-SNP GoldenGate assay was designed using SNPs that had been discovered through the resequencing of five diverse accessions that are the parents of three recombinant inbred line (RIL) mapping populations. The 384 SNPs that were selected for this custom assay were predicted to segregate in one or more of the RIL mapping populations. Allelic data were successfully generated for 89% of the SNP loci (342 of the 384) when it was used in the three RIL mapping populations, indicating that the complex nature of the soybean genome had little impact on conversion of the discovered SNPs into usable assays. In addition, 80% of the 342 mapped SNPs had a minor allele frequency >10% when this assay was used on a diverse sample of Asian landrace germplasm accessions. The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are rapidly becoming available.

Supplementary material

122_2008_726_MOESM1_ESM.doc (180 kb)
Diverse soybean landraces used in this study. (DOC 180 kb)
122_2008_726_MOESM2_ESM.xls (122 kb)
Information relating to 384 SNPs (SNP name/Locus name) in sequence tagged sites (Sequence ID) to which GoldenGate assays were designed and tested including the status of the assay and the linkage map position to which each SNP was mapped. Additional information relating to the sequence tagged sites includes the forward and reverse PCR primers and information relating to PCR amplification. (XLS 121 kb)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • David L. Hyten
    • 1
  • Qijian Song
    • 1
    • 2
  • Ik-Young Choi
    • 1
    • 3
  • Mun-Sup Yoon
    • 1
    • 4
  • James E. Specht
    • 5
  • Lakshmi K. Matukumalli
    • 6
  • Randall L. Nelson
    • 7
  • Randy C. Shoemaker
    • 8
  • Nevin D. Young
    • 9
  • Perry B. Cregan
    • 1
  1. 1.Soybean Genomics and Improvement LaboratoryU.S. Department of Agriculture, Agricultural Research ServiceBeltsvilleUSA
  2. 2.Department Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkUSA
  3. 3.National Instrumentation Center for Environmental ManagementSeoul National UniversitySeoulSouth Korea
  4. 4.Genetic Resources DivisionNational Institute of Agricultural Biotechnology, Rural Development AdministrationSuwonSouth Korea
  5. 5.Department of Agronomy and HorticultureUniversity of Nebraska LincolnLincolnUSA
  6. 6.Bovine Functional Genomics Laboratory U.S. Department of Agriculture, Agricultural Research ServiceBeltsvilleUSA
  7. 7.Soybean/Maize Germplasm, Pathology, and Genetics Research Unit and Department of Crop SciencesU.S. Department of Agriculture, Agricultural Research Service, University of IllinoisUrbanaUSA
  8. 8.Department of AgronomyU.S. Department of Agriculture, Agricultural Research Service, Iowa State UniversityAmesUSA
  9. 9.Department of Plant PathologyUniversity of MinnesotaSt. PaulUSA