Abstract:

The technically simplified approach of marker-assisted selection has directly and practically used in rice breeding. Fragrance in rice, a recessive trait, has been known to be due to an 8 bp deletion and 3 SNPs difference in a gene on chromosome 8. Rice breeders have an interest in gaining access to a simple and inexpensive method for distinguishing between fragrant and non-fragrant rice. Allele specific amplification (ASA) is a low-cost, robust technique that can be utilized to discriminate between the alleles. We used a single tube ASA assay which allows discrimination between 9 fragrant and 3 non-fragrant rice varieties and 3 F₁ plants to identify homozygous fragrant, homozygous non-fragrant, and heterozygous non-fragrant individuals. The research showed that using tetras-primer amplification refractory mutation system PCR could result in three possible outcomes. External primers generated a fragment of approximately 580 bp as a positive control for each sample. Internal and corresponding external primers produced a 355 bp fragment from a non-fragrant allele, a 257 bp fragment from a fragrant allele and both 355 bp and 257 bp fragment from a heterozygous allele allowing simple analysis on agarose gels. A single tube allele specific PCR which allows determination of the genotypic status of an individual rice plant, either homozygous fragrant, homozygous non-fragrant or heterozygous has practical utility for rice breeders worldwide.

Key words:

Rice, Fragrant gene, Allele specific amplification