@article{ajfst20221045,
author={{Sugumar, Tharanya and Gunawardhana, Tharukeshini and Rajapaksha, Kushani Akshala Dilhani and Jayawardana, Nadeeka Upamali},
title={Assessing the Allelic Diversity of <i>OsNRAMP5</i> among Sri Lankan Traditional Rice Varieties by <i>in silico</i> Analysis},
journal={American Journal of Food Science and Technology},
volume={10},
number={4},
pages={183--190},
year={2022},
url={http://pubs.sciepub.com/ajfst/10/4/5},
issn={2333-4835},
abstract={<i>OsNRAMP5</i> encodes a root expressed transporter that can significantly affect the Cd content in rice grains. An <i>in silico</i> analysis on haplotypes of <i>OsNRAMP5</i> was performed on selected traditional Sri Lankan rice varieties in order to identify potential low Cd accumulators among them. <i>OsNRAMP5</i> 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 <i>Pannithi</i> and <i>Godawel</i> showed similarities with the low Cd accumulator Nipponbare. The results did not show significant polymorphic variation in the coding region (4.88%) of <i>OsNRAMP5</i>. Haplotype analysis of the promoter region of <i>OsNRAMP5</i> in the selected rice varieties has revealed 10 haplotypes.  In the promoter region, <i>Pannithi</i> and <i>Godawel</i> 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 <i>OsNRAMP5</i> expression in <i>Pannithi</i> and <i>Godawel</i>. Therefore, there is a potential to use <i>Pannithi</i> and <i>Godawel</i> varieties in the breeding programs aimed at reducing grain Cd accumulation.},
doi={10.12691/ajfst-10-4-5}
publisher={Science and Education Publishing}
}