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

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

doi:10.9755/ejfa.v26i6.15722

Siddhi Patel, Sudeshna Chakraborty + Show 5 more

Open Access

https://doi.org/10.9755/ejfa.v26i6.15722

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Abstract

Genetic diversity analysis of 19 coloured and white rice genotypes were conducted using 14 Simple Sequence Repeat (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.

Highlights

Rice is the second most important cereal crop in the world
The seeds of 19 rice genotypes comprising of coloured rice used in the present study was obtained from the Main Rice Research Station (MRRS), Anand Agricultural University, Nawagam (Table 1)
Total of 14 Simple Sequence Repeat (SSR) and 21 Insertion Deletion (INDEL) markers were used for the study out of which 9 SSR markers and 12 INDEL markers gave polymorphic results (Table 2)

Summary

Introduction

Rice is the second most important cereal crop in the world. Among the rice growing countries in the world, India has the second largest area under rice crop (about 45 million ha) and ranks second in production next to China. In Asia, traditionally, rice with varied colours such as red, purple, brown yellow and green have been grown. Coloured rice has been preferred in the past for their special features in medicinal value and exclusive taste as compared to common rice. In India, coloured rice is prevalent in pockets of South, North western and North eastern Himalayan region (Deepa et al, 2008). The red rice was preferred by people in many parts of India, Sri-Lanka and Bhutan.

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