Development of an allele specific amplification (ASA) co-dominant marker for fragrance genotyping of rice cultivars

By Asadollah Ahmadikhah, Abodomalek Arkhy, Hojat Ghafari


Fragrance is one of critical factors in rice eating quality in rice, is a recessive trait and it has been confirmed that an 8-bp deletion as well as some SNPs within Os2AP gene on rice chromosome eight results in production of fragrance. In this research we attempted to develop an allele specific amplification (ASA) marker based on the 8-bp deletion in the gene. Arm1 primer pair flanking the 8-bp deletion region, has produced a co-dominant polymorphic banding pattern, with band size in highly fragrant and most fragrant cultivars was of 103 bp length, while in non-fragrant ones was of 111 bp length. Results suggested the use of ASA co-dominant marker Arm1 instead of phenotyping via smelling for fragrance genotyping of rice cultivars.


Key Words : Rice, fragrance, ASA marker.


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