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Related Experiment Video

Updated: Jun 10, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

High-throughput SNP discovery and assay development in common bean.

David L Hyten1, Qijian Song, Edward W Fickus

  • 1Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA. david.hyten@ars.usda.gov

BMC Genomics
|August 18, 2010
PubMed
Summary

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We developed a cost-effective method for discovering single nucleotide polymorphisms (SNPs) in organisms lacking whole genome sequences, like common bean. This approach combines Roche 454 and Illumina sequencing for efficient SNP assay development.

Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Next-generation sequencing (NGS) accelerates single nucleotide polymorphism (SNP) discovery.
  • SNP discovery is challenging and costly in species without whole genome sequences, such as common bean (Phaseolus vulgaris L.).
  • Existing methods are often limited by the need for whole genome sequencing or normalized cDNA libraries.

Purpose of the Study:

  • To develop a high-throughput method for SNP discovery in diploid organisms lacking whole genome sequences.
  • To enable efficient SNP assay development using limited genomic resources.
  • To reduce the cost and complexity of SNP discovery in non-model organisms.

Main Methods:

  • Coupling Roche 454-FLX and Illumina Genome Analyzer sequencing data.

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  • Utilizing a multi-tier reduced representation library approach.
  • Employing Sanger sequencing for SNP validation and GoldenGate assay design.

    • Main Results:

    • Discovered 3,487 SNPs, with 2,795 having sufficient flanking sequence for assay development.
    • Achieved an 86% validation rate for identified SNPs using Sanger sequencing.
    • Successfully designed a GoldenGate assay with 827 working SNPs (79% success rate) from 1,050 candidates.

    Conclusions:

    • A novel, high-throughput method for SNP discovery has been established by combining two NGS technologies.
    • This method eliminates the requirement for a whole genome sequence or normalized cDNA libraries.
    • It facilitates SNP assay development in organisms with limited genomic resources, exemplified by common bean.