Characterization of Suwandal and Heenati rice varieties for the fragrance gene using Polymerase Chain Reaction based molecular markers

Aromatic rice is ranked at the top in the rice world market. Only few recommended aromatic rice varieties are available in Sri Lanka although demand for this trait is increasing world wide. As Sri Lanka is a rich source of bio-diversity, country holds many traditional varieties with favorable qualities. Therefore, characterization of local rice varieties for the fragrance trait at molecular level is a current requirement. The genetic cause for the fragrance in Basmati and Jasmine style rice has been reported due to an eight bp deletion and several SNPs in a gene which encodes for an enzyme, Betaine Aldehyde Dehydrogenase 2 (BAD2), located in chromosome 8. Mutation of BAD2 gene, which is called fragrance gene (fgr) is associated with increased level of 2-acetyl-1-pyrroline (2AP) which can be smelled when the grains are cooked. Several molecular markers linked with mutated and wild type BAD2 gene have been previously reported. Therefore, this study was conducted to establish molecular screening system to discriminate fragrance and non-fragrance genotypes and to investigate local traditional varieties that possess fragrance gene aiming at utilizing them in rice breeding programs.

Rice seeds were obtained from the Plant Genetic Resources Center, Department of Agriculture. DNA was extracted from 2 week old rice seedlings of 25 rice accessions including several Suwandal collections, Heenati collections and several other traditional and improved varieties using a rapid DNA extraction protocol. Multiplex polymerase chain reaction amplification was performed with four primers in a single tube. Three amplified fragments that can discriminate homozygous fragrant, homozygous non- fragrant and heterozygous individuals were visualized in agarose gel. Several Basmati accessions collected from different countries and a Jasmine accession were also used as the positive control. Genotyped data revealed that some traditional rice accessions contained homozygous fragrant alleles while many other accessions contained homozygous non fragrant alleles.  Although Basmati accessions are supposed to be fragrant types some accessions exhibited non fragrant and heterozygous allele profiles. As expected improved varieties, AT306 and Lanka Samurdi expressed homozygous fragrant alleles in BAD2. The results of this study have developed a reliable ‘Marker Assisted Selection’ system for the identification of fragrance gene located in chromosome 8 of rice at early seedling stage in breeding programs. Also it has given some insight into the understanding of the aroma genes in Oriza sativa.

Keywords: fragrance gene, traditional rice, polymerase chain reaction, BAD2

1E.G.D. Priyangani,  1N.S. Kottearachchi, 1D.P.S.T.G. Attanayaka, 2B.D. Pathinayake
1Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba University of Sri Lanka, Makandura, Gonawila.
2Rice Research Institute, Ambalanthota

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