Conservation and molecular identification of traditional rice varieties collected from Kerala using matK and rbcL DNA barcode markers

Varietal identification of economically significant crops has acquired great importance in the global market especially in the terms of protection of plant varieties. Kerala is the home to several different specialty traditional rice varieties which is vital sources of nutritional and therapeutic properties. Traditional rice landraces are an integral part of the nutrition, medicine, and culture of Kerala. Most of these varieties possess similar morphological characteristics but differ in their nutritional and medicinal properties. It has become a challenge for a non-taxonomist to identify and recognize the traditional rice varieties accurately. DNA barcoding has been considered a standard method to identify species or variety which utilizes a unique pattern of variation in the DNA of the species. It can be adopted as a routine and faster approach to determine the molecular taxonomy when compared to morphological identification approaches. Currently, the most intensively applied two DNA barcode loci are maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL) for plant identification. But, the efficacy of these two loci in discriminating plant species may vary. Hence, in this study fifty-four traditional rice varieties collected from the Wayanad district of Kerala were used to generate and compare the two standard DNA barcode regions for plant matK and rbcL via PCR amplification. The varieties collected were varying in the husk color from black; red to brown and the brown rice varieties not display any morphological variation. The study identified that among the two selected markers rbcL was observed to have the potential to discriminate the intra and interspecific regions of the studied rice varieties and this would have been utilized to generate DNA barcodes for each variety. This study separates and identifies 28 traditional rice varieties among the 54 studied varieties as Oryza nivara, the wild progenitor of Asian cultivated rice. Along with other supporting information the data presented here could be used as a reference to check the authenticity and varietal purity of commercially significant rice varieties in the future.