Natural Genetic Diversity in the Potato Resistance Gene RB Confers Suppression Avoidance from Phytophthora Effector IPI-O4

Name: Hari Karki

Current Position: Molecular breeder (tomato) at Lipman Family Farms, Florida, USA

Education: M.S. and Ph.D. degrees in plant health at Louisiana State University, Baton Rouge, LA, USA

Brief Bio: Over the years, I have conducted research in the field of plant pathology, genetics, genomics, and molecular biology at Louisiana State University (LSU), The Sainsbury Laboratory (TSL) and U.S. Department of Agriculture (USDA). I was always attracted to different aspects of agriculture, which eventually led to my enrollment at the agriculture institute of Nepal. After completion of my undergraduate degree, I joined the Department of Plant Pathology and Crop Physiology at LSU to pursue a master's degree, studying the bacterial pathogen Burkholderia glumae. After completion of a M.S. degree in plant health, I continued studying for a Ph.D. degree and worked on understanding the virulence mechanism and population diversities of B. glumae through targeted sequencing and mutagenesis of pathogenic and nonpathogenic isolates. At TSL, I worked on a capture-based next-generation sequencing method, resistant gene enrichment and sequencing (RenSeq), and gene enrichment and sequencing (GenSeq) to map and clone resistance genes against late blight of potato caused by Phytophthora infestans. At the USDA, I worked on the molecular dissection of RB (also known as Rpi-blb1) mediated late blight resistance in potato. RB is a broad-spectrum late blight resistance gene cloned from Solanum bulbocastanum, which recognizes P. infestans effector IPI-O (in planta–induced gene O), also known as Avrblb1.

IPI-O is a multigene effector family that has been divided into three major classes. IPI-O class I and class II variants detect RB and initiate resistance activation; however, with class III variants, IPI-O4 not only escapes recognition by RB but is also capable of inhibiting the hypersensitive response (HR) by directly binding the RB CC domain. To identify the RB CC domain that does not interact with IPI-O4, we explored natural variations in the RB CC domain from different Solanaceae species and identified the RB CC domain from S. pinnatisectum (pnt) that does not interact directly with IPI-O4. We identified crucial amino acids in the RB CC domain that play an important role in the avoidance of suppression activity of IPI-O4 and, thus, could enable resistance activation even in the presence of this suppressor. We further modified these amino acids in a wild-type RB gene and concluded that modification of single amino acids within the RB CC domain can either diminish or increase the resistance capability of the RB gene. Our study provides a clue about engineering new variants of known R genes that can further expand the resistance spectrum.

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