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ISHS Acta Horticulturae 859: International Symposium on Molecular Markers in Horticulture

SNP DISCOVERY IN ZEA MAYS USING SEQUENCED RESTRICTION-SITE ASSOCIATED DNA MARKERS

Authors:   R.W. Nipper, T.S. Atwood, J.Q. Boone, J.M. Gribbin, E.A. Johnson
Keywords:   SNP discovery, RAD Markers, complexity reduction, linkage mapping, genotyping, Zea mays
Abstract:
Sequenced restriction-site associated DNA (RAD) markers detect genetic variation by massively parallel sequencing of genomic DNA adjacent to restriction endonuclease digestion sites. Here we describe the first extension of the RAD marker system in analysis of a plant genome. A low-resolution genome scan in Zea mays L. using the restriction endonuclease NotI interrogated 8,944 sequence loci at high coverage and produced 250.4 kilobases of sequence data. Comparison between the RAD marker sequences and the maize inbred B73 reference genome uncovered 1,116 putative single nucleotide polymorphisms (SNPs). We conclude that sequenced RAD markers are an efficient platform for SNP discovery in complex plant genomes.
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