Ali Lab



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Genome editing using the CRISPR/Cas-9 nucleases.

Genome editing has revolutionized almost all fields of biology.  In our lab, we have developed a robust genome editing method, which we are currently utilizing for knocking out and knocking in several disease resistance genes in economically important plants. In the future, we will be extending this technology to fungi and oomycetes.

Plants use two major immunity systems to defend themselves against pathogens. In one system, conserved pathogen-associated molecular patterns (PAMP) are recognized by plants through “Pattern Recognition Receptors” (PRRs) leading to the activation of defense responses. Pathogens inactivate PAMP-triggered immunity by delivering virulent disease causing effectors proteins into cells. Plants counteract by recognizing these effectors through resistance (R) proteins, which leads to a more rapid and robust defense system called effector-triggered immunity. Plant defenses include cell wall reinforcement, hypersensitive response, and expression of many defense genes including pathogenesis related (PR) genes. Introgression of resistant genes from wild relatives using traditional breeding methods is not efficient, especially in woody ornamentals, because of difficulty in sexual hybridization and potential loss of desirable traits. In addition, the gene-for-gene type R genes are in most cases rapidly overcome by new virulent pathogen strains.  Current crop transformations for fungal resistance have been using individual defense genes, which in most cases have resulted in partial resistance Durable and broad-spectrum resistance can be accomplished with heterologously expressing multiple Pattern Recognition Receptors (PRRs) along with other genes in one line. We are transforming several PRRs and other defense-related genes in unison into several economically important crops including tomatoes, Geranium and roses. Since, our approach is expected to provide broad-spectrum resistance, wherever feasible, transgenic lines will be tested against other pathogens too.



Crystal structure of Cas9-nuclease




Confocal image showing that a YFP-tagged Flagellin Sensing 2, (FLS2), apattern recognition receptor (PRR), is localized to plasma membrane to intercept potential bacterial plant pathogens.