Development of a sequence characterized amplified region (SCAR) marker for identification of Thai jasmine rice (Oryza sativa L.) variety ‘KDML105’

Abstract

The varieties of rice are difficult to be distinguished because of their similar morphological characters, therefore rice variety identification or differentiation is very important. The authentication by using molecular marker or DNA fingerprinting is the most accurate method. In this study, random amplified polymorphic DNA (RAPD) derived sequence characterized amplified region (SCAR) markers were applied to detect aromatic rice (Oryza sativa L.) variety Khao Dawk Mali (KDML) 105 from its closely related varieties. Eighty 10-mer primers were screened to identify an OPJ01KDML105-727 band which was amplified by primer OPJ-01, and this band specified to variety KDML105. SCAR marker was created by cloning and sequencing the specific band, and designing a pair of primers, SCJ01KDML105-668 to amplify the band of 668 bp. Diagnostic PCRs were performed using the primer pair with the total DNAs of O. sativa var. KDML105, and its related varieties as templates, with only O. sativa var. KDML105 being able to be amplified. This amplification is not only rapid, but is also easy to perform. Hence, it is a feasible method for identifying O. sativa var. KDML105 between rice varieties.

Key words: Oryza sativa L., varietal identification, random amplified polymorphic DNA (RAPD) marker, sequence characterized amplified region (SCAR) marker, multiplex polymerase chain reaction (PCR).