Development of Molecular Markers for Purity Testing in Thai Jasmine Rice

Varapong Chamarerk, Payorm Cobelli, Jirapong Jairin, Poonsak Mekwattanakarn, Pikul Leelakud, Jittima Wongnongwa

Abstract: Purity testing in paddy rice is sometime difficult by using phenotypic characters alone. Molecular markers can be more accurate technique for purity testing. Simple sequence repeats (SSRs) markers are widely spread throughout the rice genome and are used for purity testing in rice. DNA banding patterns from an automated DNA sequencer showed more allelic variability than those from a polyacrylamide gel electrophoresis technique. An average allelic pattern detected by using an automated DNA sequencer is 9.38 alleles per locus. The marker RM20B showed the highest allelic variation of 20 alleles, while the marker RM165 and Glu-23 showed the least allelic variation of 3 alleles. Those markers that can differentiate the rice varieties KDML105, Pathumthani 1 and Chainat 1 are RM21, RM20A, RM20B, RM209, RM3, GT11, RM232 and RM235. When using polyacrylamide gel electrophoresis technique, there was less allelic variation than detected by an automated DNA sequencer. An average allelic pattern detected by using polyacrylamide gel electrophoresis is 4.53 alleles per locus. The marker RM20A showed the highest allelic variation of 9 alleles, while the marker RM165, B03 and Glu-23 showed the least allelic variation of 2 alleles. Those markers that can differentiate the rice varieties KDML105, Pathumthani 1 and Chainat 1 are RM21, RM20A, RM20B, RM209, RM3, RM248, GT11, RM204 and RM3627. Those markers used for purity testing can be classified into 3 groups; 1) those used for identifying soft and hard cooked rice, 2) those used for identifying glutinous and non-glutinous type and 3) those used for identifying aromatic and non-aromatic variety.

Keywords: molecular markers, rice purity testing, allele standard, SSR markers.

Pages: 35 – 44 | Full PDF Paper