Title

A Single Nucleotide Polymorphism (SNP) marker linked to fragrance in rice (Oryza sativa L.)

Document Type

Article

Publication details

Jin, QS, Waters, DLE, Cordeiro, GM, Henry, RJ & Reinke, RF 2003, 'A Single Nucleotide Polymorphism (SNP) marker linked to fragrance in rice (Oryza sativa L.)', Plant Science, vol. 165, no. 2, pp. 359-364.

Plant Science journal home page available at http://www.elsevier.com/locate/plantsci Publisher's version of article available at http://dx.doi.org/10.1016/S0168-9452(03)00195-X

Peer Reviewed

Peer-Reviewed

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.