A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.)

Qingsheng Jin, Dan Waters, Giovanni M. Cordeiro, Robert J. Henry, Russell F. Reinke

    Research output: Contribution to journalArticlepeer-review

    66 Citations (Scopus)

    Abstract

    The whole rice genome sequence was used to assist in the identification of a single nucleotide polymorphism (SNP) marker linked to the fragrance gene (fgr) in rice, Genes flanked by restriction fragment length polymorphism and microsatellite markers known to be linked to the fragrance gene were identified by DNA sequence alignment of EST sequences against BAC clones covering this region of chromosome eight. Re-sequencing and comparison of parts of these genes derived from a fragrant and a non-fragrant cultivar revealed only one SNP (a C/T transition) in more than 6 kbp of sequence from 14 genes. Ten of eleven fragrant genotypes and six of 14 non-fragrant genotypes tested carried the C allele. This approach indicated a generally low level of SNP polymorphism in cultivated rice suggesting that association of SNP with phenotypes should be an efficient path to gene discovery in cultivated rice.

    Original languageEnglish
    Pages (from-to)359-364
    Number of pages6
    JournalPlant Science
    Volume165
    Issue number2
    DOIs
    Publication statusPublished - 01 Aug 2003

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