Analysis Of Wax Biosynthesis Genes In Cotton
Cotton is the largest natural fiber source. Worldly, more than 80 countries produce cotton. Pakistan is fourth main cotton growing country in the world after China, India and USA and responsible for 2/3rd manufacturing of world’s cotton. According to Economic survey of Pakistan cotton is responsible 1.6% to GDP. Cotton is facing abiotic and biotic stresses and drought stress is most important natural disaster. Waxes play major role against these stresses.
Identification of wax biosynthesis genes using bioinformatics tools is a powerful domain which saves time of researcher and wax genes in cotton (G. hirustum), protecting plant from environmental factors (like drought, pathogen attack, UV radiation etc). This research project was planned to recognize the potential genes responsible for wax biosynthesis in cotton. Identification of these genes by using bioinformatics is based on gene homology method. The already known genes from sequenced organisms (includes Arabidopsis and rice) were retrieved. Total 87 genes of Arabidopsis and rice with familiar functions were retrieved from NCBI and TAIR. The genes were organized and their function in wax biosynthesis was classified on already available literature basis. mRNA and protein sequences of 87 wax biosynthesis genes with their accession numbers were retrieved. mRNA sequences of these genes were interpreted by using BLAST tool against EST’s available at NCBI. EST’s in various crops (like cotton, potato, chilli, maize, tomato, wheat, tobacco, sorghum, etc.) were found and data related to cotton EST’s were retrieved. Total EST’s depicted from NCBI were 307414 in G. hirustum. The 26 genes were selected on basis of presence of ETS’s in G. hirustum. These genes were examined by “Multiple Sequence Alignment” and aligned with cotton EST’s which were recognized earlier. They represented significant homology with EST’s. All genes were searched for novelty and finally 6 genes were chosen as possible genes responsible for wax biosynthesis and play role in drought tolerance. These 6 genes were searched in maximum number of different species at NCBI. Only 2 genes are present in different species and relation of these genes in different species were showed by cladograms. Domains of these 6 genes were predicted and their features were studied. Regulatory elements of full gene sequence of these finally selected genes and regulatory elements in 5’ and 3’ UTR region were predicted. After regulatory element prediction, protein-protein interaction of these genes with the genes available in alkane pathway of wax biosynthesis was studied and their results were evaluated.
Conclusion and Future Recommendations
From the retrieval of wax biosynthesis genes from various plant species and their alignment with G. hirustum through BLAST tool verified the presence of wax biosynthesis genes in cotton plants. This information was reconfirmed by EST analysis from EST BLAST at NCBI of cotton. After MSA of suspected genes, 6 genes i.e. ACS4, KCS11, KCS17, KCS19, KCS21 and RGA4 are found to be novel. On classification basis functional domains and regulatory elements were predicted. Wax biosynthesis pathway genes, protein-protein interaction of KCS11, KCS17, KCS19, KCS21 with CER3, CER6, CER7, CER10, FAE1 were studied.
In future PCR primers of these genes can be designed and detected by amplification through PCR and gel electrophoresis. There are large number of wax biosynthesis genes scattered on web resources which can be gathered on single source and availability of these genes can be made easy by making user friendly databases. And these genes can be utilized for development of crops that show tolerance to abiotic and biotic stresses.