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Plant Physiol, May 2003, Vol. 132, pp. 84-91
Mining for Single Nucleotide Polymorphisms and
Insertions/Deletions in Maize Expressed Sequence Tag
Data1
Jacqueline
Batley,2
Gary
Barker,
Helen
O'Sullivan,
Keith J.
Edwards, and
David
Edwards*
Agriculture Victoria, Plant Biotechnology Centre, La Trobe
University, Bundoora, Victoria 3086, Australia (J.B., D.E.); and the
School of Biological Sciences, University of Bristol, Bristol B58 1UG,
United Kingdom (G.B., H.O., K.J.E.)
We have developed a computer based method to identify
candidate single nucleotide polymorphisms (SNPs) and small
insertions/deletions from expressed sequence tag data. Using a
redundancy-based approach, valid SNPs are distinguished from erroneous
sequence by their representation multiple times in an alignment of
sequence reads. A second measure of validity was also calculated based
on the cosegregation of the SNP pattern between multiple SNP loci in an
alignment. The utility of this method was demonstrated by applying it
to 102,551 maize (Zea mays) expressed sequence
tag sequences. A total of 14,832 candidate polymorphisms were
identified with an SNP redundancy score of two or greater. Segregation
of these SNPs with haplotype indicates that candidate SNPs with high
redundancy and cosegregation confidence scores are likely to represent
true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and cosegregation scores, in four
inbred maize lines. The SNP transition/transversion ratio and
insertion/deletion size frequencies correspond to those observed by
direct sequencing methods of SNP discovery and suggest that the
majority of predicted SNPs and insertion/deletions identified using
this approach represent true genetic variation in maize.
1
This work was supported by the Biotechnology and
Biological Sciences Research Council and the Victorian Bioinformatics
Consortum (UK; grant-aided support to IACR-Long Ashton, Investigating
Gene Function initiative grant no. IGF12403 to D.E. and G.B.,
and grant no. D14009 to H.O.). Detailed results from this study are
available on-line at www.cerealsdb.uk.net. D.E. is supported by the
Victorian Bioinformatics Consortum.
2
Present address: School of Biological Sciences,
University of Bristol, Woodland Road, Bristol BS8 1UG, UK.
*
Corresponding author; e-mail Dave.Edwards{at}nre.vic.gov.au;
fax 61-3-94793618.
© 2003 American Society of Plant Biologists
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