Development of Single Nucleotide Polymorphism (SNP) Markers and Applications in Rice Breeding

摘要

Single nucleotide polymorphisms (SNPs) are attractive because they are abundant, genetically stable, and amenable to high-throughput analysis. Using the genome sequence information of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith), we were able to identify 7805 polymorphic loci including SNPs and insertions/deletions (InDels). The frequency of SNPs in the rice genome varied between different chromosomes. To illustrate the usefulness of SNPs as a marker system, we have successfully generated 331 SNP markers (Fig.l) between an indica cultivar Guang-Lu-Ai 4 (GLA4) and a wild rice accession (Oryza rufipogon Griffith, W1943).