Abstract—Drought is a major constraint to rice production and its stability in rain-fed and poorly irrigated environments. Identifying genomic regions influencing the yield and its response to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Besides drought, the other major impediment to increased crop production is salt stress. In this context, identification of drought and salt-responsive genes assumes significance.
In this paper we carried out genome-wide analyses to explore putative genes encoding ethylene responsive factor (ERF) and dehydration-responsive element binding proteins (DREB) in the genome of indica rice. Reference nucleotides of well established molecular function, representing each of the protein families investigated, were chosen as query sequences for searches in the indica rice genome database. Clones having genomic sequences similar to the related genes were taken and converted to amino acid sequences. Putative sequences were subjected to PROSITE and Pfam databases and 31 signature sequences related to ERF family and 30 sequences related to DREB were obtained. Proteins showing more than 30% identity were taken and phylogenetic trees were generated for each family. The results of this sudy provide basic genomic information about new ERF and DREB gene families in indica rice.
Index Terms—Oryza sativa, genome wide analysis, DREB, ERF
Hemalatha N. is with the AIMIT, St.Aloysius college, Mangalore, Karnataka, India.(e-mail: hemasree71@gmail.com) Rajesh M. K. is with the Central Plantation Crops, Research Institute, Kasargod, Kerala, India. (e-mail: mkraju_cpcri@yahoo.com) Narayanan N. K. is with the School of Information Science, and Technology, Kannur University, Kannur, Kerala, India.(e-mail: csirc@rediffmail.com)
Cite: Hemalatha N, Rajesh M. K, and Narayanan N. K., "Genome-Wide Analysis of Putative ERF and DREB GENE Families in Indica Rice (O. sativa L. subsp. Indica)," International Journal of Machine Learning and Computing vol.2, no. 5, pp. 556-559, 2012.