Journal of Genetics, Genomics and Plant Breeding

ISSN (Online) : 2581-3293


Archive Issue

1 (1) 2017, AUGUST,2017

Pages: 5-9

In silico identification and development of conserved primers from DREB gene in rice

Author: Vanisri, S., Ramprasad Eruvuri, Dinesh Akula, Durga Sai, J., Sunii Lanah and P. Mamatha

Category: Bioinformatics

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Abstract:

Drought responsive element binding (DREB) proteins plays a key role as transcription factors that bind to the promoter of dehydration responsive genes such as rd29A, thereby inducing the expression of downstream genes in response to dehydration due to drought, salt and cold. We have validated hypothesis cum assumption by using bio-informatic tools in rice. Total of 19 sequences of DREB genes were downloaded from Gramene database and 14 non redundant/unigene sequences were identified. Total of 6 conserved primers were identified from the DREB gene sequences. For identification of these conserved primers, whole genome sequence of Oryza sativa (IRGCP build 5) was used as reference genome. We had used a high threshold for identification of these conserved primers. When in silico PCR studies were conducted out of 6 primers, 4 primers have yielded a product of suitable size (>300 bp amplicon). These 14 sequences were blast searched to identify the putative functions against the NCBI protein data base. Most of the sequences fall under the “fibre protein fb2” category (12 sequences) whereas, the putative function of one sequence is not available which is supposed to be unique for rice. Sequence Os12t0617000-00 had identified with a putative function of drought and salt tolerance. We had studied the localization of the proteins and found maximum of these DREB proteins are localized at intracellular regions followed by plastids, nucleus and mitochondria, which will help to understand the mechanism of drought response in rice. With these in silico studies we have validated that DREB genes are not only responsible for drought stress but also have function under cold stress. This study highlights the importance of investigating the genes which interact with markers and suggests following the behavior of marker-related genes at protein level. Identification of genes underlying drought stress will facilitate understanding of molecular mechanisms and will lead to genetic improvement of rice through marker-assisted selection (MAS). We recommend that wet lab study to validate the results obtained through present investigation

Keywords: Rice, DREB, Drought, in silico, conserved primers