Genetic diversity and DNA fingerprinting of rice varieties of Manipur using microsatellite markers

I. Meghachandra Singh
Umakanta Ngangkham
Konsam Sarika
Yengkhom Sanatombi Devi
Thounaojam Seileshkumar Singh
T. Basanta Singh
Kh. Rishikanta Singh
E. Lamalakshmi Devi
Amit Kumar
Monalisa Nameirakpam
Umananda Arambam
Thokchom Diviya
Ramgopal Laha
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Abstract

Rice variety differentiation was based on morphological descriptors (DUS) before the advent of genomic and proteomic technology. DNA fingerprinting is becoming an important molecular marker approach because of its wide application in varietal protection, classification, and conflict settlement. In the present study, genetic diversity and variability among the 11 rice varieties of Manipur at the molecular level was studied using 42 SSR markers. The genotypic data of the SSR markers revealed four sub-populations. Cluster analysis indicated the close similarity between RC Maniphou 12 and RC Maniphou 15. To create a DNA fingerprinting database for 11 rice varieties, three separate multiplex PCR systems using different combinations of 11 polymorphic SSR markers based on amplicon size were successfully developed . These were able to distinguish the distinctness of all the eleven released rice varieties. 

Keywords DNA fingerprinting, SSR, multiplex PCR, Rice, Microsatellite