Assessing the Allelic Diversity of OsNRAMP5 among Sri Lankan Traditional Rice Varieties by in silico Analysis

Tharanya Sugumar¹, Tharukeshini Gunawardhana¹, Kushani Akshala Dilhani Rajapaksha^1, and Nadeeka Upamali Jayawardana¹

¹Faculty of Agriculture, University of Peradeniya, Sri Lanka

Cite this paper:
Tharanya Sugumar, Tharukeshini Gunawardhana, Kushani Akshala Dilhani Rajapaksha and Nadeeka Upamali Jayawardana. Assessing the Allelic Diversity of OsNRAMP5 among Sri Lankan Traditional Rice Varieties by in silico Analysis. American Journal of Food Science and Technology. 2022; 10(4):183-190. doi: 10.12691/ajfst-10-4-5

Abstract

OsNRAMP5 encodes a root expressed transporter that can significantly affect the Cd content in rice grains. An in silico analysis on haplotypes of OsNRAMP5 was performed on selected traditional Sri Lankan rice varieties in order to identify potential low Cd accumulators among them. OsNRAMP5 sequences of 47 Sri Lankan traditional rice varieties from the 3000 genome project repository in the Rice SNP seek database were selected for this study. A total of 14 genic haplotypes were obtained of which Pannithi and Godawel showed similarities with the low Cd accumulator Nipponbare. The results did not show significant polymorphic variation in the coding region (4.88%) of OsNRAMP5. Haplotype analysis of the promoter region of OsNRAMP5 in the selected rice varieties has revealed 10 haplotypes. In the promoter region, Pannithi and Godawel differ by one SNP position compared to Nipponbare. Transcription Factor binding sites were not detected in the corresponding SNP position and hence, this mutation is unlikely to affect the level of OsNRAMP5 expression in Pannithi and Godawel. Therefore, there is a potential to use Pannithi and Godawel varieties in the breeding programs aimed at reducing grain Cd accumulation.

Keywords:
cadmium transporters haplotype indica rice

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