Applying Genomics to Crop Improvement

We focus on the staple food crop cassava and its pathogen, Xanthomonas axonopodis pv. manihotis (Xam). Bacterial pathogens within the genus Xanthomonas deliver type three effectors (T3Es) into the cells of their plant hosts to promote virulence. We use genomic approaches to understand the conservation of T3Es on a pathogen population level. Highly conserved effectors represent ideal targets for disease resistance. In addition, we characterize a specific class of T3Es, the transcription activator-like (TAL) effector family and report a major role for bacterial population growth and symptom development for TAL14_Xam668 and TAL20_Xam668, respectively. We identify pathogen-induced transcriptional changes using RNA-seq and identify cassava target genes for each TAL effector. TAL20_Xam668 specifically induces MeSWEET10a, a member of the sugar transporter family of susceptibility genes previously characterized in rice. TAL14_Xam668 induces a pectate lyase, a novel class of TAL-targeted susceptibility genes. We show that induction of these genes is a highly conserved virulence strategy employed by Xam during infection of cassava and propose strategies for durable engineered resistance.