Molecular Genetics and Genomics

, Volume 279, Issue 5, pp 535–543 | Cite as

Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing

  • Sadia Bekal
  • J. P. Craig
  • M. E. Hudson
  • T. L. Niblack
  • L. L. Domier
  • K. N. Lambert
Original Paper

Abstract

Heterodera glycines, the soybean cyst nematode (SCN), is a damaging agricultural pest that could be effectively managed if critical phenotypes, such as virulence and host range could be understood. While SCN is amenable to genetic analysis, lack of DNA sequence data prevents the use of such methods to study this pathogen. Fortunately, new methods of DNA sequencing that produced large amounts of data and permit whole genome comparative analyses have become available. In this study, 400 million bases of genomic DNA sequence were collected from two inbred biotypes of SCN using 454 micro-bead DNA sequencing. Comparisons to a BAC, sequenced by Sanger sequencing, showed that the micro-bead sequences could identify low and high copy number regions within the BAC. Potential single nucleotide polymorphisms (SNPs) between the two SCN biotypes were identified by comparing the two sets of sequences. Selected resequencing revealed that up to 84% of the SNPs were correct. We conclude that the quality of the micro-bead sequence data was sufficient for de novo SNP identification and should be applicable to organisms with similar genome sizes and complexities. The SNPs identified will be an important starting point in associating phenotypes with specific regions of the SCN genome.

Keywords

SNP Indel Heterodera glycines DNA Polymorphism Genetic 

Notes

Acknowledgments

This work was supported by grant 2006-35604-16731 from the United States Department of Agriculture National Research Initiative Competitive Grants Program. The CFAR program at the University of Illinois at Urbana-Champaign. The Illinois Soybean Production Operating Board, The North Central Regional Integrated Pest Management, Competitive Grants Program and the United Soybean Board. We also wish to thank Kam Colgrove for his technical support. Mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion of other products that may also be suitable. This work has been carried out in compliance with the current laws governing genetic experimentation in the United States of America.

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Sadia Bekal
    • 1
  • J. P. Craig
    • 1
  • M. E. Hudson
    • 1
  • T. L. Niblack
    • 1
  • L. L. Domier
    • 2
  • K. N. Lambert
    • 1
  1. 1.Crop SciencesUniversity of IllinoisUrbanaUSA
  2. 2.USDA-ARS, Crop SciencesUniversity of IllinoisUrbanaUSA

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