Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.)

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels),...

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Bibliographic Details
Published in:DNA research 2006-04, Vol.13 (2), p.43-51
Main Authors: MONNA, Lisa, OHTA, Rieko, MASUDA, Haruka, KOIKE, Akiko, MINOBE, Yuzo
Format: Article
Language:English
Subjects:
Alleles
Biological and medical sciences
Chromosomes, Plant
Fundamental and applied biological sciences. Psychology
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
Genome, Plant
Linkage Disequilibrium
Molecular and cellular biology
Molecular genetics
Oryza - genetics
Oryza rufipogon
Oryza sativa
Polymorphism, Single Nucleotide
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Summary:We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms are useful as DNA markers for genetic analysis or positional cloning with segregating populations of crosses. Pairwise comparison between cultivars and a neighbor-joining tree calculated from SNPs agreed very well with relationships between rice strains predicted from pedigree data or calculated with other DNA markers such as p-SINE1 and simple sequence repeats (SSRs), suggesting that whole-genome SNP information can be used for analysis of evolutionary relationships. Using multiple SNPs to identify alleles, we drew a map to illustrate the alleles shared among the eight cultivars and the accession. The map revealed that most of the genome is mono- or di-allelic among japonica cultivars, whereas alleles well conserved among modern japonica paddy rice cultivars were often shared with indica cultivars or wild rice, suggesting that the genome structure of modern cultivars is composed of chromosomal segments from various genetic backgrounds. Use of allele-sharing analysis and association analysis were also tested and are discussed.
ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/dsi030