Novel methods for genotyping diverse genomes including rice varieties


Patents filed: 

This invention is described in the following filings: 

1.  USPTO Application [PDF]    (also filed as PCT Application – PDF)


    Novel FISSR-PCR primers and methods of identifying genotyping diverse genomes of plant and animal systems including rice varieties, a kit thereof. 


    J. Nagaraju 


    The present invention relates to set of 37 inter-simple sequence repeats (ISSR)-PCR primers for genotyping eukaryotes and a method of genotyping diverse genomes of plant and animal systems using FISSR-PCR primers and SSR markers; more particularly, a FISSR and SSR method of distinguishing Basmati rice varieties from Non-Basmati (NB) rice varieties, and Traditional Basmati (TB) rice varieties from Evolved Basmati (NB) rice varieties, and also, a method for determining adulteration of Basmati rice with other rice varieties and a kit thereof. 


2.  USPTO – Continuation-in-part (CIP) Application[PDF] 


    Single tube multiplex assay for detection of adulterants in basmati rice samples 


    J. Nagaraju et al. 


    The present invention relates to a single tube multiplex assay for distinguishing basmati from non-basmati rice varieties and thereby the adulteration, said assay comprising steps of running multiplex PCR with sample using eight loci, and distinguishing the basmati from non-basmati rice varieties and thereby the adulteration on the basis of varietal specific multiplex allele profile; and also, a method of quantifying adulteration in basmati rice varieties, said method comprising steps of constructing a standard curve on the basis of ratio of quantity of amplified products of the alleles of adulterant and the basmati rice against the progressive proportion of adulteration, and quantifying the adulteration in basmati rice variety on the basis of peak area of the alleles corresponding to basmati and that of the adulterant. 

Commercial potential:   [DOC] 

Research publications: 

Kumar, L.D., Kathirvel, M., Rao, G.V., and Nagaraju, J. 2001. DNA profiling of disputed chilli samples
           (Capsicum annum) using ISSR-PCR and FISSR-PCR marker assays. Forensic Sci. Int. 116: 63-68. [PDF] 

Nagaraju, J., Kathirvel, M., Subbaiah, E.V., Muthulakshmi, M., and Kumar L.D. 2002. FISSR-PCR: A simple and
           sensitive assay for highthroughput genotyping and genetic mapping. Mol. Cell. Probes Bact. 16: 67-72. [PDF] 

Nagaraju, J., Kathirvel, M., Kumar R.R., Siddiq, E.A., and Hasnain, S.E. 2002. Genetic analysis of traditional and
           evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers.
            Proc. Natl. Acad. Sci. USA. 99: 5836-5841. [PDF] 

Archak, S., Lakshminarayanareddy, V. and Nagaraju, J. 2007. High-throughput multiplex microsatellite marker
           assay for detection and quantification of adulteration in Basmati rice (Oryza sativa). Electrophoresis (In press).

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