Optimization of the choice of molecular markers for identification of commercially used rice varieties in India using rapid DNA extraction protocol

Abstract

The present investigating aimed at the development of molecular marker for cultivar identification and genetic purity assessment. A total of four SSR markers and six SRAP primer were developed for the identification of sixteen different commercial varieties of rice. Traditional practice like grow-out-test based on morphological traits is time consuming and sometimes environmentally influenced. After development of molecular marker, it is using as an alternative to grow –out –test because of its rapid, accurate detection. We have assessed the potential of simple sequence repeat and sequence-related amplified polymorphism markers in distinguishing rice varieties and four simple sequence repeat markers namely CT-14, CT-25 CT XY-1 and ATC-3 and six sequence-related amplified polymorphism markers primers could be clearly distinguished sixteen commercially cultivar rice varieties. In addition to single markers, it’s better to try with marker combinations, which were amenable for PCR and capable of distinguishing the varieties. Larger differences for each crop were found between cultivers from different seed companies than within the same company. These DNA markers can provide an easier and faster reliable genetic identification of rice cultivars.