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Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm

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Abstract

The development of single nucleotide polymorphism (SNP) markers in maize offers the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. We mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe. We then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered. We also describe the development of a 768 marker multiplex assay for use on the Illumina® BeadArray™ platform. SNP markers were mapped on the IBM2 intermated B73 × Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets. A high degree of colinearity was found with the genetic nested association map. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina® platform.

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Authors and Affiliations

  1. Pioneer Hi-Bred International, Inc. (DuPont Agriculture and Nutrition), 7300 NW 62nd Avenue, P.O. Box 1004, Johnston, IA, 51031-1004, USA

    Elizabeth Jones, Mulu Ayele, Ed Bruggeman, Ken Yourstone, Oscar S. Smith, Jana Warren, Jean Babayev, Sutirtha Basu & Stephen Smith

  2. Pioneer Hi-Bred International, Inc. (DuPont Agriculture and Nutrition), 810 Sugar Grove Ave-Highway 44, Dallas Center, IA, 50063-2005, USA

    Wen-Chy Chu & Chethana Bezawada

  3. Pioneer Hi-Bred International, Inc. (DuPont Agriculture and Nutrition), 1039 S Milton-Shopiere, P.O. BOX 668, Janesville, WI, 53547-0668, USA

    Julie Ho

  4. DuPont Agriculture and Nutrition, Route 141, Henry Clay Bldg #353, Wilmington, DE, 19880-0353, USA

    Antoni Rafalski

  5. Plant Genetics Research Unit, USDA-Agricultural Research Service, 302 Curtis Hall, Columbia, MO, USA

    Michael D. McMullen

  6. Division of Plant Sciences, University of Missouri, Columbia, MO, 65211-7020, USA

    Michael D. McMullen

Authors
  1. Elizabeth Jones
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  2. Wen-Chy Chu
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  3. Mulu Ayele
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  4. Julie Ho
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  7. Antoni Rafalski
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  8. Oscar S. Smith
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  9. Michael D. McMullen
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  10. Chethana Bezawada
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  11. Jana Warren
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  12. Jean Babayev
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  13. Sutirtha Basu
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  14. Stephen Smith
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Correspondence to Elizabeth Jones.

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Jones, E., Chu, WC., Ayele, M. et al. Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm. Mol Breeding 24, 165–176 (2009). https://doi.org/10.1007/s11032-009-9281-z

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  • DOI: https://doi.org/10.1007/s11032-009-9281-z

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