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TitleAn SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments
AuthorsF. Alex Feltus, Jun Wan, Stefan R. Schulze, James C. Estill, Ning Jiang, and
Andrew H. Paterson
Year2004
Taxonrice
PDF1812.pdf
PublicationGenome Research 14:1812-1819
Journal_linkhttp://www.genome.org
Publisher_note
Supplemental
AbstractDense coverage of the rice genome with polymorphic DNA markers is an invaluable tool for DNA marker-assisted breeding, positional cloning, and a wide range of evolutionary studies. We have aligned drafts of two rice subspecies, indica and japonica, and analyzed levels and patterns of genetic diversity. After filtering multiple copy and low quality sequence, 408,898 candidate DNA polymorphisms (SNPs/INDELs) were discerned between the two subspecies. These filters have the consequence that our data set includes only a subset of the available SNPs (in particular excluding large numbers of SNPs that may occur between repetitive DNA alleles) but increase the likelihood that this subset is useful: Direct sequencing suggests that 79.8%

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