Abstract
The present communication is aimed to find out determinants of molecular marker based classification of rice (Oryza sativa L) germplasm using the available data from an experiment conducted for development of molecular fingerprints of diverse varieties of Basmati and non Basmati rice adapted to irrigated and aerobic agro-eco systems. The distance-matrix based dendrogram was developed following UPGMA method that grouped all the 44 varieties agro-eco systems wise. We examined the clustering of Basmati and non- Basmati varieties in detail. The results suggest that the easily distinguishable simple characters viz. plant height, photosensitivity, leaf color, awn’s color, awns’ number etc., governed by major genes did not contribute significantly towards classification of rice genotypes used. The complex characters such as adaptation to agro-eco systems and rice quality may play vital role in determination of molecular marker based classification of rice genotypes. Key word: Basmati rice, molecular markers, genetic diversity, agro-eco systems, rice quality.  
Highlights
The traditional varieties of Basmati rice are tall, long duration, photosensitive and contained minimum genetic diversity
The present study was undertaken with the objective to fingerprint/characterize different varieties of Basmati and non-Basmati rice adapted to different agroecological systems by using SSR and its alternative approach inter-SSR assays (Zietkiewicz et al, 1994, Singh et al, 2000a, 2000b) and to examine the results in order to work out efficient determinants for molecular marker based classification
The molecular marker based available techniques are used to estimate genetic diversity that may correspond to contribution of different characteristics in the categoryzation of germplasm
Summary
The traditional varieties of Basmati rice are tall, long duration, photosensitive and contained minimum genetic diversity. This crop could not be genetically benefitted even during green revolution era. Low yielding, disease susceptible traditional varieties of Basmati rice still remained in cultivation due to their high quality that fetch high premium price in the local as well as international market. The present study was undertaken with the objective to fingerprint/characterize different varieties of Basmati and non-Basmati rice adapted to different agroecological systems by using SSR and its alternative approach inter-SSR assays (Zietkiewicz et al, 1994, Singh et al, 2000a, 2000b) and to examine the results in order to work out efficient determinants for molecular marker based classification
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