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PMID: 15342564 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments.

Genome research ·Vol. 14 ·No. 9 ·2004-09-00 ·Pages 1812-9

Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH

Abstract

Dense 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% +/- 7.5% of the in silico SNPs are real. The SNP sample in our database is not randomly distributed across the genome. In fact, 566 rice genomic regions had unusually high (328 contigs/48.6 Mb/13.6% of genome) or low (237 contigs/64.7 Mb/18.1% of genome) polymorphism rates. Many SNP-poor regions were substantially longer than most SNP-rich regions, covering up to 4 Mb, and possibly reflecting introgression between the respective gene pools that may have occurred hundreds of years ago. Although 46.2% +/- 8.3% of the SNPs differentiate other pairs of japonica and indica genotypes, SNP rates in rice were not predictive of evolutionary rates for corresponding genes in another grass species, sorghum. The data set is freely available at http://www.plantgenome.uga.edu/snp.

MeSH Terms
Breeding Genetic Variation Genome, Plant Molecular Sequence Data Oryza/classification,genetics Polymorphism, Single Nucleotide Recombination, Genetic Sequence Alignment Sorghum
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Feltus F Alex
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
Wan Jun
Schulze Stefan R
Estill James C
Jiang Ning
Paterson Andrew H
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.2479404
Published
2004-09-00
Pages
1812-9
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC515328
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1101/gr.2479404 PMC Full Text View journal details
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