GENOME-WIDE IN SILICO PREDICTION OF PUTATIVE TRANSCRIPTION FACTOR BINDING SITES FOR COTTON FIBER STRENGTH
Journal Title: International Journal of Agriculture Sciences - Year 2016, Vol 8, Issue 19
Abstract
Transcription factors are the early responsive genes which up on receiving stimulus from both biotic and abiotic stress lead to expression of various kind of proteins which can cope up with stress. Furthermore, the expression of genes takes place only when specific transcription factor (TF) binds to 6 to 15 nucleotide region present in upstream of corresponding gene called as transcription factor binding site (TFBSs). In present study, in silico based approach was used to predict the putative TFBSs and their TF responsible for fiber strength in G.barbadense. The data pertaining to differential expression of genes corresponding to fiber strength was retrieved from NCBI GEO database. A total of 70 significantly up regulated and down regulated ESTs were retrieved and assembled to 5 contigs. The contigs were functional annotated to know its exact role. The upstream sequences of the contigs were retrieved from G. raimondii genome. The upstream sequence subjected to NNPP software for promoter prediction. Using position weight matrix of experimentally validated TFBSs deposited in JASPAR database was used to predict the TFBS in promoter regions. The newly identified TFBSs were in the range from 6 to 20 nucleotides with multiple binding sites, except for Glucuronosyl transferases. With discovery of TFBSs and their TF for fiber strength will lead to better understanding of fiber strength development, which intern may lead to genetic manipulation of TFs and their introgression in G. hirsutum species which could help in achieving high fiber strength in addition to higher yields
Authors and Affiliations
A. DINESH
Keywords
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