Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing |
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Authors: | Sadia Bekal J P Craig M E Hudson T L Niblack L L Domier K N Lambert |
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Institution: | (1) Crop Sciences, University of Illinois, 1102 S. Goodwin Ave., Urbana, IL 61801, USA;(2) USDA-ARS, Crop Sciences, University of Illinois, 1102 S. Goodwin Ave., Urbana, IL 61801, USA |
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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. |
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Keywords: | SNP Indel Heterodera glycines DNA Polymorphism Genetic |
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