Of gene expression and self expression

I wrote this essay a few years ago, as part of an application process to attend a workshop on gene expression and microarray. I got accepted and had to visit The Institute of Genomic Research (TIGR) in Rockville, MD.

Here goes:

One of the major constraints to rice production is the variety of diseases present in different rice growing environments. The most viable practice to manage rice disease is still through the use of resistant cultivars. Over the years, it has been found that the use of major genes (R genes) for disease resistance are not the only strategy needed to combat a diverse array of pathogens. Genes downstream from the R genes also contribute to the overall defense response to pathogens. It has also come to light that there is cross-talk between metabolic pathways related to responses to different pathogens.
What genes are expressed in response to a particular pathogen? What genes are commonly expressed in response to more than one pathogen? Can we pool a combination of these genes to come up with a variety exhibiting broad spectrum resistance to multiple pathogens? These are the questions that have guided my PhD dissertation in the last four years. By integrating molecular, phenotypic and in silico approaches to studying broad spectrum to fungal pathogens of rice, we have identified several promising lines that are more resistant to rice blast across multiple environments. By analyzing the functional annotation, organization and characteristics of each candidate genes, we were able to validate genetic mapping data with the rice physical map and generate additional molecular markers for analysis. We have developed PCR markers for defense response candidate genes that are now being used for other mapping populations of rice. We have shown that by marker-assisted selection, candidate genes with quantitative effects may be combined efficiently. I hope I would be able to answer in the course of my PhD dissertation at the International Rice Research Institute. I am currently working on rice mutants exhibiting loss of resistance to rice blast, as well as to bacterial blight. We have started testing their reaction to the sheath blight and brown spot pathogens. I am also working on Vandana x Moroberekan rice population which exhibit quantitative resistance to rice blast. We have made intercrosses of progenies from this cross to pool different mechanisms of resistance to a single plant. These mechanisms of resistance are candidate genes identified from multiple experiments. However, these candidate genes may not be the only genes involved in quantitative resistance and there may other loci which also contribute to resistance.
This is where the impact of oligonucleotide arrays come in. With microarrays, I hope to be able to identify candidate genes in the rice materials I am working on that contribute resistance to different rice pathogens. Most especially, BC3F6 lines of the Vandana x Moroberekan intercrosses will be used for multilocation testing for reaction to rice blast. The effectiveness of gene combinations contributing to blast resistance in these intercrosses would be validated in the field. These results will not only be useful for genetic studies but also has practical applications in marker-aided selection of resistant lines in rice breeding.
Just as in the field of human medicine, where the ideal scenario is that doctor works in the lab looking for medicines against diseases and once found crosses the hallway to bring the medicine to the patient, the use of oligonucleotide chips in my research would allow me to identify genes for broad spectrum resistance against a plethora of rice pathogens and validate their efficacy in the field to come up with a resistant variety, which is the ultimate goal of rice research.

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I am on the last leg of my PhD studies. As the days go by, so fast and so many deadlines, the need for self expression becomes adamant. So here I am, putting down my thoughts, my feelings on what is happening in my life.