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Genetic diversity analysis of colored and white rice genotypes using Microsatellite (SSR) and Insertion-Deletion (INDEL) markers

Siddhi Patel, Rallapalli Ravikiran, Sudeshna Chakraborty, Sneha Macwana, N. Sasidharan, Ruchi Trivedi, Bhushan Aher.


Genetic diversity analysis of 19 coloured and white rice genotypes were conducted using 14 Simple SequenceRepeat (SSR) and 21 Insertion Deletion (INDEL) markers. Among them, polymorphic results were obtained for 9 SSR and 12 INDEL markers. The PIC values ranged from 0.36(RM484) to 0.78 (RM 167) and 0.50 (R9M20) and 0.81 (R9M10) for SSR and INDEL markers respectively. In the case of both SSR and INDEL markers highest genetic diversity was observed between Krishna Kamod (White pericarp) and IRST 1 (Red pericarp) whereas least genetic diversity was observed between Lal Kada (Red pericarp) and Krishna Kamod (White pericarp). However, it was also found that brown, black and red pericarp share more similarity among themselves. It was also observed that INDEL markers reveals greater diversity among the genotypes as compared to SSR markers which was indent from the low average similarity index observed in the former. On the whole INDEL markers were found to be more efficient than SSR markers for diversity analysis.

Key words: Red rice, SSR, INDEL, Polymorphism, Heterozygosity

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